Integrative analysis reveals regulatory programs in endometriosis
Open accessAbstract
Endometriosis is a common gynecological disease found in approximately 10% of reproductive-age women. Gene expression analysis has been performed to explore alterations in gene expression associated with endometriosis; however, the underlying transcription factors (TFs) governing such expression changes have not been investigated in a systematic way. In this study, we propose a method to integrate gene expression with TF binding data and protein-protein interactions to construct an integrated regulatory network (IRN) for endometriosis. The IRN has shown that the most regulated gene in endometriosis is RUNX1, which is targeted by 14 of 26 TFs also involved in endometriosis. Using 2 published cohorts, GSE7305 (Hover, n = 20) and GSE7307 (Roth, n = 36) from the Gene Expression Omnibus database, we identified a network of TFs, which bind to target genes that are differentially expressed in endometriosis. Enrichment analysis based on the hypergeometric distribution allowed us to predict the TFs involved in endometriosis (n = 40). This included known TFs such as androgen receptor (AR) and critical factors in the pathology of endometriosis, estrogen receptor α, and estrogen receptor β. We also identified several new ones from which we selected FOXA2 and TFAP2C, and their regulation was confirmed by quantitative real-time polymerase chain reaction and immunohistochemistry (IHC). Further, our analysis revealed that the function of AR and p53 in endometriosis is regulated by posttranscriptional changes and not by differential gene expression. Our integrative analysis provides new insights into the regulatory programs involved in endometriosis.
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RNA expression of ESR2 is 40- to 140-fold higher in stromal cells obtained from ovarian endometriomas compared to healthy eutopic endometrial stromal cells.
“RNA expression of ESR2 is 40-to 140-fold higher in stromal cells obtained from ovarian endometriomas compared to healthy eutopic endometrial stromal cells”
From Endometriosis and nuclear receptors (2019) · cites this paper as Yang et al., 2015
The Discussion reports that ESR2 expression was upregulated in endometriosis samples. It does not report a 40- to 140-fold increase or establish that comparison specifically for stromal cells from ovarian endometriomas versus healthy eutopic endometrial stromal cells. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe androgen receptor has been identified as an endometriosis-associated transcription factor.
“the androgen receptor has been identified as an endometriosis-associated transcription factor.16”
From Steroid hormone profiling reveals altered adrenal androgen production in endometriosis (2026) · cites this paper as [16]
Androgens can regulate processes associated with the formation of endometriosis lesions.
“Androgens can regulate processes associated with the formation of endometriosis lesions”
From Steroid hormone profiling reveals altered adrenal androgen production in endometriosis (2026) · cites this paper as [16]
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OMICs Studies and Endometriosis Biomarker Identification
Saare, M., Peters, M., Aints, A., Laisk, T., Salumets, A., & Altmäe, S. (2017) · Springer eBooks · doi:10.1007/978-3-319-59856-7_12 · Cited by 8 · see citing works
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Rahman, M. S., Kim, T. H., Barrier, B. F., Spencer, T. E., Kelleher, A. M., & Jeong, J. (2025) · The FASEB Journal · doi:10.1096/fj.202403182r · Cited by 6 · see citing works
Zheng, Q., Wei, X.-Y., Rao, J., & Zhou, C. (2020) · PeerJ · doi:10.7717/peerj.9000 · Cited by 4 · see citing works
Androgens modulate endometrial function
Yamagata, K., Mizuno, Y., Mizuno, Y., Tamaru, S., & Kajihara, T. (2025) · Medical Molecular Morphology · doi:10.1007/s00795-025-00430-6 · Cited by 3 · see citing works
Steroid hormone profiling reveals altered adrenal androgen production in endometriosis
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“16 We propose that androgen excess, described herein, may drive endometriosis pathophysiology through direct regulation of androgen-dependent processes (via T and 11KT) and by acting as obligate substrates for aromatase (via A4 and T) to fuel estrogenic processes in lesions.”
Transcription factor addictions: exploring the potential Achilles’ Heel of endometriosis
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A Promising Novel Treatment for Endometriosis
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Molecular and Cellular Changes in the Pathogenesis of Endometriosis
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Progesterone receptor in uterine glands is required for pregnancy establishment in mice
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- Authors
- Yang, H., Kang, K., Cheng, C., Mamillapalli, R., & Taylor, H. S.
- Affiliations
- Capital Medical University (CN)
- Dartmouth College (US)
- Yale University (US)
- Corresponding author
- Mamillapalli, Ramanaiah
- Venue
- Reproductive Sciences
- Published
- 2015-09
- Volume
- 22
- Issue
- 9
- Pages
- 1060-1072
- ISSN
- 1933-7191 (ISSN-L)
- 1933-7205
- PMC
- PMC5933170
- OpenAlex
- W2096174862
- Cited by
- 39
- References
- 73
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 6 · 2023: 2 · 2022: 2 · 2021: 3 · 2020: 7 · 2019: 2 · 2018: 2 · 2017: 5 · 2016: 1
- FWCI
- 3.05
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Reproductive Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (81300467)
- National Institutes of Health (NIH-R01)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD076422, NIH R01 HD076422)
- Topics
- Health Sciences › Medicine › Reproductive Medicine › Endometriosis Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Estrogen and related hormone effects
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant and fungal interactions
- Keywords
- endometriosis, transcription factors, gene expression, transcription factor binding sites, protein-protein interaction, RUNX1, androgen receptor, estrogen receptor alpha, estrogen receptor beta, FOXA2, TFAP2C, p53, post-transcriptional regulation, differentially expressed genes
- MeSH terms
- Endometriosis, Female, Gene Expression Regulation, Genetic Markers, Humans, Protein Binding, Receptors, Androgen, Transcription, Genetic, Case-Control Studies, Tumor Suppressor Protein p53, Computational Biology, Gene Expression Profiling, Protein Interaction Mapping, Databases, Genetic, Chromatin Immunoprecipitation, Estrogen Receptor alpha, Estrogen Receptor beta, Transcription Factor AP-2, Core Binding Factor Alpha 2 Subunit, Hepatocyte Nuclear Factor 3-beta, Gene Regulatory Networks, Genetic Association Studies, Protein Interaction Maps
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