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Samare-Najaf M, Razavinasab SA, Samareh A, Jamali N. Omics-based novel strategies in the diagnosis of endometriosis. Crit Rev Clin Lab Sci 2024; 61:205-225. [PMID: 37878077 DOI: 10.1080/10408363.2023.2270736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
Endometriosis, an enigmatic and chronic disorder, is considered a debilitating condition despite being benign. Globally, this gynecologic disorder affects up to 10% of females of reproductive age, impacting almost 190 million individuals. A variety of genetic and environmental factors are involved in endometriosis development, hence the pathophysiology and etiology of endometriosis remain unclear. The uncertainty of the etiology of the disease and its complexity along with nonspecific symptoms have led to misdiagnosis or lack of diagnosis of affected people. Biopsy and laparoscopy are referred to as the gold standard for endometriosis diagnosis. However, the invasiveness of the procedure, the unnecessary operation in disease-free women, and the dependence of the reliability of diagnosis on experience in this area are considered the most significant limitations. Therefore, continuous studies have attempted to offer a noninvasive and reliable approach. The recent advances in modern technologies have led to the generation of large-scale biological data sets, known as -omics data, resulting in the proceeding of the -omics century in biomedical sciences. Thereby, the present study critically reviews novel and noninvasive biomarkers that are based on -omics approaches from 2020 onward. The findings reveal that biomarkers identified based on genomics, epigenomics, transcriptomics, proteomics, and metabolomics are potentially able to diagnose endometriosis, predict prognosis, and stage patients, and potentially, in the near future, a multi-panel of these biomarkers will generate clinical benefits.
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Affiliation(s)
- Mohammad Samare-Najaf
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Kerman Regional Blood Transfusion Center, Kerman, Iran
- Biochemistry Department, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Ali Samareh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Navid Jamali
- Department of Laboratory Sciences, Sirjan School of Medical Sciences, Sirjan, Iran
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2
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Wei S, Tang W, Chen D, Xiong J, Xue L, Dai Y, Guo Y, Wu C, Dai J, Wu M, Wang S. Multiomics insights into the female reproductive aging. Ageing Res Rev 2024; 95:102245. [PMID: 38401570 DOI: 10.1016/j.arr.2024.102245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
The human female reproductive lifespan significantly diminishes with age, leading to decreased fertility, reduced fertility quality and endocrine function disorders. While many aspects of aging in general have been extensively documented, the precise mechanisms governing programmed aging in the female reproductive system remain elusive. Recent advancements in omics technologies and computational capabilities have facilitated the emergence of multiomics deep phenotyping. Through the application and refinement of various high-throughput omics methods, a substantial volume of omics data has been generated, deepening our comprehension of the pathogenesis and molecular underpinnings of reproductive aging. This review highlights current and emerging multiomics approaches for investigating female reproductive aging, encompassing genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics. We elucidate their influence on fundamental cell biology and translational research in the context of reproductive aging, address the limitations and current challenges associated with multiomics studies, and offer a glimpse into future prospects.
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Affiliation(s)
- Simin Wei
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Weicheng Tang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Dan Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Jiaqiang Xiong
- Department of Obstetrics and Gynecology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Liru Xue
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yican Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Chuqing Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
| | - Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
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Winkler I, Tolkachov A, Lammers F, Lacour P, Daugelaite K, Schneider N, Koch ML, Panten J, Grünschläger F, Poth T, Ávila BMD, Schneider A, Haas S, Odom DT, Gonçalves Â. The cycling and aging mouse female reproductive tract at single-cell resolution. Cell 2024; 187:981-998.e25. [PMID: 38325365 DOI: 10.1016/j.cell.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 04/21/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction.
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Affiliation(s)
- Ivana Winkler
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany
| | - Alexander Tolkachov
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Fritjof Lammers
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Perrine Lacour
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Klaudija Daugelaite
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Nina Schneider
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany
| | - Marie-Luise Koch
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Jasper Panten
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany; German Cancer Research Center (DKFZ), Division of Computational Genomics and Systems Genetics, 69120 Heidelberg, Germany
| | - Florian Grünschläger
- Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany; German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Division of Stem Cells and Cancer, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Tanja Poth
- CMCP - Center for Model System and Comparative Pathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | | | - Augusto Schneider
- Universidade Federal de Pelotas, Faculdade de Nutrição, 96010-610 Pelotas, RS, Brazil
| | - Simon Haas
- German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Division of Stem Cells and Cancer, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Charité - Universitätsmedizin Berlin, Department of Hematology, Oncology and Cancer Immunology, 10115 Berlin, Germany
| | - Duncan T Odom
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Ângela Gonçalves
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany.
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Bedrick BS, Courtright L, Zhang J, Snow M, Amendola ILS, Nylander E, Cayton-Vaught K, Segars J, Singh B. A Systematic Review of Epigenetics of Endometriosis. F&S REVIEWS 2024; 5:100070. [PMID: 38524912 PMCID: PMC10956470 DOI: 10.1016/j.xfnr.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Objective To assess the current literature evaluating the epigenetics of endometriosis in humans. Evidence Review A systematic review was conducted in accordance with the PRISMA guidelines within PubMed, EBSCOhost, Cochrane Library, Embase, Scopus, and Web of Science Core Collection. A comprehensive search strategy was developed by a data informationist. Observational and interventional studies assessing epigenetics in humans published in English up to January 15th, 2023, were included. Two reviewers independently screened studies evaluating the role of epigenetics in endometriosis. The risk of bias was assessed using Cochrane RoB 2.0 tool and the Newcastle-Ottawa scale. Extracted data were analyzed descriptively. Results We identified 18.639 studies, of which 57 were included, comprising 1.623 patients with endometriosis and 1.243 controls. Among the 57 studies included, 50 (88%) were case-control studies, and 7 (12%) were cross-sectional. Fifty-nine percent of the studies were Asian, 25% were from America, 14% were European, and 2% were from Africa. Acetylation and methylation were the two main key histone modifications that were centered in this review. Accordingly, we classified the studies as those focusing on genome-wide methylation and those on histone acetylation. Several studies identified an association between endometriosis and hypermethylated genes, including the PGR-B, SF-1, and RASSF1A. The genes HOXA10, COX-2, IL-12B, and GATA6 were found to be hypomethylated in endometriotic tissue by several studies. In regards to histone modification, multiple studies reported that the acetylation levels of histones H3 and H4 affect multiple genes associated with endometriosis. In addition, HDAC2 was found to be elevated in endometriosis patients in two studies. Conclusion Several studies reported a significant difference between specific genes' methylation levels in endometrial biopsies and normal tissue, which suggests that DNA methylation may play an important role in the modulation of the genotype in endometriotic tissue. Acetylation and methylation are the two key histone modifications leading to differential gene expression in endometriotic tissues. The alterations in gene expression reported by the 57 studies can have direct implications on cell cycle growth, cell cycle arrest, and apoptosis and, therefore, might play a key role in the pathogenesis of endometriosis. This review offers insight that histone modifications need further research to evaluate their role as potential biomarkers and treatment targets for endometriosis. Although several key similarities were reported, there were some disagreements among the results, which might be attributable to the heterogeneity between studies. Further research with a more robust standardization is needed to validate the epigenetic changes in endometriosis.
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Affiliation(s)
- Bronwyn S. Bedrick
- Department of Gynecology & Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura Courtright
- Division of Reproductive Sciences & Women’s Health Research, Department of Gynecology & Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiahui Zhang
- Department of Obstetrics & Gynecology, University of Vermont Medical Center, Burlington, VT, USA
| | - Morgan Snow
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Isabela Landsteiner Sampaio Amendola
- Division of Reproductive Sciences & Women’s Health Research, Department of Gynecology & Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elisabeth Nylander
- Informationist Services, Welch Medical Library, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kamaria Cayton-Vaught
- Division of Reproductive Sciences & Women’s Health Research, Department of Gynecology & Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James Segars
- Division of Reproductive Sciences & Women’s Health Research, Department of Gynecology & Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bhuchitra Singh
- Division of Reproductive Sciences & Women’s Health Research, Department of Gynecology & Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Hu X, Wu H, Yong X, Wang Y, Yang S, Fan D, Xiao Y, Che L, Shi K, Li K, Xiong C, Zhu H, Qian Z. Cyclical endometrial repair and regeneration: Molecular mechanisms, diseases, and therapeutic interventions. MedComm (Beijing) 2023; 4:e425. [PMID: 38045828 PMCID: PMC10691302 DOI: 10.1002/mco2.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/21/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
The endometrium is a unique human tissue with an extraordinary ability to undergo a hormone-regulated cycle encompassing shedding, bleeding, scarless repair, and regeneration throughout the female reproductive cycle. The cyclical repair and regeneration of the endometrium manifest as changes in endometrial epithelialization, glandular regeneration, and vascularization. The mechanisms encompass inflammation, coagulation, and fibrinolytic system balance. However, specific conditions such as endometriosis or TCRA treatment can disrupt the process of cyclical endometrial repair and regeneration. There is uncertainty about traditional clinical treatments' efficacy and side effects, and finding new therapeutic interventions is essential. Researchers have made substantial progress in the perspective of regenerative medicine toward maintaining cyclical endometrial repair and regeneration in recent years. Such progress encompasses the integration of biomaterials, tissue-engineered scaffolds, stem cell therapies, and 3D printing. This review analyzes the mechanisms, diseases, and interventions associated with cyclical endometrial repair and regeneration. The review discusses the advantages and disadvantages of the regenerative interventions currently employed in clinical practice. Additionally, it highlights the significant advantages of regenerative medicine in this domain. Finally, we review stem cells and biologics among the available interventions in regenerative medicine, providing insights into future therapeutic strategies.
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Affiliation(s)
- Xulin Hu
- Clinical Medical College and Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduSichuanChina
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Haoming Wu
- Clinical Medical College and Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduSichuanChina
| | - Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapySichuan UniversityChengduSichuanChina
| | - Yao Wang
- Clinical Medical College and Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduSichuanChina
| | - Shuhao Yang
- Department of OrthopedicsThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Diyi Fan
- Clinical Medical College and Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduSichuanChina
| | - Yibo Xiao
- Clinical Medical College and Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduSichuanChina
| | - Lanyu Che
- Clinical Medical College and Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduSichuanChina
| | - Kun Shi
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Kainan Li
- Clinical Medical College and Affiliated Hospital of Chengdu UniversityChengdu UniversityChengduSichuanChina
| | | | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of EducationWest China Second University Hospital of Sichuan UniversityChengduSichuanChina
| | - Zhiyong Qian
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduSichuanChina
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Pathare ADS, Loid M, Saare M, Gidlöf SB, Zamani Esteki M, Acharya G, Peters M, Salumets A. Endometrial receptivity in women of advanced age: an underrated factor in infertility. Hum Reprod Update 2023; 29:773-793. [PMID: 37468438 PMCID: PMC10628506 DOI: 10.1093/humupd/dmad019] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/24/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Modern lifestyle has led to an increase in the age at conception. Advanced age is one of the critical risk factors for female-related infertility. It is well known that maternal age positively correlates with the deterioration of oocyte quality and chromosomal abnormalities in oocytes and embryos. The effect of age on endometrial function may be an equally important factor influencing implantation rate, pregnancy rate, and overall female fertility. However, there are only a few published studies on this topic, suggesting that this area has been under-explored. Improving our knowledge of endometrial aging from the biological (cellular, molecular, histological) and clinical perspectives would broaden our understanding of the risks of age-related female infertility. OBJECTIVE AND RATIONALE The objective of this narrative review is to critically evaluate the existing literature on endometrial aging with a focus on synthesizing the evidence for the impact of endometrial aging on conception and pregnancy success. This would provide insights into existing gaps in the clinical application of research findings and promote the development of treatment options in this field. SEARCH METHODS The review was prepared using PubMed (Medline) until February 2023 with the keywords such as 'endometrial aging', 'receptivity', 'decidualization', 'hormone', 'senescence', 'cellular', 'molecular', 'methylation', 'biological age', 'epigenetic', 'oocyte recipient', 'oocyte donation', 'embryo transfer', and 'pregnancy rate'. Articles in a language other than English were excluded. OUTCOMES In the aging endometrium, alterations occur at the molecular, cellular, and histological levels suggesting that aging has a negative effect on endometrial biology and may impair endometrial receptivity. Additionally, advanced age influences cellular senescence, which plays an important role during the initial phase of implantation and is a major obstacle in the development of suitable senolytic agents for endometrial aging. Aging is also accountable for chronic conditions associated with inflammaging, which eventually can lead to increased pro-inflammation and tissue fibrosis. Furthermore, advanced age influences epigenetic regulation in the endometrium, thus altering the relation between its epigenetic and chronological age. The studies in oocyte donation cycles to determine the effect of age on endometrial receptivity with respect to the rates of implantation, clinical pregnancy, miscarriage, and live birth have revealed contradictory inferences indicating the need for future research on the mechanisms and corresponding causal effects of women's age on endometrial receptivity. WIDER IMPLICATIONS Increasing age can be accountable for female infertility and IVF failures. Based on the complied observations and synthesized conclusions in this review, advanced age has been shown to have a negative impact on endometrial functioning. This information can provide recommendations for future research focusing on molecular mechanisms of age-related cellular senescence, cellular composition, and transcriptomic changes in relation to endometrial aging. Additionally, further prospective research is needed to explore newly emerging therapeutic options, such as the senolytic agents that can target endometrial aging without affecting decidualization. Moreover, clinical trial protocols, focusing on oocyte donation cycles, would be beneficial in understanding the direct clinical implications of endometrial aging on pregnancy outcomes.
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Affiliation(s)
- Amruta D S Pathare
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Marina Loid
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Merli Saare
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Sebastian Brusell Gidlöf
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Masoud Zamani Esteki
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Ganesh Acharya
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Medicine, Women’s Health and Perinatology Research Group, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maire Peters
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Andres Salumets
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
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7
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Ding H, Xu H, Zhang T, Shi C. Identification and validation of M2 macrophage-related genes in endometriosis. Heliyon 2023; 9:e22258. [PMID: 38058639 PMCID: PMC10695979 DOI: 10.1016/j.heliyon.2023.e22258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023] Open
Abstract
Aims M2 macrophage is believed to play an important role in the development of endometriosis. This study aimed to identify several key genes related to the M2 macrophage in endometriosis. Method Differential expressed genes between endometriosis and non-endometriosis were identified based on three microarray datasets from the Gene Expression Omnibus database. Gene modules significantly associated with M2 macrophage were identified from the weighted gene co-expression network analysis. Furthermore, by intersecting the differential expressed genes and M2 macrophage-associated module genes, M2 macrophage-related genes in endometriosis were identified. Functional analyses of the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes for these genes were then performed. Following, the least absolute shrinkage and selection operator, random forest, and receiver operating characteristic curves were further conducted to identify the key M2 macrophage-related genes in endometriosis. Finally, the expressions of key genes in endometriosis, as well as their correlations with M2 macrophages were verified in an independent validation cohort. Results Totally, 185 M2 macrophage-related genes were identified, and they were mainly enriched in functions associated with the cell cycle, oocyte maturation, and immune response. Following machine learning algorithms, eight key genes were selected in the endometriosis: PGR, OLFM4, PIP5K1B, CCNA1, BRIP1, CADM1, PRAME, and GCNT1. The eight key genes were confirmed to be negative with M2 macrophage infiltration levels. Furthermore, the expression levels of these genes were significantly lower in the middle secretory stage while relevantly higher in the proliferative stage. The validation analysis also showed similar outcomes with the above results. Conclusion Eight M2 macrophage-related genes were identified as potential biomarkers of endometriosis, providing novel understanding of immune cells in the endometriosis.
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Affiliation(s)
- Hongyan Ding
- Department of Obstetrics and Gynecology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, PR China
| | - Hongge Xu
- Department of Obstetrics and Gynecology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, PR China
| | - Ting Zhang
- Department of Obstetrics and Gynecology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, PR China
| | - Can Shi
- Department of Obstetrics and Gynecology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, PR China
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8
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Meltsov A, Saare M, Teder H, Paluoja P, Arffman RK, Piltonen T, Laudanski P, Wielgoś M, Gianaroli L, Koel M, Peters M, Salumets A, Krjutškov K, Palta P. Targeted gene expression profiling for accurate endometrial receptivity testing. Sci Rep 2023; 13:13959. [PMID: 37633957 PMCID: PMC10460380 DOI: 10.1038/s41598-023-40991-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/20/2023] [Indexed: 08/28/2023] Open
Abstract
Expressional profiling of the endometrium enables the personalised timing of the window of implantation (WOI). This study presents and evaluates a novel analytical pipeline based on a TAC-seq (Targeted Allele Counting by sequencing) method for endometrial dating. The expressional profiles were clustered, and differential expression analysis was performed on the model development group, using 63 endometrial biopsies spanning over proliferative (PE, n = 18), early-secretory (ESE, n = 18), mid-secretory (MSE, n = 17) and late-secretory (LSE, n = 10) endometrial phases of the natural cycle. A quantitative predictor model was trained on the development group and validated on sequenced samples from healthy women, consisting of 52 paired samples taken from ESE and MSE phases and five LSE phase samples from 31 individuals. Finally, the developed test was applied to 44 MSE phase samples from a study group of patients diagnosed with recurrent implantation failure (RIF). In validation samples (n = 57), we detected displaced WOI in 1.8% of the samples from fertile women. In the RIF study group, we detected a significantly higher proportion of the samples with shifted WOI than in the validation set of samples from fertile women, 15.9% and 1.8% (p = 0.012), respectively. The developed model was evaluated with an average cross-validation accuracy of 98.8% and an accuracy of 98.2% in the validation group. The developed beREADY screening model enables sensitive and dynamic detection of selected transcriptome biomarkers, providing a quantitative and accurate prediction of endometrial receptivity status.
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Affiliation(s)
- Alvin Meltsov
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Merli Saare
- Competence Centre On Health Technologies, 50411, Tartu, Estonia.
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia.
| | - Hindrek Teder
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Institute of Biomedicine and Translational Medicine, University of Tartu, 50411, Tartu, Estonia
| | - Priit Paluoja
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Riikka K Arffman
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, FI-90014, Oulu, Finland
| | - Terhi Piltonen
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, FI-90014, Oulu, Finland
| | - Piotr Laudanski
- Oviklinika Infertility Center, 01-377, Warsaw, Poland
- Women's Health Research Institute, Calisia University, 62-800, Kalisz, Poland
- Department of Obstetrics, Gynecology and Gynaecological Oncology, Medical University of Warsaw, 02-091, Warsaw, Poland
| | | | - Luca Gianaroli
- SISMeR, Reproductive Medicine Institute, 40138, Bologna, Italy
| | - Mariann Koel
- Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Maire Peters
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Andres Salumets
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, SE-141 52, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Priit Palta
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
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9
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Mortlock S, Houshdaran S, Kosti I, Rahmioglu N, Nezhat C, Vitonis AF, Andrews SV, Grosjean P, Paranjpe M, Horne AW, Jacoby A, Lager J, Opoku-Anane J, Vo KC, Manvelyan E, Sen S, Ghukasyan Z, Collins F, Santamaria X, Saunders P, Kober K, McRae AF, Terry KL, Vallvé-Juanico J, Becker C, Rogers PAW, Irwin JC, Zondervan K, Montgomery GW, Missmer S, Sirota M, Giudice L. Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function. Commun Biol 2023; 6:780. [PMID: 37587191 PMCID: PMC10432557 DOI: 10.1038/s42003-023-05070-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/23/2023] [Indexed: 08/18/2023] Open
Abstract
Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Herein, we characterize variation in DNA methylation (DNAm) and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genotype data and methylation in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles associated with stage III/IV endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. Menstrual cycle phase was a major source of DNAm variation suggesting cellular and hormonally-driven changes across the cycle can regulate genes and pathways responsible for endometrial physiology and function. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis, highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.
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Affiliation(s)
- Sally Mortlock
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Sahar Houshdaran
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Nilufer Rahmioglu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Camran Nezhat
- Stanford University Medical Center, Palo Alto, CA, USA
- University of California San Francisco, San Francisco, CA, USA
- Camran Nezhat Institute, Center for Special Minimally Invasive and Robotic Surgery, Woodside, CA, USA
| | - Allison F Vitonis
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shan V Andrews
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Parker Grosjean
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Manish Paranjpe
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Andrew W Horne
- MRC Centre for Reproductive Health, University of Edinburgh, QMRI, Edinburgh, UK
| | - Alison Jacoby
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jeannette Lager
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Opoku-Anane
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kim Chi Vo
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Evelina Manvelyan
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sushmita Sen
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zhanna Ghukasyan
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Frances Collins
- MRC Centre for Reproductive Health, University of Edinburgh, QMRI, Edinburgh, UK
| | - Xavier Santamaria
- Carlos Simon Foundation, Health Research Institute, Valencia, Spain
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Philippa Saunders
- Centre for Inflammation Research, Institute for Regeneration and Repair University of Edinburgh, Edinburgh, UK
| | - Kord Kober
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Allan F McRae
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, MA, USA
| | - Júlia Vallvé-Juanico
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Christian Becker
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter A W Rogers
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women's Hospital, Melbourne, Australia
| | - Juan C Irwin
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Krina Zondervan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Stacey Missmer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Division of Neonatology, University of California San Francisco, San Francisco, CA, USA
| | - Linda Giudice
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA.
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10
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Ferrari AJ, Rawat P, Rendulich HS, Annapragada AV, Kinose Y, Zhang X, Devins K, Budina A, Scharpf RB, Mitchell MA, Tanyi JL, Morgan MA, Schwartz LE, Soong TR, Velculescu VE, Drapkin R. H2Bub1 loss is an early contributor to clear cell ovarian cancer progression. JCI Insight 2023; 8:e164995. [PMID: 37345659 PMCID: PMC10371241 DOI: 10.1172/jci.insight.164995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/04/2023] [Indexed: 06/23/2023] Open
Abstract
Epigenetic aberrations, including posttranslational modifications of core histones, are major contributors to cancer. Here, we define the status of histone H2B monoubiquitylation (H2Bub1) in clear cell ovarian carcinoma (CCOC), low-grade serous carcinoma, and endometrioid carcinomas. We report that clear cell carcinomas exhibited profound loss, with nearly all cases showing low or negative H2Bub1 expression. Moreover, we found that H2Bub1 loss occurred in endometriosis and atypical endometriosis, which are established precursors to CCOCs. To examine whether dysregulation of a specific E3 ligase contributes to the loss of H2Bub1, we explored expression of ring finger protein 40 (RNF40), ARID1A, and UBR7 in the same case cohort. Loss of RNF40 was significantly and profoundly correlated with loss of H2Bub1. Using genome-wide DNA methylation profiles of 230 patients with CCOC, we identified hypermethylation of RNF40 in CCOC as a likely mechanism underlying the loss of H2Bub1. Finally, we demonstrated that H2Bub1 depletion promoted cell proliferation and clonogenicity in an endometriosis cell line. Collectively, our results indicate that H2Bub1 plays a tumor-suppressive role in CCOCs and that its loss contributes to disease progression.
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Affiliation(s)
- Adam J. Ferrari
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
- Graduate Program in Cell and Molecular Biology; and
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Priyanka Rawat
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Hannah S. Rendulich
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Akshaya V. Annapragada
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yasuto Kinose
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Xiaoming Zhang
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Devins
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Budina
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert B. Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marilyn A. Mitchell
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Janos L. Tanyi
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Mark A. Morgan
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Lauren E. Schwartz
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - T. Rinda Soong
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Victor E. Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
- Graduate Program in Cell and Molecular Biology; and
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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11
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DNA Methylation of Window of Implantation Genes in Cervical Secretions Predicts Ongoing Pregnancy in Infertility Treatment. Int J Mol Sci 2023; 24:ijms24065598. [PMID: 36982674 PMCID: PMC10051225 DOI: 10.3390/ijms24065598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/17/2023] Open
Abstract
Window of implantation (WOI) genes have been comprehensively identified at the single cell level. DNA methylation changes in cervical secretions are associated with in vitro fertilization embryo transfer (IVF-ET) outcomes. Using a machine learning (ML) approach, we aimed to determine which methylation changes in WOI genes from cervical secretions best predict ongoing pregnancy during embryo transfer. A total of 2708 promoter probes were extracted from mid-secretory phase cervical secretion methylomic profiles for 158 WOI genes, and 152 differentially methylated probes (DMPs) were selected. Fifteen DMPs in 14 genes (BMP2, CTSA, DEFB1, GRN, MTF1, SERPINE1, SERPINE2, SFRP1, STAT3, TAGLN2, TCF4, THBS1, ZBTB20, ZNF292) were identified as the most relevant to ongoing pregnancy status. These 15 DMPs yielded accuracy rates of 83.53%, 85.26%, 85.78%, and 76.44%, and areas under the receiver operating characteristic curves (AUCs) of 0.90, 0.91, 0.89, and 0.86 for prediction by random forest (RF), naïve Bayes (NB), support vector machine (SVM), and k-nearest neighbors (KNN), respectively. SERPINE1, SERPINE2, and TAGLN2 maintained their methylation difference trends in an independent set of cervical secretion samples, resulting in accuracy rates of 71.46%, 80.06%, 80.72%, and 80.68%, and AUCs of 0.79, 0.84, 0.83, and 0.82 for prediction by RF, NB, SVM, and KNN, respectively. Our findings demonstrate that methylation changes in WOI genes detected noninvasively from cervical secretions are potential markers for predicting IVF-ET outcomes. Further studies of cervical secretion of DNA methylation markers may provide a novel approach for precision embryo transfer.
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12
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Lee YX, Su PH, Do AQ, Tzeng CR, Hu YM, Chen CH, Chen CW, Liao CC, Chen LY, Weng YC, Wang HC, Lai HC. Cervical Secretion Methylation Is Associated with the Pregnancy Outcome of Frozen-Thawed Embryo Transfer. Int J Mol Sci 2023; 24:ijms24021726. [PMID: 36675243 PMCID: PMC9863254 DOI: 10.3390/ijms24021726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The causes of implantation failure remain a black box in reproductive medicine. The exact mechanism behind the regulation of endometrial receptivity is still unknown. Epigenetic modifications influence gene expression patterns and may alter the receptivity of human endometrium. Cervical secretions contain endometrial genetic material, which can be used as an indicator of the endometrial condition. This study evaluates the association between the cervical secretion gene methylation profile and pregnancy outcome in a frozen-thawed embryonic transfer (FET) cycle. Cervical secretions were collected from women who entered the FET cycle with a blastocyst transfer (36 pregnant and 36 non-pregnant women). The DNA methylation profiles of six candidate genes selected from the literature review were measured by quantitative methylation-specific PCR (qMSP). Bioinformatic analysis of six selected candidate genes showed significant differences in DNA methylation between receptive and pre-receptive endometrium. All candidate genes showed different degrees of correlation with the pregnancy outcomes in the logistic regression model. A machine learning approach showed that the combination of candidate genes' DNA methylation profiles could differentiate pregnant from non-pregnant samples with an accuracy as high as 86.67% and an AUC of 0.81. This study demonstrated the association between cervical secretion methylation profiles and pregnancy outcomes in an FET cycle and provides a basis for potential clinical application as a non-invasive method for implantation prediction.
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Affiliation(s)
- Yi-Xuan Lee
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11030, Taiwan
- Taipei Fertility Center, Taipei 11030, Taiwan
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
| | - Po-Hsuan Su
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
| | - Anh Q. Do
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
- Department of Obstetrics and Gynecology, Hai Phong University of Medicine and Pharmacy, Hai Phong 04254, Vietnam
| | - Chii-Ruei Tzeng
- Taipei Fertility Center, Taipei 11030, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11303, Taiwan
| | - Yu-Ming Hu
- Taipei Fertility Center, Taipei 11030, Taiwan
| | - Chi-Huang Chen
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11303, Taiwan
- Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei 11030, Taiwan
| | - Chien-Wen Chen
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
| | - Chi-Chun Liao
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
| | - Lin-Yu Chen
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11303, Taiwan
| | - Yu-Chun Weng
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
| | - Hui-Chen Wang
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan
| | - Hung-Cheng Lai
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11030, Taiwan
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei 23504, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11303, Taiwan
- Correspondence: or ; Tel.: +886-2-2249-0088 (ext. 8868)
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13
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Jin M, Ji J, Chen X, Zhou Y, Wang D, Liu A. The emerging role of TET enzymes in the immune microenvironment at the maternal-fetal interface during decidualization and early pregnancy. Front Immunol 2023; 13:1066599. [PMID: 36685517 PMCID: PMC9850229 DOI: 10.3389/fimmu.2022.1066599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
A dysregulated immune microenvironment at the maternal-fetal interface in early pregnancy may lead to early pregnancy loss, fetal growth restriction, and preeclampsia. However, major questions about how epigenetic modifications regulate the immune microenvironment during the decidualization process and embryo implantation remain unanswered. DNA methylation, the main epigenetic mechanism involved in the endometrial cycle, is crucial for specific transcriptional networks associated with endometrial stromal cell (ESC) proliferation, hormone response, decidualization, and embryo implantation. Ten-eleven translocation (TET) enzymes, responsible for catalyzing the conversion of 5-methylcytosine to 5-hydroxymethylcyosine, 5-formylytosine, and 5-carboxylcyosine to achieve the DNA demethylation process, appear to play a critical role in decidualization and embryo implantation. Here, we provide a comprehensive view of their structural similarities and the common mechanism of regulation in the microenvironment at the maternal-fetal interface during decidualization and early pregnancy. We also discuss their physiological role in the decidual immune microenvironment. Finally, we propose a key hypothesis regarding TET enzymes at the maternal-fetal interface between decidual immune cells and ESCs. Future work is needed to elucidate their functional role and examine therapeutic strategies targeting these enzymes in pregnancy-related disease preclinical models, which would be of great value for future implications in disease diagnosis or treatment.
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Affiliation(s)
- Mengmeng Jin
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Jianxiong Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xi Chen
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Ying Zhou
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Dimin Wang
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China,*Correspondence: Aixia Liu, ; Dimin Wang,
| | - Aixia Liu
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China,Department of Reproductive Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China,*Correspondence: Aixia Liu, ; Dimin Wang,
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14
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Lei L, Xu X, Gong C, Lin B, Li F. Integrated analysis of genome-wide gene expression and DNA methylation profiles reveals candidate genes in ovary endometriosis. Front Endocrinol (Lausanne) 2023; 14:1093683. [PMID: 37033258 PMCID: PMC10076879 DOI: 10.3389/fendo.2023.1093683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND The incidence of endometriosis (EMs), a common disease in gynecology, has increased over the years. Women suffer from the symptoms caused by EMs, such as chronic pelvic pain, dysmenorrhea, and infertility. However, the etiology and pathophysiology of EMs remain unclear. This study aimed to identify candidate genes of endometriosis through integrated analysis of genome-wide gene expression and DNA methylation profiles. RESULTS Eutopic and ectopic endometrial tissues were collected from patients who were diagnosed as ovarian EMs. Genome-wide methylation profiling identified 17551 differentially methylated loci, with 9777 hypermethylated and 7774 hypomethylated loci. Differentially methylated loci were mainly concentrated in the gene body and intergenic regions. Genome-wide gene expression profiling identified 1837 differentially expressed genes (DEGs), with 1079 genes upregulated and 758 downregulated in ectopic groups. Integrated analysis revealed that DNA methylation was negatively correlated to gene expression in most genomic regions, such as exon, 3'UTR, 5'UTR, and promoter. We also identified promoter-related (53 downregulated and 113 upregulated) and enhancer-related DMGs (212 downregulated and 232 upregulated), which were significantly correlated to the gene expression. Further validation of the top-ranked genes belonging to differentially methylated genes (DMGs) and DEGs revealed that TMEM184A, GREM2, SFN, KIR3DX1, HPGD, ESR1, BST2, PIK3CG and RNASE1 were significant candidate genes in ovarian endometriosis. CONCLUSION Our study revealed the significance of DNA methylation in the gene expression in ovary endometriosis, which provides new insights and a molecular foundation for understanding the underlying mechanisms of endometriosis.
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Affiliation(s)
- Lei Lei
- Department of Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xinxin Xu
- Department of Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chengchen Gong
- Department of Dermatology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bowen Lin
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Fang Li, ; Bowen Lin,
| | - Fang Li
- Department of Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Fang Li, ; Bowen Lin,
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15
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Li Piani L, Vigano' P, Somigliana E. Epigenetic clocks and female fertility timeline: A new approach to an old issue? Front Cell Dev Biol 2023; 11:1121231. [PMID: 37025178 PMCID: PMC10070683 DOI: 10.3389/fcell.2023.1121231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Worldwide increase in life expectancy has boosted research on aging. Overcoming the concept of chronological age, higher attention has been addressed to biological age, which reflects a person's real health state, and which may be the resulting combination of both intrinsic and environmental factors. As epigenetics may exert a pivotal role in the biological aging, epigenetic clocks were developed. They are based on mathematical models aimed at identifying DNA methylation patterns that can define the biological age and that can be adopted for different clinical scopes (i.e., estimation of the risks of developing age-related disorders or predicting lifespan). Recently, epigenetic clocks have gained a peculiar attention in the fertility research field, in particular in the female counterpart. The insight into the possible relations between epigenetic aging and women's infertility might glean additional information about certain conditions that are still not completely understood. Moreover, they could disclose significant implications for health promotion programs in infertile women. Of relevance here is that the impact of biological age and epigenetics may not be limited to fertility status but could translate into pregnancy issues. Indeed, epigenetic alterations of the mother may transfer into the offspring, and pregnancy itself as well as related complications could contribute to epigenetic modifications in both the mother and newborn. However, even if the growing interest has culminated in the conspicuous production of studies on these topics, a global overview and the availability of validated instruments for diagnosis is still missing. The present narrative review aims to explore the possible bonds between epigenetic aging and fertility timeline. In the "infertility" section, we will discuss the advances on epigenetic clocks focusing on the different tissues examined (endometrium, peripheral blood, ovaries). In the "pregnancy" section, we will discuss the results obtained from placenta, umbilical cord and peripheral blood. The possible role of epigenetic aging on infertility mechanisms and pregnancy outcomes represents a question that may configure epigenetic clock as a bond between two apparently opposite worlds: infertility and pregnancy.
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Affiliation(s)
- Letizia Li Piani
- Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy
- *Correspondence: Letizia Li Piani,
| | - Paola Vigano'
- Infertility Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Edgardo Somigliana
- Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy
- Infertility Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
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Deryabin PI, Borodkina AV. Epigenetic clocks provide clues to the mystery of uterine ageing. Hum Reprod Update 2022; 29:259-271. [PMID: 36515535 DOI: 10.1093/humupd/dmac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Rising maternal ages and age-related fertility decline are a global challenge for modern reproductive medicine. Clinicians and researchers pay specific attention to ovarian ageing and hormonal insufficiency in this regard. However, uterine ageing is often left out of the picture, with the majority of reproductive clinicians being close to unanimous on the absence of age-related functional decline in the uterine tissues. Therefore, most existing techniques to treat an age-related decline in implantation rates are based primarily on hormonal supplementation and oocyte donation. Solving the issue of uterine ageing might lead to an adjustment to these methods. OBJECTIVE AND RATIONALE A focus on uterine ageing and the possibility of slowing it emerged with the development of the information theory of ageing, which identifies genomic instability and erosion of the epigenetic landscape as important drivers of age-related decline in the functionality of most cells and tissues. Age-related smoothing of this landscape and a decline in tissue function can be assessed by measuring the ticking of epigenetic clocks. Within this review, we explore whether the uterus experiences age-related alterations using this elegant approach. We analyse existing data on epigenetic clocks in the endometrium, highlight approaches to improve the accuracy of the clocks in this cycling tissue, speculate on the endometrial pathologies whose progression might be predicted by the altered speed of epigenetic clocks and discuss the possibilities of slowing down the ticking of these clocks. SEARCH METHODS Data for this review were identified by searches of Medline, PubMed and Google Scholar. References from relevant articles using the search terms 'ageing', 'maternal age', 'female reproduction', 'uterus', 'endometrium', 'implantation', 'decidualization', 'epigenetic clock', 'biological age', 'DNA methylation', 'fertility' and 'infertility' were selected. A total of 95 articles published in English between 1985 and 2022 were included, six of which describe the use of the epigenetic clock to evaluate uterine/endometrium ageing. OUTCOMES Application of the Horvath and DNAm PhenoAge epigenetic clocks demonstrated a poor correlation with chronological age in the endometrium. Several approaches were suggested to enhance the predictive power of epigenetic clocks for the endometrium. The first was to increase the number of samples in the training dataset, as for the Zang clock, or to use more sophisticated clock-building algorithms, as for the AltumAge clock. The second method is to adjust the clocks according to the dynamic nature of the endometrium. Using either approach revealed a strong correlation with chronological age in the endometrium, providing solid evidence for age-related functional decline in this tissue. Furthermore, age acceleration/deceleration, as estimated by epigenetic clocks, might be a promising tool to predict or to gain insights into the origin of various endometrial pathologies, including recurrent implantation failure, cancer and endometriosis. Finally, there are several strategies to slow down or even reverse epigenetic clocks that might be applied to reduce the risk of age-related uterine impairments. WIDER IMPLICATIONS The uterine factor should be considered, along with ovarian issues, to correct for the decline in female fertility with age. Epigenetic clocks can be tested to gain a deeper understanding of various endometrial disorders.
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Affiliation(s)
- Pavel I Deryabin
- Mechanisms of Cellular Senescence Group, Institute of Cytology of the Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Aleksandra V Borodkina
- Mechanisms of Cellular Senescence Group, Institute of Cytology of the Russian Academy of Sciences, Saint-Petersburg, Russia
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Epigenetic age provides insight into tissue origin in endometriosis. Sci Rep 2022; 12:21281. [PMID: 36481772 PMCID: PMC9732286 DOI: 10.1038/s41598-022-25416-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Endometriosis is a common reproductive disease with a heterogeneous presentation. Classification attempts have thus far not offered insight into its cause or its symptoms. Endometriosis may result from the migration of shed endometrium to the peritoneal cavity. However, there are cases reported in girls without uteruses and men. While a non-retrograde menstruation origin of ectopic tissue is certain in these cases, we explored the use of DNA methylation age (DNAm age) to distinguish between retrograde and non-retrograde tissue origin in endometriosis. Using publicly available DNA methylation data and Horvath's pan-tissue epigenetic clock, we compared DNAm age and epigenetic age acceleration (EAA) of ectopic lesions to eutopic endometrium of diseased and control endometrium. We examined EAA in cancer metastasis and teratomas to control for migration and developmental origin. Disease status does not change DNAm age of eutopic endometrium, but the effect of ectopic status was profound: - 16.88 years (p = 4.82 × 10-7). There were no differences between EAA of primary/metastatic tumor paired samples, suggesting that the observed effect is not due to tissue migration or ectopic location. Immature or mature teratoma compartments decreased DNAm age by 9.44 and 7.40 years respectively, suggesting that developmental state correlates with DNAm age. Ectopic endometriotic tissue exhibits decelerated DNAm age, similar to that observed in teratomas composed of multipotent tissue, but distinct from eutopic tissue. The migration process does not change DNAm age and eutopic endometrium is concordant with chronological age regardless of disease status. We conclude that DNAm age of ectopic lesions suggests a distinct developmental origin for a subset of lesions. This finding may assist in classifying endometriosis into distinct subtypes that may be clinically relevant.
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Adamczyk M, Rawłuszko-Wieczorek AA, Wirstlein P, Nowicki M, Jagodziński PP, Wender-Ozegowska E, Kedzia M. Assessment of TET1 gene expression, DNA methylation and H3K27me3 level of its promoter region in eutopic endometrium of women with endometriosis and infertility. Biomed Pharmacother 2022; 150:112989. [PMID: 35489280 DOI: 10.1016/j.biopha.2022.112989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 11/02/2022] Open
Abstract
Endometriosis is the cause of infertility. The eutopic endometrium of women with endometriosis showed an aberrant expression pattern of multitude genes. The role of TET1 protein in the pathogenesis of endometriosis and related infertility is not sufficiently known. Further, knowledge on TET1 transcriptional control still remains incomplete. The aim of the study was assessment of TET1 gene expression, DNA methylation and H3K27me3 level of its promoter region in eutopic endometrium of women with endometriosis and infertility. The study included 44 infertile patients with endometriosis (IWE) and 77 infertile (IW) and fertile (FW) patients without endometriosis. The research material was eutopic endometrium. The TET1 mRNA level was analyzed by qPCR. Western blot was used to evaluate the level of TET1 protein. The level of DNA methylation and H3K27me3 level of TET1 gene's promoter region were assessed using HRM and ChIP qPCR, respectively. The level of TET1 expression (TET1 mRNA; TET1 protein level) was lower in IWE during the implantation window (p < 0.001; p = 0.0329). The level of TET1 DNA methylation was higher in the secretory endometrium in mild and advanced IWE (p < 0.004; p < 0.008). H3K27me3 level did not differ between the study groups. The diminished expression of TET1 gene during the secretory phase, may account for the aberrant process of embryonic implantation in infertile endometriosis patients. DNA hypermethylation of TET1 gene is a potential relevant regulator of its expression. H3K27me3 occupancy does not affect the expression of TET1 gene in our study group.
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Affiliation(s)
- Magdalena Adamczyk
- Department of Reproduction, Poznan University of Medical Sciences, 60-535, Poland.
| | | | - Przemysław Wirstlein
- Department of Reproduction, Poznan University of Medical Sciences, 60-535, Poland
| | - Michał Nowicki
- Department of Histology and Embriology, Poznan University of Medical Sciences, 60-781, Poland
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 60-781, Poland
| | - Ewa Wender-Ozegowska
- Department of Reproduction, Poznan University of Medical Sciences, 60-535, Poland
| | - Malgorzata Kedzia
- Department of Reproduction, Poznan University of Medical Sciences, 60-535, Poland
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Epigenetic Factors in Eutopic Endometrium in Women with Endometriosis and Infertility. Int J Mol Sci 2022; 23:ijms23073804. [PMID: 35409163 PMCID: PMC8998720 DOI: 10.3390/ijms23073804] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Eutopic endometrium in patients with endometriosis is characterized by aberrant expression of essential genes during the implantation window. It predisposes to disturbance of endometrial receptivity. The pathomechanism of implantation failures in women with endometriosis remains unclear. This paper aims to summarize the knowledge on epigenetic mechanisms in eutopic endometrium in the group of patients with both endometriosis and infertility. The impaired DNA methylation patterns of gene promoter regions in eutopic tissue was established. The global profile of histone acetylation and methylation and the analysis of selected histone modifications showed significant differences in the endometrium of women with endometriosis. Aberrant expression of the proposed candidate genes may promote an unfavorable embryonic implantation environment of the endometrium due to an immunological dysfunction, inflammatory reaction, and apoptotic response in women with endometriosis. The role of the newly discovered proteins regulating gene expression, i.e., TET proteins, in endometrial pathology is not yet completely known. The cells of the eutopic endometrium in women with endometriosis contain a stable, impaired methylation pattern and a histone code. Medication targeting critical genes responsible for the aberrant gene expression pattern in eutopic endometrium may help treat infertility in women with endometriosis.
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Chen CW, Huang RL, Do AQ, Wang HC, Lee YX, Wang CW, Hsieh CC, Tzeng CR, Hu YM, Chen CH, Weng YC, Su PH, Chen LY, Lai HC. Genome-wide analysis of cervical secretions obtained during embryo transfer reveals the association between deoxyribonucleic acid methylation and pregnancy outcomes. F&S SCIENCE 2022; 3:74-83. [PMID: 35559997 DOI: 10.1016/j.xfss.2021.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To study whether the methylation status of cervical secretions can reflect the ability of the endometrium to allow embryo implantation. DESIGN Case-control study. SETTING In vitro fertilization centers. PATIENT(S) Women undergoing embryo transfer cycles, in which at least 1 good-quality embryo was transferred. INTERVENTION(S) Collection of cervical secretions during the procedure of embryo transfer. MAIN OUTCOME MEASURE(S) Methylation profiles of cervical secretions in relation to pregnancy outcomes. RESULT(S) Genome-wide methylation profiles differ between cervical secretions from pregnancy and nonpregnancy cycles. Clustering analysis on the basis of the top 2,000 differentially methylated probes of cervical secretions from 28 pregnancy and 29 nonpregnancy cycles correctly categorized 86.0% of the samples in terms of conceptional status, which was verified in selected genes by quantitative methylation-specific polymerase chain reaction and validated in another independent sample set. The combination of selected genes was estimated to predict pregnancy outcomes with a maximal area under the receiver operating characteristic curve of 0.83. CONCLUSION(S) The methylation profiles of cervical secretions were associated with pregnancy outcomes in embryo transfer cycles. Although not clinically useful at present, deoxyribonucleic acid methylation in cervical secretions may shed new light on the less invasive assessment of endometrial receptivity.
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Affiliation(s)
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Anh Q Do
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Obstetrics and Gynecology, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam; International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hui-Chen Wang
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Xuan Lee
- Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Graduate Institute of Clinical Medicine, Taipei Medical University, Taipei, Taiwan; Taipei Fertility Center, Taipei, Taiwan
| | | | | | | | | | - Chi-Huang Chen
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yu-Chun Weng
- Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Po-Hsuan Su
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Lin-Yu Chen
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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Frincu F, Carp-Veliscu A, Petca A, Badiu DC, Bratila E, Cirstoiu M, Mehedintu C. Maternal-Fetal Outcomes in Women with Endometriosis and Shared Pathogenic Mechanisms. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:1258. [PMID: 34833476 PMCID: PMC8625694 DOI: 10.3390/medicina57111258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 12/20/2022]
Abstract
The connection between endometriosis and pregnancy outcomes is trending among the research topics. Until recently, endometriosis and its painful symptomatology were considered to be alleviated by pregnancy. However, these beliefs have shifted, as emerging literature has demonstrated the role of this condition in affecting pregnancy evolution. The underlying pathogenesis of endometriosis is still poorly understood, all the more when pregnancy complications are involved. Debatable opinions on endometriosis associated with obstetric complications exist because of the potential bias resulting from the heterogeneity of preceding evidence. This review aims to evaluate the connection between endometriosis and adverse pregnancy outcomes and their shared pathogenic mechanisms. We searched PubMed and EMBASE and focused on the studies that include placenta praevia, premature rupture of membranes, spontaneous preterm birth, gestational hypertension, preeclampsia, obstetric hemorrhages (ante- and postpartum bleeding, abruptio placentae), miscarriage, stillbirth, neonatal death, gestational diabetes mellitus, gestational cholestasis, small for gestational age, and their association with endometriosis. Not only the risks of emergence were highlighted, but also the pathogenic connections. Epigenetic alterations of some genes were found to be mirrored both in endometriosis and obstetric complications. This review issues a warning for providing increased attention to pregnant women with endometriosis and newborns as higher risks of preeclampsia, placental issues, and preterm deliveries are associated.
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Affiliation(s)
- Francesca Frincu
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (F.F.); (A.P.); (E.B.); (M.C.); (C.M.)
| | - Andreea Carp-Veliscu
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (F.F.); (A.P.); (E.B.); (M.C.); (C.M.)
| | - Aida Petca
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (F.F.); (A.P.); (E.B.); (M.C.); (C.M.)
| | - Dumitru-Cristinel Badiu
- Department of General Surgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Elvira Bratila
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (F.F.); (A.P.); (E.B.); (M.C.); (C.M.)
| | - Monica Cirstoiu
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (F.F.); (A.P.); (E.B.); (M.C.); (C.M.)
| | - Claudia Mehedintu
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (F.F.); (A.P.); (E.B.); (M.C.); (C.M.)
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Retis-Resendiz AM, González-García IN, León-Juárez M, Camacho-Arroyo I, Cerbón M, Vázquez-Martínez ER. The role of epigenetic mechanisms in the regulation of gene expression in the cyclical endometrium. Clin Epigenetics 2021; 13:116. [PMID: 34034824 PMCID: PMC8146649 DOI: 10.1186/s13148-021-01103-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The human endometrium is a highly dynamic tissue whose function is mainly regulated by the ovarian steroid hormones estradiol and progesterone. The serum levels of these and other hormones are associated with three specific phases that compose the endometrial cycle: menstrual, proliferative, and secretory. Throughout this cycle, the endometrium exhibits different transcriptional networks according to the genes expressed in each phase. Epigenetic mechanisms are crucial in the fine-tuning of gene expression to generate such transcriptional networks. The present review aims to provide an overview of current research focused on the epigenetic mechanisms that regulate gene expression in the cyclical endometrium and discuss the technical and clinical perspectives regarding this topic. MAIN BODY The main epigenetic mechanisms reported are DNA methylation, histone post-translational modifications, and non-coding RNAs. These epigenetic mechanisms induce the expression of genes associated with transcriptional regulation, endometrial epithelial growth, angiogenesis, and stromal cell proliferation during the proliferative phase. During the secretory phase, epigenetic mechanisms promote the expression of genes associated with hormone response, insulin signaling, decidualization, and embryo implantation. Furthermore, the global content of specific epigenetic modifications and the gene expression of non-coding RNAs and epigenetic modifiers vary according to the menstrual cycle phase. In vitro and cell type-specific studies have demonstrated that epithelial and stromal cells undergo particular epigenetic changes that modulate their transcriptional networks to accomplish their function during decidualization and implantation. CONCLUSION AND PERSPECTIVES Epigenetic mechanisms are emerging as key players in regulating transcriptional networks associated with key processes and functions of the cyclical endometrium. Further studies using next-generation sequencing and single-cell technology are warranted to explore the role of other epigenetic mechanisms in each cell type that composes the endometrium throughout the menstrual cycle. The application of this knowledge will definitively provide essential information to understand the pathological mechanisms of endometrial diseases, such as endometriosis and endometrial cancer, and to identify potential therapeutic targets and improve women's health.
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Affiliation(s)
- Alejandra Monserrat Retis-Resendiz
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Ixchel Nayeli González-García
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Moisés León-Juárez
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Marco Cerbón
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Edgar Ricardo Vázquez-Martínez
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico.
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Joshi NR, Kohan-Ghadr HR, Roqueiro DS, Yoo JY, Fru K, Hestermann E, Yuan L, Ho SM, Jeong JW, Young SL, Lessey BA, Fazleabas AT. Genetic and epigenetic changes in the eutopic endometrium of women with endometriosis: association with decreased endometrial αvβ3 integrin expression. Mol Hum Reprod 2021; 27:6163298. [PMID: 33693877 DOI: 10.1093/molehr/gaab018] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 02/09/2021] [Indexed: 01/10/2023] Open
Abstract
About 40% of women with infertility and 70% of women with pelvic pain suffer from endometriosis. The pregnancy rate in women undergoing IVF with low endometrial integrin αvβ3 (LEI) expression is significantly lower compared to the women with high endometrial integrin αvβ3 (HEI). Mid-secretory eutopic endometrial biopsies were obtained from healthy controls (C; n=3), and women with HEI (n=4) and LEI (n=4) and endometriosis. Changes in gene expression were assessed using human gene arrays and DNA methylation data were derived using 385 K Two-Array Promoter Arrays. Transcriptional analysis revealed that LEI and C groups clustered separately with 396 differentially expressed genes (DEGs) (P<0.01: 275 up and 121 down) demonstrating that transcriptional and epigenetic changes are distinct in the LEI eutopic endometrium compared to the C and HEI group. In contrast, HEI vs C and HEI vs LEI comparisons only identified 83 and 45 DEGs, respectively. The methylation promoter array identified 1304 differentially methylated regions in the LEI vs C comparison. The overlap of gene and methylation array data identified 14 epigenetically dysregulated genes and quantitative RT-PCR analysis validated the transcriptomic findings. The analysis also revealed that aryl hydrocarbon receptor (AHR) was hypomethylated and significantly overexpressed in LEI samples compared to C. Further analysis validated that AHR transcript and protein expression are significantly (P<0.05) increased in LEI women compared to C. The increase in AHR, together with the altered methylation status of the 14 additional genes, may provide a diagnostic tool to identify the subset of women who have endometriosis-associated infertility.
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Affiliation(s)
- Niraj R Joshi
- Michigan State University, College of Human Medicine, Grand Rapids, MI, USA
| | | | | | - Jung Yoon Yoo
- Department of Biochemistry and Molecular Biology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
| | - Karenne Fru
- Coastal Reproductive Endocrinology and Infertility, Wilmington, NC, USA
| | | | - Lingwen Yuan
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Shuk-Mei Ho
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jae-Wook Jeong
- Michigan State University, College of Human Medicine, Grand Rapids, MI, USA
| | - Steven L Young
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
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Xiao L, Pei T, Huang W, Zhou M, Fu J, Tan J, Liu T, Song Y, Yang S. MicroRNA22-5p targets ten-eleven translocation and regulates estrogen receptor 2 expression in infertile women with minimal/mild endometriosis during implantation window. PLoS One 2020; 15:e0234086. [PMID: 32658928 PMCID: PMC7357761 DOI: 10.1371/journal.pone.0234086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/18/2020] [Indexed: 11/19/2022] Open
Abstract
Based on microRNA (miR) microarray analysis, we previously found that miR22-5p expression is decreased in the mid-luteal endometrium of women with minimal/mild endometriosis. Bioinformatics analysis predicted that miR22-5p targets ten-eleven translocation (TET2) 3'-untranslated region. This study aimed to determine the regulation and roles of miR22-5p in the pathogenesis of minimal/mild endometriosis-associated infertility. MiR22-5p and TET2 expression in the mid-luteal endometrium from women with or without minimal/mild endometriosis was analyzed. After transfection with miR22-5p mimics or inhibitor, TET2 expression was analyzed by quantitative reverse transcription (RT-q) PCR, western blotting and immunohistochemistry. 5-Hydroxymethylcytosine was determined by immunofluorescence and dot blotting. Expression and promoter methylation of estrogen receptor 2 (ESR2) was measured by RT-qPCR and western blotting, and by bisulfite sequencing, respectively. We first established that miR22-5p expression decreased and TET2 expression increased in minimal/mild endometriosis during implantation window. TET2 was found to be a direct target of miR22-5p. MiR22-5p regulated the expression of ESR2, but did not directly affect methylation of its promoter region (-197/+359). Our results suggest that an imbalance in miR22-5p expression in the mid-luteal endometrium may be involved in minimal/mild endometriosis-associated infertility.
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Affiliation(s)
- Li Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Tianjiao Pei
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Wei Huang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
- * E-mail:
| | - Min Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Jing Fu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Jing Tan
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Tingting Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Yong Song
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Shiyuan Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
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Prašnikar E, Knez J, Kovačič B, Kunej T. Molecular signature of eutopic endometrium in endometriosis based on the multi-omics integrative synthesis. J Assist Reprod Genet 2020; 37:1593-1611. [PMID: 32474803 PMCID: PMC7376782 DOI: 10.1007/s10815-020-01833-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/14/2020] [Indexed: 12/31/2022] Open
Abstract
PURPOSE To synthesise data from genome-wide studies reporting molecular signature of eutopic endometrium through the phases of the menstrual cycle in endometriosis. METHODS Extraction of data from publications reporting genetic signatures characterising endometrium associated with endometriosis. The nomenclature of extracted differentially expressed transcripts and proteins was adopted according to the HUGO Gene Nomenclature Committee (HGNC). Loci were further sorted according to the different phases of the menstrual cycle, i.e. menstrual (M), proliferative (P), secretory (S), early-secretory (ES), mid-secretory (MS), late-secretory (LS), and not specified (N/S) if the endometrial dating was not available. Enrichment analysis was performed using the DAVID bioinformatics tool. RESULTS Altered molecular changes were reported by 21 studies, including 13 performed at the transcriptomic, 6 at proteomic, and 2 at epigenomic level. Extracted data resulted in a catalogue of total 670 genetic causes with available 591 official gene symbols, i.e. M = 3, P = 188, S = 81, ES = 82, MS = 173, LS = 36, and N/S = 28. Enriched pathways included oestrogen signalling pathway, extracellular matrix organization, and endothelial cell chemotaxis. Our study revealed that knowledge of endometrium biology in endometriosis is fragmented due to heterogeneity of published data. However, 15 genes reported as dysregulated by at least two studies within the same phase and 33 significantly enriched GO-BP terms/KEGG pathways associated with different phases of the menstrual cycle were identified. CONCLUSIONS A multi-omics insight into molecular patterns underlying endometriosis could contribute towards identification of endometrial pathological mechanisms that impact fertility capacities of women with endometriosis.
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Affiliation(s)
- Erika Prašnikar
- Department of Reproductive Medicine and Gynecological Endocrinology, University Medical Centre Maribor, 2000, Maribor, Slovenia
| | - Jure Knez
- Department of Gynecological and Breast Oncology, University Medical Centre Maribor, 2000, Maribor, Slovenia
| | - Borut Kovačič
- Department of Reproductive Medicine and Gynecological Endocrinology, University Medical Centre Maribor, 2000, Maribor, Slovenia.
| | - Tanja Kunej
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, 1000, Ljubljana, Slovenia.
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26
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Jhamat N, Niazi A, Guo Y, Chanrot M, Ivanova E, Kelsey G, Bongcam-Rudloff E, Andersson G, Humblot P. LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function. BMC Genomics 2020; 21:385. [PMID: 32493210 PMCID: PMC7268755 DOI: 10.1186/s12864-020-06777-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/10/2020] [Indexed: 12/18/2022] Open
Abstract
Background Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometrial function. Following in vitro culture, bEECs from three cows were either untreated (0) or exposed to 2 and 8 μg/mL LPS for 24 h. Results DNA samples extracted at 0 h and 24 h were sequenced using reduced representation bisulfite sequencing (RRBS). When comparing DNA methylation results at 24 h to time 0 h, a larger proportion of hypomethylated regions were identified in the LPS-treated groups, whereas the trend was opposite in controls. When comparing LPS groups to controls at 24 h, a total of 1291 differentially methylated regions (DMRs) were identified (55% hypomethylated and 45% hypermethylated). Integration of DNA methylation data obtained here with our previously published gene expression data obtained from the same samples showed a negative correlation (r = − 0.41 for gene promoter, r = − 0.22 for gene body regions, p < 0.05). Differential methylation analysis revealed that effects of LPS treatment were associated with methylation changes for genes involved in regulation of immune and inflammatory responses, cell adhesion, and external stimuli. Gene ontology and pathway analyses showed that most of the differentially methylated genes (DMGs) were associated with cell proliferation and apoptotic processes; and pathways such as calcium-, oxytocin- and MAPK-signaling pathways with recognized roles in innate immunity. Several DMGs were related to systemic inflammation and tissue re-modelling including HDAC4, IRAK1, AKT1, MAP3K6, Wnt7A and ADAMTS17. Conclusions The present results show that LPS altered the DNA methylation patterns of bovine endometrial epithelial cells. This information, combined with our previously reported changes in gene expression related to endometrial function, confirm that LPS activates pro-inflammatory mechanisms leading to perturbed immune balance and cell adhesion processes in the endometrium.
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Affiliation(s)
- Naveed Jhamat
- Department of Animal Breeding and Genetics, Section of Molecular Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.,SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.,Department of Information Technology, University of the Punjab, Gujranwala Campus, Gujranwala, Pakistan
| | - Adnan Niazi
- Department of Animal Breeding and Genetics, Section of Molecular Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden. .,SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.
| | - Yongzhi Guo
- Department of Clinical Sciences, Division of Reproduction, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Metasu Chanrot
- Department of Clinical Sciences, Division of Reproduction, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.,Faculty of Veterinary Science, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat, 802 40, Thailand
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Section of Molecular Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.,SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Section of Molecular Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.,Centre for Reproductive Biology in Uppsala, CRU, P.O. Box 7054, 750 07, Uppsala, Sweden
| | - Patrice Humblot
- Department of Clinical Sciences, Division of Reproduction, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
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27
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Houshdaran S, Oke AB, Fung JC, Vo KC, Nezhat C, Giudice LC. Steroid hormones regulate genome-wide epigenetic programming and gene transcription in human endometrial cells with marked aberrancies in endometriosis. PLoS Genet 2020; 16:e1008601. [PMID: 32555663 PMCID: PMC7299312 DOI: 10.1371/journal.pgen.1008601] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 01/09/2020] [Indexed: 01/03/2023] Open
Abstract
Programmed cellular responses to cycling ovarian-derived steroid hormones are central to normal endometrial function. Abnormalities therein, as in the estrogen-dependent, progesterone-"resistant" disorder, endometriosis, predispose to infertility and poor pregnancy outcomes. The endometrial stromal fibroblast (eSF) is a master regulator of pregnancy success. However, the complex hormone-epigenome-transcriptome interplay in eSF by each individual steroid hormone, estradiol (E2) and/or progesterone (P4), under physiologic and pathophysiologic conditions, is poorly understood and was investigated herein. Genome-wide analysis in normal, early and late stage eutopic eSF revealed: i) In contrast to P4, E2 extensively affected the eSF DNA methylome and transcriptome. Importantly, E2 resulted in a more open versus closed chromatin, confirmed by histone modification analysis. Combined E2 with P4 affected a totally different landscape than E2 or P4 alone. ii) P4 responses were aberrant in early and late stage endometriosis, and mapping differentially methylated CpG sites with progesterone receptor targets from the literature revealed different but not decreased P4-targets, leading to question the P4-"resistant" phenotype in endometriosis. Interestingly, an aberrant E2-response was noted in eSF from endometriosis women; iii) Steroid hormones affected specific genomic contexts and locations, significantly enriching enhancers and intergenic regions and minimally involving proximal promoters and CpG islands, regardless of hormone type and eSF disease state. iv) In eSF from women with endometriosis, aberrant hormone-induced methylation signatures were mainly due to existing DNA methylation marks prior to hormone treatments and involved known endometriosis genes and pathways. v) Distinct DNA methylation and transcriptomic signatures revealed early and late stage endometriosis comprise unique disease subtypes. Taken together, the data herein, for the first time, provide significant insight into the hormone-epigenome-transcriptome interplay of each steroid hormone in normal eSF, and aberrant E2 response, distinct disease subtypes, and pre-existing epigenetic aberrancies in the setting of endometriosis, provide mechanistic insights into how endometriosis affects endometrial function/dysfunction.
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Affiliation(s)
- Sahar Houshdaran
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Ashwini B. Oke
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Jennifer C. Fung
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Kim Chi Vo
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Camran Nezhat
- Camran Nezhat Institute, Palo Alto, California, United States of America
| | - Linda C. Giudice
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
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28
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Goulielmos GN, Matalliotakis M, Matalliotaki C, Eliopoulos E, Matalliotakis I, Zervou MI. Endometriosis research in the -omics era. Gene 2020; 741:144545. [PMID: 32165309 DOI: 10.1016/j.gene.2020.144545] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/18/2022]
Abstract
Endometriosis is a pathological condition extensively studied, but its pathogenesis is not completely understood, since its pathophysiology stems from a broad spectrum of environmental influences and genetic factors. Moreover, the nature of this condition is heterogeneous and includes different anatomical entities. Scientists actively pursue discovery of novel biomarkers in the hope of better identifying susceptible individuals in early stages of the disease. High-throughput technologies have substantially revolutionized medical research and, as a first step, the advent of genotyping arrays led to large-scale genome-wide association studies (GWAS) and enabled the assessment of global transcript levels, thus giving rise to integrative genetics. In this framework, comprehensive studies have been conducted at multiple biological levels by using the "omics" platforms, thus allowing to re-examine endometriosis at a greater degree of molecular resolution. -Omics technologies can detect and analyze hundreds of markers in the same experiment and their increasing use in the field of gynecology comes from an urgent need to find new diagnostic and therapeutic tools that improve the diagnosis of endometriosis and the efficacy of assisted reproductive techniques. Proteomics and metabolomics have been introduced recently into the every day methodology of researchers collaborating with gynecologists and, importantly, multi-omics approach is advantageous to gain insight of the total information that underlies endometriosis, compared to studies of any single -omics type. In this review, we expect to present multiple studies based on the high-throughput-omics technologies and to shed light in all considerable advantages that they may confer to a proper management of endometriosis.
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Affiliation(s)
- George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece
| | - Michail Matalliotakis
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece; Third Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki, Greece; Department of Obstetrics and Gynecology, Venizeleio and Pananio General Hospital of Heraklion, Heraklion, Greece
| | - Charoula Matalliotaki
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece; Third Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki, Greece; Department of Obstetrics and Gynecology, Venizeleio and Pananio General Hospital of Heraklion, Heraklion, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Ioannis Matalliotakis
- Department of Obstetrics and Gynecology, Venizeleio and Pananio General Hospital of Heraklion, Heraklion, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece.
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29
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Shared Molecular Features Linking Endometriosis and Obstetric Complications. Reprod Sci 2020; 27:1089-1096. [PMID: 32046439 DOI: 10.1007/s43032-019-00119-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
Recent epidemiological research has shown the increased risk of adverse pregnancy outcomes in women with endometriosis compared with the general population. The aim of this review is to explore common pathophysiologic mechanisms between endometriosis and obstetric complications. A computerized literature search was performed to identify relevant studies. The search covered the period between January 2008 and October 2018. One of the potential mechanisms driving the initiation and progression of endometriosis is the accumulation of a variety of epigenetic changes in endometrial cells. Epigenetic control of gene expression which is considered to be responsible for the development of endometriosis is commonly seen in patients with preeclampsia, small for gestational age (SGA), or preterm birth. DLX5 and GATA3, paternally imprinted genes, and CDKN1C, a maternally imprinted gene, were aberrantly expressed in placenta tissues of the preeclampsia; CDKN1C, the growth inhibitor gene, was upregulated in human SGA placentas; and hypomethylation of PTGER2 would be associated with preterm birth. Preeclampsia, SGA, or preterm birth may share common epigenetic alterations with endometriosis, which raises the possibility that the occurrence of two conditions might be nonrandom. To date, however, there is a lack of evidence that links endometriosis and other obstetric complications, such as postpartum hemorrhage or placental abruption, at the epigenetic level. In conclusion, epigenetic changes may be a common hallmark of two conditions: endometriosis and obstetrical complications, such as preeclampsia, SGA, or preterm birth.
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30
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Gerkowicz SA, Curtis SW, Knight AK, Cobb DO, Spencer JB, Conneely KN, Terrell ML, Marcus M, Smith AK. Endometriosis, endocrine disrupters, and epigenetics: an investigation into the complex interplay in women with polybrominated biphenyl exposure and endometriosis. J Assist Reprod Genet 2020; 37:427-436. [PMID: 32026200 PMCID: PMC7056781 DOI: 10.1007/s10815-020-01695-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/10/2020] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Endocrine disrupting compounds (EDCs) have been shown to affect multiple biologic processes especially steroid-hormone processes. We sought to determine differences in DNA methylation exists between women with and without endometriosis following exposure to polybrominated biphenyl (PBB). METHODS Cross-sectional study of 305 females in the Michigan PBB Registry. DNA was extracted, and DNA methylation was interrogated using the MethylationEPIC BeadChip (Illumina, San Diego, California). Demographic data was analyzed using Chi-squared and T tests. Linear regressions were performed for each cytosine-guanine dinucleotide (CpG) site, modeling the logit transformation of the β value as a linear function of the presence of endometriosis. Sensitivity analyses were conducted controlling for estradiol levels and menopausal status. Replication study performed evaluating for any association between CpGs reported in the literature and our findings. RESULTS In total, 39,877 CpGs nominally associated with endometriosis (p < 0.05) after adjusting for age and cellular heterogeneity, although none remained significant after correction for multiple comparisons (FDR < 0.05). Pathway analysis of these CpGs showed enrichment in 68 biologic pathways involved in various endocrine, immunologic, oncologic, and cell regulation processes as well as embryologic reproductive tract development and function (FoxO, Wnt, and Hedgehog signaling). We identified 42,261 CpG sites in the literature reported to be associated with endometriosis; 2012 of these CpG sites were also significant in our cohort. CONCLUSION We found 39,877 CpG sites that nominally associated with endometriosis (p < 0.05) after adjusting for age and cellular heterogeneity; however, none remained significant after correction for multiple comparisons (FDR < 0.05).
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Affiliation(s)
- Sabrina A Gerkowicz
- Department of Gynecology and Obstetrics, Division of Reproductive Endocrinology and Infertility, Emory University, Atlanta, GA, USA
| | - Sarah W Curtis
- Genetics and Molecular Biology Program, Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Anna K Knight
- Department of Gynecology and Obstetrics, Emory University, 101 Woodruff Circle NE, Suite 4217, Atlanta, GA, 30322, USA
| | - Dawayland O Cobb
- Department of Gynecology and Obstetrics, Emory University, 101 Woodruff Circle NE, Suite 4217, Atlanta, GA, 30322, USA
| | - Jessica B Spencer
- Department of Gynecology and Obstetrics, Division of Reproductive Endocrinology and Infertility, Emory University, Atlanta, GA, USA
| | - Karen N Conneely
- Genetics and Molecular Biology Program, Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Metrecia L Terrell
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Michele Marcus
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alica K Smith
- Department of Gynecology and Obstetrics, Emory University, 101 Woodruff Circle NE, Suite 4217, Atlanta, GA, 30322, USA.
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 101 Woodruff Circle NE, Suite 4217, Atlanta, GA, 30322, USA.
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31
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Mahajan V, Farquhar C, Ponnampalam AP. Could DNA hydroxymethylation be crucial in influencing steroid hormone signaling in endometrial biology and endometriosis? Mol Reprod Dev 2019; 87:7-16. [PMID: 31749216 DOI: 10.1002/mrd.23299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Endometriosis affects 10% of reproductive-aged women. It is characterized by the growth of the endometrium, outside the uterus and is associated with infertility and chronic abdominal pain. Lack of noninvasive diagnostic tools and early screening tests results in delayed treatment and subsequently increased disease severity. Endometriosis is a disease associated with a deregulated hormonal response, therefore, understanding the molecular mechanisms that govern this hormonal interplay is of paramount importance. DNA methylation is an epigenetic mark that regulates gene expression and is often associated with genes that code for steroid receptors and enzymes associated with estrogen synthesis and metabolism in endometriosis. DNA hydroxymethylation, which is structurally similar to methylation but functionally different, is a biologically critical mechanism that is also known to regulate gene expression. Ten Eleven Translocation (TET) proteins mediate hydroxymethylation. However, the role of DNA hydroxymethylation or TETs in the endometrium remains relatively unexplored. Currently, the "gold standard" technique used to study methylation patterns is bisulfite genomic sequencing. This technique also detects hydroxymethylation but fails to distinguish between the two, thereby limiting our understanding of these two processes. The presence of TETs in the male and female reproductive tract and its contribution to endometrial cancer makes it an important factor to study in endometriosis. This review summarizes the role of DNA methylation in aberrant steroid hormone signaling and hypothesizes that hydroxymethylation could be a factor influencing hormonal instability seen in endometriosis.
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Affiliation(s)
- Vishakha Mahajan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Cynthia Farquhar
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Anna P Ponnampalam
- The Liggins Institute, The University of Auckland, Auckland, New Zealand.,Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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32
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Barjaste N, Shahhoseini M, Afsharian P, Sharifi-Zarchi A, Masoudi-Nejad A. Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues. J Assist Reprod Genet 2019; 36:1743-1752. [PMID: 31273584 DOI: 10.1007/s10815-019-01508-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/13/2019] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Endometriosis is a gynecological disease that causes the uterine lining to appear in other organs outside the uterus. As DNA methylation has an important role in this disorder, its profiling can reveal new information to improve the diagnosis and treatment of endometriosis patients. METHODS We conducted a genome-wide methylation profiling of ectopic and eutopic endometrial tissues from women with and without endometriosis using Infinium Human Methylation 450K BeadChip arrays. DNA methylation samples were collected from nine ectopic and nine eutopic endometrial tissues of endometriosis and six endometrial tissues of healthy controls. RESULTS Correlation heatmaps and the principal component analysis divided the samples into two clusters, one consisting of all ectopic samples and the other consisting of both eutopic and control samples unexpectedly without segregation between them. The assay identified a group of methylated genes that were overrepresented in biological processes, including abnormality in signaling, development, and adhesion of cells. Pathway analysis revealed disruption in HTLV infection pathways, PI3K-Akt, oxytocin, and relaxin signaling. Moreover, we found eutopic lesions are strongly associated with autoimmune disease. CONCLUSIONS Our results confirmed the role of DNA methylation alternations in endometriosis development and pathogenesis. Our finding suggests aberrant DNA methylation can activate several signaling pathways including PI3k-AKT signaling, relaxin, and oxytocin which are associated with the pathogenesis of endometriosis.
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Affiliation(s)
- Nadia Barjaste
- Laboratory of Bioinformatics and Systems Biology, Department of Bioinformatics, University of Tehran, Kish International Campus, Kish, Iran
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Maryam Shahhoseini
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Parvaneh Afsharian
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Bioinformatics and Systems Biology, Department of Bioinformatics, University of Tehran, Kish International Campus, Kish, Iran.
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Pisarska MD, Chan JL, Lawrenson K, Gonzalez TL, Wang ET. Genetics and Epigenetics of Infertility and Treatments on Outcomes. J Clin Endocrinol Metab 2019; 104:1871-1886. [PMID: 30561694 PMCID: PMC6463256 DOI: 10.1210/jc.2018-01869] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/12/2018] [Indexed: 02/08/2023]
Abstract
CONTEXT Infertility affects 10% of the reproductive-age population. Even the most successful treatments such as assisted reproductive technologies still result in failed implantation. In addition, adverse pregnancy outcomes associated with infertility have been attributed to these fertility treatments owing to the presumed epigenetic modifications of in vitro fertilization and in vitro embryo development. However, the diagnosis of infertility has been associated with adverse outcomes, and the etiologies leading to infertility have been associated with adverse pregnancy and long-term outcomes. EVIDENCE ACQUISITION We have comprehensively summarized the data available through observational, experimental, cohort, and randomized studies to better define the effect of the underlying infertility diagnosis vs the epigenetics of infertility treatments on treatment success and overall outcomes. EVIDENCE SYNTHESIS Most female infertility results from polycystic ovary syndrome, endometriosis, and unexplained infertility, with some cases resulting from a polycystic ovary syndrome phenotype or underlying endometriosis. In addition to failed implantation, defective implantation can lead to problems with placentation that leads to adverse pregnancy outcomes, affecting both mother and fetus. CONCLUSION Current research, although limited, has suggested that genetics and epigenetics of infertility diagnosis affects disease and overall outcomes. In addition, other fertility treatments, which also lead to adverse outcomes, are aiding in the identification of factors, including the supraphysiologic hormonal environment, that might affect the overall success and healthy outcomes for mother and child. Further studies, including genome-wide association studies, epigenomics studies, and experimental studies, are needed to better identify the factors leading to these outcomes.
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Affiliation(s)
- Margareta D Pisarska
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, California
- David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jessica L Chan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Kate Lawrenson
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Tania L Gonzalez
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Erica T Wang
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, California
- David Geffen School of Medicine at UCLA, Los Angeles, California
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Kulski JK. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019; 8:cells8050480. [PMID: 31137555 PMCID: PMC6562477 DOI: 10.3390/cells8050480] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
The HCP5 RNA gene (NCBI ID: 10866) is located centromeric of the HLA-B gene and between the MICA and MICB genes within the major histocompatibility complex (MHC) class I region. It is a human species-specific gene that codes for a long noncoding RNA (lncRNA), composed mostly of an ancient ancestral endogenous antisense 3′ long terminal repeat (LTR, and part of the internal pol antisense sequence of endogenous retrovirus (ERV) type 16 linked to a human leukocyte antigen (HLA) class I promoter and leader sequence at the 5′-end. Since its discovery in 1993, many disease association and gene expression studies have shown that HCP5 is a regulatory lncRNA involved in adaptive and innate immune responses and associated with the promotion of some autoimmune diseases and cancers. The gene sequence acts as a genomic anchor point for binding transcription factors, enhancers, and chromatin remodeling enzymes in the regulation of transcription and chromatin folding. The HCP5 antisense retroviral transcript also interacts with regulatory microRNA and immune and cellular checkpoints in cancers suggesting its potential as a drug target for novel antitumor therapeutics.
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Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA 6009, Australia.
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan.
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35
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Mortlock S, Restuadi R, Levien R, Girling JE, Holdsworth-Carson SJ, Healey M, Zhu Z, Qi T, Wu Y, Lukowski SW, Rogers PAW, Yang J, McRae AF, Fung JN, Montgomery GW. Genetic regulation of methylation in human endometrium and blood and gene targets for reproductive diseases. Clin Epigenetics 2019; 11:49. [PMID: 30871624 PMCID: PMC6416889 DOI: 10.1186/s13148-019-0648-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/06/2019] [Indexed: 02/02/2023] Open
Abstract
Background Major challenges in understanding the functional consequences of genetic risk factors for human disease are which tissues and cell types are affected and the limited availability of suitable tissue. The aim of this study was to evaluate tissue-specific genotype-epigenetic characteristics in DNA samples from both endometrium and blood collected from women at different stages of the menstrual cycle and relate results to genetic risk factors for reproductive traits and diseases. Results We analysed DNA methylation (DNAm) data from endometrium and blood samples from 66 European women. Methylation profiles were compared between stages of the menstrual cycle, and changes in methylation overlaid with changes in transcription and genotypes. We observed large changes in methylation (27,262 DNAm probes) across the menstrual cycle in endometrium that were not observed in blood. Individual genotype data was tested for association with methylation at 443,016 and 443,101 DNAm probes in endometrium and blood respectively to identify methylation quantitative trait loci (mQTLs). A total of 4546 sentinel cis-mQTLs (P < 1.13 × 10−10) and 434 sentinel trans-mQTLs (P < 2.29 × 10−12) were detected in endometrium and 6615 sentinel cis-mQTLs (P < 1.13 × 10−10) and 590 sentinel trans-mQTLs (P < 2.29 × 10−12) were detected in blood. Following secondary analyses, conducted to test for overlap between mQTLs in the two tissues, we found that 62% of endometrial cis-mQTLs were also observed in blood and the genetic effects between tissues were highly correlated. A number of mQTL SNPs were associated with reproductive traits and diseases, including one mQTL located in a known risk region for endometriosis (near GREB1). Conclusions We report novel findings characterising genetic regulation of methylation in endometrium and the association of endometrial mQTLs with endometriosis risk and other reproductive traits and diseases. The high correlation of genetic effects between tissues highlights the potential to exploit the power of large mQTL datasets in endometrial research and identify target genes for functional studies. However, tissue-specific methylation profiles and genetic effects also highlight the importance of also using disease-relevant tissues when investigating molecular mechanisms of disease risk. Electronic supplementary material The online version of this article (10.1186/s13148-019-0648-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sally Mortlock
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia.
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Rupert Levien
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Jane E Girling
- Department of Obstetrics and Gynaecology, and Gynaecology Research Centre, University of Melbourne, Royal Women's Hospital, Parkville, VIC, 3052, Australia.,Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Sarah J Holdsworth-Carson
- Department of Obstetrics and Gynaecology, and Gynaecology Research Centre, University of Melbourne, Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Martin Healey
- Department of Obstetrics and Gynaecology, and Gynaecology Research Centre, University of Melbourne, Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Ting Qi
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Peter A W Rogers
- Department of Obstetrics and Gynaecology, and Gynaecology Research Centre, University of Melbourne, Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Jenny N Fung
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Building 80, St Lucia, QLD, 4072, Australia
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36
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Wang L, Zhao J, Li Y, Wang Z, Kang S. Genome-wide analysis of DNA methylation in endometriosis using Illumina Human Methylation 450 K BeadChips. Mol Reprod Dev 2019; 86:491-501. [PMID: 30740831 DOI: 10.1002/mrd.23127] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 12/13/2022]
Abstract
Endometriosis is a common chronic gynecologic disorder characterized by the presence and growth of endometrial-like tissue outside of the uterine cavity. Although the exact etiology remains unclear, epigenetic modifications, such as DNA methylation, are thought to contribute to the pathogenesis of endometriosis. Here, we used the Illumina Human Methylation 450 K BeadChip Array to analyze the genome-wide DNA methylation profiles of six endometriotic lesions and six eutopic endometria from patients with ovarian endometriosis and six endometria of women without endometriosis. Compared with the eutopic endometria of women with endometriosis, 12,159 differentially methylated CpG sites and 375 differentially methylated promoter regions were identified in endometriotic lesions. GO analyses showed that these putative differentially methylated genes were primarily associated with immune response, inflammatory response, response to steroid hormone stimulus, cell adhesion, negative regulation of apoptosis, and activation of the MAPK activity. In addition, the expression levels of DNMT1, DNMT3A, DNMT3B, and MBD2 in endometriotic lesions and eutopic endometria were significantly decreased compared with control endometria. Our findings suggest that aberrant DNA methylation status in endometriotic lesions may play a significant role in the pathogenesis and progression of endometriosis.
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Affiliation(s)
- Lixian Wang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jian Zhao
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yan Li
- Department of Molecular Biology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zihe Wang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shan Kang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, China
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37
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Abstract
Nucleobases are water-soluble compounds that need specific transporters to cross biological membranes. Cumulative evidence based on studies using animal tissues and cells indicates that the carrier-mediated transport systems for purine and pyrimidine nucleobases can be classified into the following two types: concentrative transport systems that mediate nucleobase transport depending on the sodium ion concentration gradient; and other systems that mediate facilitated diffusion depending on the concentration gradient of the substrate. Recently, several molecular transporters that are involved in both transport systems have been identified. The function and activity of these transporters could be of pharmacological significance considering the roles that they play not only in nucleotide synthesis and metabolism but also in the pharmacokinetics and delivery of a variety of nucleobase analogues used in anticancer and antiviral drug therapy. The present review provides an overview of the recent advances in our understanding of the molecular basis of nucleobase transport systems, focusing on the transporters that mediate purine nucleobases, and discusses the involvement of intracellular metabolism in purine nucleobase transport and chemotherapy using ganciclovir.
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Affiliation(s)
- Katsuhisa Inoue
- Department of Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
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38
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Rahmioglu N, Drong AW, Lockstone H, Tapmeier T, Hellner K, Saare M, Laisk-Podar T, Dew C, Tough E, Nicholson G, Peters M, Morris AP, Lindgren CM, Becker CM, Zondervan KT. Variability of genome-wide DNA methylation and mRNA expression profiles in reproductive and endocrine disease related tissues. Epigenetics 2017; 12:897-908. [PMID: 29099281 PMCID: PMC5750814 DOI: 10.1080/15592294.2017.1367475] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies in the fields of reproductive medicine and endocrinology are yielding robust genetic variants associated with disease. Integrated genomic, transcriptomic, and epigenomic molecular profiling studies are common methodologies used to understand the biologic pathways perturbed by these variants. However, molecular profiling resources do not include the tissue most relevant to many female reproductive traits, the endometrium, while the parameters influencing variability of results from its molecular profiling are unclear. We investigated the sources of DNA methylation and RNA expression profile variability in endometrium (n = 135), endometriotic disease tissue (endometriosis), and subcutaneous abdominal fat samples from 24 women, quantifying between-individual, within-tissue (cellular heterogeneity), and technical variation. DNA samples (n = 96) were analyzed using Illumina HumanMethlylation450 BeadChip arrays; RNA samples (n = 39) were analyzed using H12-expression arrays. Variance-component analyses showed that, for the top 10–50% variable DNA methylation/RNA expression sites, between-individual variation far exceeded within-tissue and technical variation. Menstrual-phase accounted for most variability in methylation/expression patterns in endometrium (Pm = 7.8 × 10−3, Pe = 8.4 × 10−5) but not in fat and endometriotic tissue; age was significantly associated with DNA methylation profile of endometrium (Pm = 9 × 10−5) and endometriotic disease tissue (Pm = 2.4 × 10−5); and smoking was significantly associated with DNA methylation in adipose tissue (Pm = 1.8 × 10−3). Hierarchical cluster analysis showed significantly different methylation signatures between endometrium and endometriotic tissue enriched for WNT signaling, angiogenesis, cadherin signaling, and gonadotropin-releasing-hormone-receptor pathways. Differential DNA methylation/expression analyses suggested detection of a limited number of sites with large fold changes (FC > 4), but power calculations accounting for different sources of variability showed that for robust detection >500 tissue samples are required. These results enable appropriate study design for large-scale expression and methylation tissue-based profiling relevant to many reproductive and endocrine traits.
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Affiliation(s)
- Nilufer Rahmioglu
- a Wellcome Centre for Human Genetics, University of Oxford , Roosevelt Drive, Oxford , OX3 7BN , UK
| | - Alexander W Drong
- a Wellcome Centre for Human Genetics, University of Oxford , Roosevelt Drive, Oxford , OX3 7BN , UK
| | - Helen Lockstone
- a Wellcome Centre for Human Genetics, University of Oxford , Roosevelt Drive, Oxford , OX3 7BN , UK
| | - Thomas Tapmeier
- b Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology , John Radcliffe Hospital, University of Oxford , Oxford , OX3 7BN , UK
| | - Karin Hellner
- b Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology , John Radcliffe Hospital, University of Oxford , Oxford , OX3 7BN , UK
| | - Merli Saare
- c Competence Centre on Health Technologies, Tartu, Estonia and Women's Clinic, Institute of Clinical Medicine, University of Tartu , Tartu , Estonia
| | - Triin Laisk-Podar
- c Competence Centre on Health Technologies, Tartu, Estonia and Women's Clinic, Institute of Clinical Medicine, University of Tartu , Tartu , Estonia
| | - Christine Dew
- b Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology , John Radcliffe Hospital, University of Oxford , Oxford , OX3 7BN , UK
| | - Emily Tough
- b Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology , John Radcliffe Hospital, University of Oxford , Oxford , OX3 7BN , UK
| | - George Nicholson
- a Wellcome Centre for Human Genetics, University of Oxford , Roosevelt Drive, Oxford , OX3 7BN , UK
| | - Maire Peters
- c Competence Centre on Health Technologies, Tartu, Estonia and Women's Clinic, Institute of Clinical Medicine, University of Tartu , Tartu , Estonia
| | - Andrew P Morris
- a Wellcome Centre for Human Genetics, University of Oxford , Roosevelt Drive, Oxford , OX3 7BN , UK.,d Department of Biostatistics , University of Liverpool , Liverpool , OX3 7BN , UK
| | - Cecilia M Lindgren
- a Wellcome Centre for Human Genetics, University of Oxford , Roosevelt Drive, Oxford , OX3 7BN , UK
| | - Christian M Becker
- b Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology , John Radcliffe Hospital, University of Oxford , Oxford , OX3 7BN , UK
| | - Krina T Zondervan
- a Wellcome Centre for Human Genetics, University of Oxford , Roosevelt Drive, Oxford , OX3 7BN , UK.,b Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology , John Radcliffe Hospital, University of Oxford , Oxford , OX3 7BN , UK
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39
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Olesen MS, Starnawska A, Bybjerg-Grauholm J, Bielfeld AP, Agerholm I, Forman A, Overgaard MT, Nyegaard M. Biological age of the endometrium using DNA methylation. Reproduction 2017; 155:167-172. [PMID: 29162648 DOI: 10.1530/rep-17-0601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/19/2022]
Abstract
Age has a detrimental effect on reproduction and as an increasing number of women postpone motherhood, it is imperative to assess biological age in terms of fertility prognosis and optimizing fertility treatment individually. Horvath's epigenetic clock is a mathematical algorithm that calculates the biological age of human cells, tissues or organs based on DNA methylation levels. The clock, however, was previously shown to be highly inaccurate for the human endometrium, most likely because of the hormonal responsive nature of this tissue. The aim of this study was to determine if epigenetically based biological age of the human endometrium correlated with chronological age, when strictly timed to the same time point in the menstrual cycle. Endometrial biopsies from nine women were obtained in two consecutive cycles, both strictly timed to the LH surge (LH + 7) and additionally, peripheral whole blood samples were analyzed. Using the Illumina HumanMethylation 450 K array and Horvath's epigenetic clock, we found a significant correlation between the biological age of the endometrium and the chronological age of the participants, although the endometrial biological age was accelerated by comparison with blood and chronological age. Moreover, similar biological ages were found in pairs of consecutive biopsies, indicating that an endometrial biopsy does not alter the biological age in the following cycle. In conclusion, as long as endometrial samples are timed to the same time point in the menstrual cycle, Horvath's epigenetic clock could be a powerful new biomarker of reproductive aging in the human endometrium.
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Affiliation(s)
- Mia S Olesen
- The Fertility ClinicHorsens Regional Hospital, Horsens, Denmark
| | - Anna Starnawska
- Department of BiomedicineAarhus University, Aarhus C, Denmark.,iPSYCH: The Lundbeck Foundation Initiative for Integrative Psychiatric ResearchAarhus, Denmark
| | | | - Alexandra P Bielfeld
- Department of GynaecologyObstetrics and REI (UniKiD), Medical Faculty, University Duesseldorf, Duesseldorf, Germany
| | - Inge Agerholm
- The Fertility ClinicHorsens Regional Hospital, Horsens, Denmark
| | - Axel Forman
- Department of Gynaecology and ObstetricsAarhus University Hospital, Skejby, Denmark
| | - Michael T Overgaard
- Department of Chemistry and BioscienceAalborg University, Aalborg E, Denmark
| | - Mette Nyegaard
- Department of BiomedicineAarhus University, Aarhus C, Denmark
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40
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Kukushkina V, Modhukur V, Suhorutšenko M, Peters M, Mägi R, Rahmioglu N, Velthut-Meikas A, Altmäe S, Esteban FJ, Vilo J, Zondervan K, Salumets A, Laisk-Podar T. DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase. Sci Rep 2017. [PMID: 28634372 PMCID: PMC5478666 DOI: 10.1038/s41598-017-03682-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The inner uterine lining (endometrium) is a unique tissue going through remarkable changes each menstrual cycle. Endometrium has its characteristic DNA methylation profile, although not much is known about the endometrial methylome changes throughout the menstrual cycle. The impact of methylome changes on gene expression and thereby on the function of the tissue, including establishing receptivity to implanting embryo, is also unclear. Therefore, this study used genome-wide technologies to characterize the methylome and the correlation between DNA methylation and gene expression in endometrial biopsies collected from 17 healthy fertile-aged women from pre-receptive and receptive phase within one menstrual cycle. Our study showed that the overall methylome remains relatively stable during this stage of the menstrual cycle, with small-scale changes affecting 5% of the studied CpG sites (22,272 out of studied 437,022 CpGs, FDR < 0.05). Of differentially methylated CpG sites with the largest absolute changes in methylation level, approximately 30% correlated with gene expression measured by RNA sequencing, with negative correlations being more common in 5' UTR and positive correlations in the gene 'Body' region. According to our results, extracellular matrix organization and immune response are the pathways most affected by methylation changes during the transition from pre-receptive to receptive phase.
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Affiliation(s)
- Viktorija Kukushkina
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Marina Suhorutšenko
- Competence Centre on Health Technologies, Tartu, Estonia.,Women's Clinic, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tartu, Estonia.,Women's Clinic, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Nilufer Rahmioglu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Signe Altmäe
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm, Sweden
| | | | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Krina Zondervan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Women's Clinic, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Triin Laisk-Podar
- Competence Centre on Health Technologies, Tartu, Estonia. .,Women's Clinic, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.
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41
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Ito F, Yamada Y, Shigemitsu A, Akinishi M, Kaniwa H, Miyake R, Yamanaka S, Kobayashi H. Role of Oxidative Stress in Epigenetic Modification in Endometriosis. Reprod Sci 2017; 24:1493-1502. [PMID: 28443478 DOI: 10.1177/1933719117704909] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrant DNA methylation and histone modification are associated with an increased risk of reproductive disorders such as endometriosis. However, a cause-effect relationship between epigenetic mechanisms and endometriosis development has not been fully determined. This review provides current information based on oxidative stress in epigenetic modification in endometriosis. This article reviews the English-language literature on epigenetics, DNA methylation, histone modification, and oxidative stress associated with endometriosis in an effort to identify epigenetic modification that causes a predisposition to endometriosis. Oxidative stress, secondary to the influx of hemoglobin, heme, and iron during retrograde menstruation, is involved in the expression of CpG demethylases, ten-eleven translocation, and jumonji (JMJ). Ten-eleven translocation and JMJ recognize a wide range of endogenous DNA methyltransferases (DNMTs). The increased expression levels of DNMTs may be involved in the subsequent downregulation of the decidualization-related genes. This review supports the hypothesis that there are at least 2 distinct phases of epigenetic modification in endometriosis: the initial wave of iron-induced oxidative stress would be followed by the second big wave of epigenetic modulation of endometriosis susceptibility genes. We summarize the recent advances in our understanding of the underlying epigenetic mechanisms focusing on oxidative stress in endometriosis.
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Affiliation(s)
- Fuminori Ito
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Yuki Yamada
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Aiko Shigemitsu
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Mika Akinishi
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Hiroko Kaniwa
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Ryuta Miyake
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Shoichiro Yamanaka
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Hiroshi Kobayashi
- 1 Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
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42
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Biomarkers in endometriosis: challenges and opportunities. Fertil Steril 2017; 107:523-532. [PMID: 28189296 DOI: 10.1016/j.fertnstert.2017.01.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/27/2016] [Accepted: 01/06/2017] [Indexed: 02/07/2023]
Abstract
Endometriosis is a debilitating gynecologic disease affecting millions of women across the world, with symptoms including dysmenorrhea, chronic pelvic pain, and infertility. Theorized to stem from the phenomenon of retrograde menstruation, the diagnosis of endometriosis is typically delayed by 8-10 years owing to misinterpretation of symptoms as common menstrual cramps in adolescent girls and young women. With increased incidence of endometriosis in young girls correlated with earlier menarche, the development of diagnostic biomarkers is imperative for diagnosing and treating women afflicted with endometriosis as early as we can. In the past few years, multiple reviews highlighted the list of potential diagnostic candidates in peritoneal fluid, blood, urine, and endometrial biopsies from endometriosis patients in different stages of disease and menstrual cycle. In this review, we explore the opportunities and challenges facing the field of diagnostic biomarkers for endometriosis. We highlight the importance of eutopic endometrium as a source of potential diagnostic biomarkers by looking at the expression levels of noncoding RNA in tissue as well as in blood. Finally, we discuss some of the challenges that hinder our efforts in validating candidate diagnostic biomarkers for endometriosis.
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43
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Rogers PAW, Adamson GD, Al-Jefout M, Becker CM, D’Hooghe TM, Dunselman GAJ, Fazleabas A, Giudice LC, Horne AW, Hull ML, Hummelshoj L, Missmer SA, Montgomery GW, Stratton P, Taylor RN, Rombauts L, Saunders PT, Vincent K, Zondervan KT. Research Priorities for Endometriosis. Reprod Sci 2017; 24:202-226. [PMID: 27368878 PMCID: PMC5933154 DOI: 10.1177/1933719116654991] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The 3rd International Consensus Workshop on Research Priorities in Endometriosis was held in São Paulo on May 4, 2014, following the 12th World Congress on Endometriosis. The workshop was attended by 60 participants from 19 countries and was divided into 5 main sessions covering pathogenesis/pathophysiology, symptoms, diagnosis/classification/prognosis, disease/symptom management, and research policy. This research priorities consensus statement builds on earlier efforts to develop research directions for endometriosis. Of the 56 research recommendations from the 2011 meeting in Montpellier, a total of 41 remained unchanged, 13 were updated, and 2 were deemed to be completed. Fifty-three new research recommendations were made at the 2014 meeting in Sao Paulo, which in addition to the 13 updated recommendations resulted in a total of 66 new recommendations for research. The research recommendations published herein, as well as those from the 2 previous papers from international consensus workshops, are an attempt to promote high-quality research in endometriosis by identifying and agreeing on key issues that require investigation. New areas included in the 2014 recommendations include infertility, patient stratification, and research in emerging nations, in addition to an increased focus on translational research. A revised and updated set of research priorities that builds on this document will be developed at the 13th World Congress on Endometriosis to be held on May 17-20, 2017, in Vancouver, British Columbia, Canada.
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Affiliation(s)
| | - G. David Adamson
- Palo Alto Medical Foundation Fertility Physicians of Northern California,
Palo Alto, CA, USA
- World Endometriosis Research Foundation (WERF), London, United Kingdom
| | | | - Christian M. Becker
- Nuffield Department of Obstetrics & Gynaecology, Endometriosis Care
Centre, Oxford, United Kingdom
| | | | - Gerard A. J. Dunselman
- Department of Obstetrics & Gynaecology, Research Institute GROW,
Maastricht University Medical Centre, Maastricht, the Netherlands
| | | | - Linda C. Giudice
- World Endometriosis Research Foundation (WERF), London, United Kingdom
- University of California, San Francisco, CA, USA
- World Endometriosis Society (WES), Vancouver, Canada
| | - Andrew W. Horne
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh,
United Kingdom
| | - M. Louise Hull
- The Robinson Institute, University of Adelaide, Adelaide, Australia
| | - Lone Hummelshoj
- World Endometriosis Research Foundation (WERF), London, United Kingdom
- World Endometriosis Society (WES), Vancouver, Canada
| | - Stacey A. Missmer
- World Endometriosis Research Foundation (WERF), London, United Kingdom
- Harvard Schools of Medicine and Public Health, Boston, MA, USA
| | | | | | - Robert N. Taylor
- World Endometriosis Society (WES), Vancouver, Canada
- Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Luk Rombauts
- World Endometriosis Research Foundation (WERF), London, United Kingdom
- World Endometriosis Society (WES), Vancouver, Canada
- Monash University, Clayton, Australia
| | - Philippa T. Saunders
- MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh,
United Kingdom
| | - Katy Vincent
- Nuffield Department of Obstetrics & Gynaecology, Endometriosis Care
Centre, Oxford, United Kingdom
| | - Krina T. Zondervan
- Nuffield Department of Obstetrics & Gynaecology, Endometriosis Care
Centre, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford,
United Kingdom
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Yotova I, Hsu E, Do C, Gaba A, Sczabolcs M, Dekan S, Kenner L, Wenzl R, Tycko B. Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis. PLoS One 2017; 12:e0170859. [PMID: 28125717 PMCID: PMC5268815 DOI: 10.1371/journal.pone.0170859] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. Genes found to have DM included examples encoding transporters (SLC22A23), signaling components (BDNF, DAPK1, ROR1, and WNT5A) and transcription factors (GATA family, HAND2, HOXA cluster, NR5A1, OSR2, TBX3). Intriguingly, among the TF genes with DM we also found JAZF1, a proto-oncogene affected by chromosomal translocations in endometrial stromal tumors. Using RNA-Seq we identified a subset of the DM genes showing differential expression (DE), with the likelihood of DE increasing with the extent of the DM and its location in enhancer elements. Supporting functional relevance, treatment of stromal cells with the hypomethylating drug 5aza-dC led to activation of DAPK1 and SLC22A23 and repression of HAND2, JAZF1, OSR2, and ROR1 mRNA expression. We found that global 5hmC is decreased in endometriotic versus normal epithelial but not stroma cells, and for JAZF1 and BDNF examined by oxidative bis-seq, found that when 5hmC is detected, patterns of 5hmC paralleled those of 5mC. Together with prior studies, these results define a consistent epigenetic signature in endometriosis stromal cells and nominate specific transcriptional and signaling pathways as therapeutic targets.
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Affiliation(s)
- Iveta Yotova
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
- * E-mail:
| | - Emily Hsu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Catherine Do
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Aulona Gaba
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Matthias Sczabolcs
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Sabine Dekan
- Department of Experimental Pathology, Clinical Institute of Pathology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Department of Experimental Pathology, Clinical Institute of Pathology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
- Pathology Laboratory Animal Pathology University of Veterinary Medicine Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Rene Wenzl
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
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45
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Houshdaran S, Nezhat CR, Vo KC, Zelenko Z, Irwin JC, Giudice LC. Aberrant Endometrial DNA Methylome and Associated Gene Expression in Women with Endometriosis. Biol Reprod 2016; 95:93. [PMID: 27535958 PMCID: PMC5178151 DOI: 10.1095/biolreprod.116.140434] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/10/2016] [Indexed: 12/17/2022] Open
Abstract
Endometriosis is an estrogen-dependent, progesterone-resistant disorder largely derived from retrograde transplantation of menstrual tissue/cells into the pelvis, eliciting an inflammatory response, pelvic pain, and infertility. Eutopic endometrium (within the uterus), giving rise to pelvic disease, displays cycle-dependent transcriptomic, proteomic, and signaling abnormalities, and although its DNA methylation profiles dynamically change across the cycle in healthy women, studies in endometriosis are limited. Herein, we investigated the DNA methylome and associated gene expression in three phases of the cycle in eutopic endometrium of women with severe endometriosis versus controls, matched for ethnicity, medications, smoking, and no recent contraceptive steroid use. Genome-wide DNA methylation and gene expression were coassessed in each sample. Cycle phase was determined by histology, serum hormone levels, and unsupervised principal component and hierarchical cluster analyses of microarray data. Altered endometrial DNA methylation in endometriosis was most prominent in the midsecretory phase (peak progesterone), with disruption of the normal pattern of cycle-dependent DNA methylation changes, including a bias toward methylation of CpG islands, suggesting wide-range abnormalities of the chromatin remodeling machinery in endometriosis. DNA methylation changes were associated with altered gene expression relevant to endometrial function/dysfunction, including cell proliferation, inflammation/immune response, angiogenesis, and steroid hormone response. The data provide insight into epigenetic reprogramming and steroid hormone actions in endometrium contributing to the pathogenesis and pathophysiology of endometriosis.
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Affiliation(s)
- Sahar Houshdaran
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California
| | - Camran R Nezhat
- Center for Special Minimally Invasive and Robotic Surgery, Palo Alto, California
| | - Kim Chi Vo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California
| | - Zara Zelenko
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California
| | - Juan C Irwin
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California
| | - Linda C Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California
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Bruner-Tran KL, Gnecco J, Ding T, Glore DR, Pensabene V, Osteen KG. Exposure to the environmental endocrine disruptor TCDD and human reproductive dysfunction: Translating lessons from murine models. Reprod Toxicol 2016; 68:59-71. [PMID: 27423904 DOI: 10.1016/j.reprotox.2016.07.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 07/06/2016] [Accepted: 07/09/2016] [Indexed: 12/31/2022]
Abstract
Humans and other animals are exposed to a wide array of man-made toxicants, many of which act as endocrine disruptors that exhibit differential effects across the lifespan. In humans, while the impact of adult exposure is known for some compounds, the potential consequences of developmental exposure to endocrine disrupting chemicals (EDCs) is more difficult to ascertain. Animal studies have revealed that exposure to EDCs prior to puberty can lead to adult reproductive disease and dysfunction. Specifically, in adult female mice with an early life exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), we demonstrated a transgenerational occurrence of several reproductive diseases that have been linked to endometriosis in women. Herein, we review the evidence for TCDD-associated development of adult reproductive disease as well as known epigenetic alterations associated with TCDD and/or endometriosis. We will also introduce new "Organ-on-Chip" models which, combined with our established murine model, are expected to further enhance our ability to examine alterations in gene-environment interactions that lead to heritable disease.
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Affiliation(s)
- Kaylon L Bruner-Tran
- Women's Reproductive Health Research Center, Department of Obstetrics & Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | - Juan Gnecco
- Women's Reproductive Health Research Center, Department of Obstetrics & Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tianbing Ding
- Women's Reproductive Health Research Center, Department of Obstetrics & Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Dana R Glore
- Women's Reproductive Health Research Center, Department of Obstetrics & Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Virginia Pensabene
- Women's Reproductive Health Research Center, Department of Obstetrics & Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kevin G Osteen
- Women's Reproductive Health Research Center, Department of Obstetrics & Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare System, Nashville TN 37212, USA
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