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Cuadrado-Torroglosa I, García-Velasco JA, Alecsandru D. The Impacts of Inflammatory and Autoimmune Conditions on the Endometrium and Reproductive Outcomes. J Clin Med 2024; 13:3724. [PMID: 38999290 PMCID: PMC11242609 DOI: 10.3390/jcm13133724] [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: 05/23/2024] [Revised: 06/17/2024] [Accepted: 06/23/2024] [Indexed: 07/14/2024] Open
Abstract
Background: A healthy pregnancy begins with an adequate endometrial state, even before the arrival of a blastocyst. Proper endometrial priming and the development of a tolerogenic decidua are key steps in creating the perfect environment for implantation and pregnancy. In these processes, the involvement of the maternal immune system seems to be of great relevance, modulating the different decidual immune populations to prepare the endometrium for a potential pregnancy. However, certain local pathologies of an inflammatory and autoimmune nature appear to have a direct impact on these phenomena, thus altering patients' reproductive outcomes. Methods: This literature review analyzes original articles, reviews, systematic reviews, and meta-analyses published between 1990 and 2024, concerning the impact of different inflammatory and autoimmune conditions on endometrial status and fertility. The included papers were obtained from Medline (Pubmed) and the Cochrane library. Results: There is evidence that endometriosis, adenomyosis, and chronic endometritis, through the promotion of a chronic inflammatory environment, are capable of altering endometrial immune populations, and, thus, processes essential for early pregnancy. Among other effects, these conditions have been linked to impaired decidualization, alterations in progesterone responsiveness, and hindered placentation. Similarly, antiphospholipid syndrome (APS), thyroid dysfunction, diabetes, and other pathologies related to glucose and gluten metabolism, due to their autoimmune nature, also appear to have a local impact on the uterine environment, affecting reproductive success through different mechanisms, including altered hormonal response and, again, impaired decidualization. Conclusions: The management of inflammatory and autoimmune diseases in assisted reproduction patients is gaining importance due to their direct impact on the endometrium. It is necessary to follow current expert recommendations and established therapeutic approaches in order to improve patients' prospects, ranging from antibiotic treatment in chronic endometritis to heparin and aspirin in APS, as well as hormonal treatments for endometriosis/adenomyosis or a gluten-free diet in celiac disease. All of them and the rest of the therapeutic perspectives, both current and under investigation, are presented throughout this work, assessing the possible improvements for reproductive outcomes.
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Affiliation(s)
- Isabel Cuadrado-Torroglosa
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Avenida Fernando Abril Martorell, 106, Torre A, Planta 1a, 46026 Valencia, Spain; (I.C.-T.); (J.A.G.-V.)
| | - Juan A. García-Velasco
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Avenida Fernando Abril Martorell, 106, Torre A, Planta 1a, 46026 Valencia, Spain; (I.C.-T.); (J.A.G.-V.)
- IVIRMA Global Research Alliance, IVIRMA Madrid, Av. del Talgo, 68, 28023 Madrid, Spain
- Department of Obstetrics and Gynaecology, Rey Juan Carlos University, Av. de Atenas, s/n, 28922 Alcorcón, Spain
| | - Diana Alecsandru
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Avenida Fernando Abril Martorell, 106, Torre A, Planta 1a, 46026 Valencia, Spain; (I.C.-T.); (J.A.G.-V.)
- IVIRMA Global Research Alliance, IVIRMA Madrid, Av. del Talgo, 68, 28023 Madrid, Spain
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Madasu C, Liao Z, Parks SE, Sharma KL, Bohren KM, Ye Q, Li F, Palaniappan M, Tan Z, Yuan F, Creighton CJ, Tang S, Masand RP, Guan X, Young DW, Monsivais D, Matzuk MM. Identification of potent pan-ephrin receptor kinase inhibitors using DNA-encoded chemistry technology. Proc Natl Acad Sci U S A 2024; 121:e2322934121. [PMID: 38701119 PMCID: PMC11087803 DOI: 10.1073/pnas.2322934121] [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: 12/28/2023] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
EPH receptors (EPHs), the largest family of tyrosine kinases, phosphorylate downstream substrates upon binding of ephrin cell surface-associated ligands. In a large cohort of endometriotic lesions from individuals with endometriosis, we found that EPHA2 and EPHA4 expressions are increased in endometriotic lesions relative to normal eutopic endometrium. Because signaling through EPHs is associated with increased cell migration and invasion, we hypothesized that chemical inhibition of EPHA2/4 could have therapeutic value. We screened DNA-encoded chemical libraries (DECL) to rapidly identify EPHA2/4 kinase inhibitors. Hit compound, CDD-2693, exhibited picomolar/nanomolar kinase activity against EPHA2 (Ki: 4.0 nM) and EPHA4 (Ki: 0.81 nM). Kinome profiling revealed that CDD-2693 bound to most EPH family and SRC family kinases. Using NanoBRET target engagement assays, CDD-2693 had nanomolar activity versus EPHA2 (IC50: 461 nM) and EPHA4 (IC50: 40 nM) but was a micromolar inhibitor of SRC, YES, and FGR. Chemical optimization produced CDD-3167, having picomolar biochemical activity toward EPHA2 (Ki: 0.13 nM) and EPHA4 (Ki: 0.38 nM) with excellent cell-based potency EPHA2 (IC50: 8.0 nM) and EPHA4 (IC50: 2.3 nM). Moreover, CDD-3167 maintained superior off-target cellular selectivity. In 12Z endometriotic epithelial cells, CDD-2693 and CDD-3167 significantly decreased EFNA5 (ligand) induced phosphorylation of EPHA2/4, decreased 12Z cell viability, and decreased IL-1β-mediated expression of prostaglandin synthase 2 (PTGS2). CDD-2693 and CDD-3167 decreased expansion of primary endometrial epithelial organoids from patients with endometriosis and decreased Ewing's sarcoma viability. Thus, using DECL, we identified potent pan-EPH inhibitors that show specificity and activity in cellular models of endometriosis and cancer.
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Affiliation(s)
- Chandrashekhar Madasu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Zian Liao
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
| | - Sydney E. Parks
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Kiran L. Sharma
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Kurt M. Bohren
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Qiuji Ye
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Feng Li
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Murugesan Palaniappan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Zhi Tan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Fei Yuan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX77030
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX77030
- Department of Medicine, Baylor College of Medicine, Houston, TX77030
| | - Suni Tang
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Ramya P. Masand
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX77030
| | - Xiaoming Guan
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX77030
| | - Damian W. Young
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Diana Monsivais
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Martin M. Matzuk
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
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Li R, Tran DN, Lessey BA, Young SL, Kim TH, Jeong JW. Transcriptomic changes in eutopic endometrium and ectopic lesions during endometriosis progression in a mouse model. F&S SCIENCE 2024; 5:182-194. [PMID: 38342342 PMCID: PMC11116064 DOI: 10.1016/j.xfss.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
OBJECTIVE To identify the transcriptomic changes of ectopic lesions and eutopic endometrial tissues during the progression of endometriosis, we performed transcriptomic analysis in the eutopic endometrium and ectopic lesions. DESIGN Laboratory study. SETTING Academic medical center. ANIMALS Four fertile and 4 subfertile Pgrcre/+Rosa26mTmG/+ mice with endometriosis, and 4 sham mice for each group of endometriosis mice as control. These mice underwent either surgery to induce endometriosis or sham surgery. Fertile sham and mice with endometriosis were used 1 month after surgery, whereas subfertile ones were used 3 months after surgery. INTERVENTIONS Early and chronic effects of endometriosis on transcriptomics of ectopic lesions and eutopic endometrium. MAIN OUTCOME MEASURES RNA-sequencing analysis and identification of differentially expressed genes and pathways in the ectopic lesions and eutopic uteri from mice with endometriosis and sham mice at day 3.5 of pregnancy. RESULTS Our mouse model recapitulates the transcriptomic changes of ectopic lesions in humans. RNA-sequencing analysis was performed in ectopic lesions and eutopic uteri from mice with or without endometriosis during the progression of the disease. Estrogen activity, inflammation, angiogenesis, and fibrosis pathways were consistently elevated in all the ectopic lesions compared with eutopic endometrium. Cholesterol/glucose synthesis and stem cell pluripotency pathways were more enhanced in ectopic lesions from subfertile mice compared with their eutopic endometrium. Dysregulation of infiltration of macrophage, dendritic, T and B cells was validated with the use of immunohistochemistry in ectopic lesions. Multiple ligand-receptor pairs between the ectopic and eutopic endometrium were altered compared with the sham endometrium. Suppressed WNT and EGF pathways were only found in the eutopic endometrium from subfertile not fertile mice compared with sham. CONCLUSIONS Our mouse endometriosis model recapitulates the transcriptomics of ectopic lesions in humans. Our transcriptomic analysis during endometriosis progression in our mouse model will help us understand the pathophysiology of endometriosis.
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Affiliation(s)
- Rong Li
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, Missouri
| | - Dinh Nam Tran
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, Missouri
| | - Bruce A Lessey
- Department of Obstetrics and Gynecology, Wake Forest Baptist Health, Winston-Salem, North Carolina
| | - Steven L Young
- Department of Obstetrics, Gynecology and Women's Health, Duke University, Durham, North Carolina
| | - Tae Hoon Kim
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, Missouri
| | - Jae-Wook Jeong
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, Missouri.
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4
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Liang Q, Yang S, Mai M, Chen X, Zhu X. Mining phase separation-related diagnostic biomarkers for endometriosis through WGCNA and multiple machine learning techniques: a retrospective and nomogram study. J Assist Reprod Genet 2024; 41:1433-1447. [PMID: 38456992 PMCID: PMC11143086 DOI: 10.1007/s10815-024-03079-9] [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: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the role of phase separation-related genes in the development of endometriosis (EMs) and to identify potential characteristic genes associated with the condition. METHODS We used GEO database data, including 74 non-endometriosis and 74 varying-degree EMs patients. Our approach involved identifying significant gene modules, exploring gene intersections, identifying core genes, and screening for potential EMs biomarkers using weighted gene co-expression network analysis (WGCNA) and various machine learning approaches. We also performed gene set enrichment analysis (GSEA) to understand relevant pathways. This comprehensive approach helps investigate EMs genetics and potential biomarkers. RESULTS Nine genes were identified at the intersection, suggesting their involvement in EMs. GSEA linked DEGs to pathways like complement and coagulation cascades, DNA replication, chemokines, apical plasma membrane processes, and diseases such as Hepatitis B, Human T-cell leukemia virus 1 infection, and COVID-19. Five feature genes (FOS, CFD, CCNA1, CA4, CST1) were selected by machine learning for an effective EMs diagnostic nomogram. GSEA indicated their roles in mismatch repair, cell cycle regulation, complement and coagulation cascades, and IL-17 inflammation. Notable differences in immune cell proportions (CD4 T cells, CD8 T cells, DCs, macrophages) were observed between normal and disease groups, suggesting immune involvement. CONCLUSIONS This study suggests the potential involvement of phase separation-related genes in the pathogenesis of endometriosis (EMs) and identifies promising biomarkers for diagnosis. These findings have implications for further research and the development of new therapeutic strategies for EMs.
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Affiliation(s)
- Qiuyi Liang
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Shengmei Yang
- Obstetrical Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meiyi Mai
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiurong Chen
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China.
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5
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Oskotsky TT, Bhoja A, Bunis D, Le BL, Tang AS, Kosti I, Li C, Houshdaran S, Sen S, Vallvé-Juanico J, Wang W, Arthurs E, Govil A, Mahoney L, Lang L, Gaudilliere B, Stevenson DK, Irwin JC, Giudice LC, McAllister SL, Sirota M. Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach. iScience 2024; 27:109388. [PMID: 38510116 PMCID: PMC10952035 DOI: 10.1016/j.isci.2024.109388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Existing medical treatments for endometriosis-related pain are often ineffective, underscoring the need for new therapeutic strategies. In this study, we applied a computational drug repurposing pipeline to stratified and unstratified disease signatures based on endometrial gene expression data to identify potential therapeutics from existing drugs, based on expression reversal. Of 3,131 unique genes differentially expressed by at least one of six endometriosis signatures, only 308 (9.8%) were in common; however, 221 out of 299 drugs identified, (73.9%) were shared. We selected fenoprofen, an uncommonly prescribed NSAID that was the top therapeutic candidate for further investigation. When testing fenoprofen in an established rat model of endometriosis, fenoprofen successfully alleviated endometriosis-associated vaginal hyperalgesia, a surrogate marker for endometriosis-related pain. These findings validate fenoprofen as a therapeutic that could be utilized more frequently for endometriosis and suggest the utility of the aforementioned computational drug repurposing approach for endometriosis.
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Affiliation(s)
- Tomiko T. Oskotsky
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Arohee Bhoja
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel Bunis
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Brian L. Le
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Alice S. Tang
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Christine Li
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Sahar Houshdaran
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, CA, USA
| | - Sushmita Sen
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, CA, USA
| | - Júlia Vallvé-Juanico
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, CA, USA
| | - Wanxin Wang
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, CA, USA
| | - Erin Arthurs
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Arpita Govil
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Lauren Mahoney
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Lindsey Lang
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, CA, USA
| | | | - Juan C. Irwin
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, CA, USA
| | - Linda C. Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, CA, USA
| | | | - Marina Sirota
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
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6
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Cook CJ, Wiggin N, Fogg KC. Characterizing the Extracellular Matrix Transcriptome of Endometriosis. Reprod Sci 2024; 31:413-429. [PMID: 37789126 PMCID: PMC10827821 DOI: 10.1007/s43032-023-01359-w] [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: 03/13/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023]
Abstract
In recent years, the matrisome, a set of proteins that make up the extracellular matrix (ECM) or are closely involved in ECM behavior, has been shown to have great importance for characterizing and understanding disease pathogenesis and progression. The matrisome is especially critical for examining diseases characterized by extensive tissue remodeling. Endometriosis is characterized by the extrauterine growth of endometrial tissue, making it an ideal condition to study through the lens of matrisome gene expression. While large gene expression datasets have become more available and gene dysregulation in endometriosis has been the target of several studies, the gene expression profile of the matrisome specifically in endometriosis has not been well characterized. In our study, we explored four Gene Expression Omnibus (GEO) DNA microarray datasets containing eutopic endometrium of people with and without endometriosis. After batch correction, menstrual cycle phase accounted for 53% of variance and disease accounted for 23%; thus, the data were separated by menstrual cycle phase before performing differential expression analysis, statistical and machine learning modeling, and enrichment analysis. We established that matrisome gene expression alone can effectively differentiate endometriosis samples from healthy ones, demonstrating the potential of matrisome gene expression for diagnostic applications. Furthermore, we identified specific matrisome genes and gene networks whose expression can distinguish endometriosis stages I/II from III/IV. Taken together, these findings may aid in developing future in vitro models of disease, offer insights into novel treatment strategies, and advance diagnostic tools for this underserved patient population.
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Affiliation(s)
- Carson J Cook
- Bioengineering, Oregon State University, Corvallis, OR, 97331, USA
| | - Noah Wiggin
- Computer Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Kaitlin C Fogg
- Bioengineering, Oregon State University, Corvallis, OR, 97331, USA.
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7
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Yang X, Yan K, Zhan Q, Chen H, Pei CZ, Zhu L. Exploration of Diagnostic Deubiquitinating Enzymes in Endometriosis and Its Immune Infiltration. Biochem Genet 2024:10.1007/s10528-023-10653-w. [PMID: 38302849 DOI: 10.1007/s10528-023-10653-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024]
Abstract
The mechanism involved in the pathogenesis of endometriosis is poorly understood. The purpose of this study is to identify key deubiquitinating enzymes (DUBs) for endometriosis diagnosis and elucidate the possible mechanism, offering novel insights for noninvasive early diagnosis and treatment. Four gene expression datasets were employed from the Gene Expression Omnibus to identify differentially expressed genes (DEGs) between endometriosis and normal controls. GO and KEGG pathways were performed for enrichment analysis. Calibration curves, ROC, DCA, and clinical impact curves verified the clinical usefulness of the nomogram model. In addition, the ssGSEA method was conducted to estimate 23 types of immune cells. A specific DUB gene signature was constructed with Lasso regression, univariate logistic regression, and SVM analysis. RT-qPCR validated the expression of biomarkers. A total of 85 endometriosis-related DUBs were identified in the eutopic endometrium. Among them, 20 DUBs were found to be correlated with the severity of endometriosis. A diagnostic risk model based on five DUB-related genes (USP21, USP48, ZRANB1, COPS5, and EIF3F) was developed using lasso-cox regression analysis. The nomogram model exhibited a strong predictive ability to diagnose endometriosis. KEGG analysis revealed that ubiquitin-mediated proteolysis was activated in patients suffering from severe symptoms. Analysis of immune cell infiltration revealed a positive correlation between USP21 and multiple immune cells in the eutopic endometrium. However, EIF3F showed an opposite relationship. Dysregulation of DUBs was related to the immune microenvironment in endometriosis. Results from RT-qPCR confirmed the expression of DEGs in clinical samples. In summary, the diagnostic model for endometriosis constructed using five differentially expressed DUB genes demonstrates strong diagnostic capability, suggesting that these genes could serve as potential candidate biomarkers and therapeutic targets.
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Affiliation(s)
- Xinyun Yang
- Department of Reproductive Endocrinology, Zhejiang University School of Medicine, Women's Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Kai Yan
- Department of Reproductive Endocrinology, Zhejiang University School of Medicine, Women's Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Qitao Zhan
- Department of Reproductive Endocrinology, Zhejiang University School of Medicine, Women's Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Hao Chen
- Department of Pathology, Hangzhou Women's Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Chang-Zhu Pei
- Reproductive Medicine Center, Yanbian University Hospital, Yanji, Jilin, People's Republic of China.
| | - Linling Zhu
- Department of Reproductive Endocrinology, Zhejiang University School of Medicine, Women's Hospital, Hangzhou, Zhejiang, People's Republic of China.
- Department of Gynecology, Hangzhou Women's Hospital, Hangzhou, Zhejiang, People's Republic of China.
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8
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Zhang H, Zhang H, Yang H, Shuid AN, Sandai D, Chen X. Machine learning-based integrated identification of predictive combined diagnostic biomarkers for endometriosis. Front Genet 2023; 14:1290036. [PMID: 38098472 PMCID: PMC10720908 DOI: 10.3389/fgene.2023.1290036] [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: 09/06/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Background: Endometriosis (EM) is a common gynecological condition in women of reproductive age, with diverse causes and a not yet fully understood pathogenesis. Traditional diagnostics rely on single diagnostic biomarkers and does not integrate a variety of different biomarkers. This study introduces multiple machine learning techniques, enhancing the accuracy of predictive models. A novel diagnostic approach that combines various biomarkers provides a new clinical perspective for improving the diagnostic efficiency of endometriosis, holding significant potential for clinical application. Methods: In this study, GSE51981 was used as a test set, and 11 machine learning algorithms (Lasso, Stepglm, glmBoost, Support Vector Machine, Ridge, Enet, plsRglm, Random Forest, LDA, XGBoost, and NaiveBayes) were employed to construct 113 predictive models for endometriosis. The optimal model was determined based on the AUC values derived from various algorithms. These genes were then evaluated using nine machine learning algorithms (Random Forest, SVM, Gradient Boosting Machine, LASSO, XGB, NNET, Generalized Linear Model, KNN, and Decision Tree) to assess significance scores and identify diagnostic genes for each algorithm. The diagnostic value of these genes was further validated in external datasets from GSE7305, GSE11691, and GSE120103. Results: Analysis of the GSE51981 dataset revealed 62 DEGs. The Stepglm [Both] and plsRglm algorithms identified 30 genes with the most potential using the AUC evaluation. Subsequently, nine machine learning algorithms were applied to select diagnostic genes, leading to the identification of five key diagnostic genes using the LASSO algorithm. The ADAT1 gene exhibited the best single-gene predictive performance, with an AUC of 0.785. A combination of genes (FOS, EPHX1, DLGAP5, PCSK5, and ADAT1) achieves an AUC of 0.836 in the test dataset. Moreover, these genes consistently exhibited an AUC exceeding 0.78 in all validation datasets, demonstrating superior predictive performance. Furthermore, correlation analysis with immune infiltration strengthened their predictive value by demonstrating the close relationship of the diagnostic genes with immune infiltrating cells. Conclusion: A combination of biomarkers consisting of FOS, EPHX1, DLGAP5, PCSK5, and ADAT1 can serve as a diagnostic tool for endometriosis, enhancing diagnostic efficiency. The association of these genes with immune infiltrating cells reveals their potential role in the pathogenesis of endometriosis, providing new insights for early detection and treatment.
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Affiliation(s)
- Haolong Zhang
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Haoling Zhang
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Huadi Yang
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Ahmad Naqib Shuid
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Doblin Sandai
- Department of Community Health, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Xingbei Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
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Giudice LC, Oskotsky TT, Falako S, Opoku‐Anane J, Sirota M. Endometriosis in the era of precision medicine and impact on sexual and reproductive health across the lifespan and in diverse populations. FASEB J 2023; 37:e23130. [PMID: 37641572 PMCID: PMC10503213 DOI: 10.1096/fj.202300907] [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: 05/05/2023] [Accepted: 07/26/2023] [Indexed: 08/31/2023]
Abstract
Endometriosis is a common estrogen-dependent disorder wherein uterine lining tissue (endometrium) is found mainly in the pelvis where it causes inflammation, chronic pelvic pain, pain with intercourse and menses, and infertility. Recent evidence also supports a systemic inflammatory component that underlies associated co-morbidities, e.g., migraines and cardiovascular and autoimmune diseases. Genetics and environment contribute significantly to disease risk, and with the explosion of omics technologies, underlying mechanisms of symptoms are increasingly being elucidated, although novel and effective therapeutics for pain and infertility have lagged behind these advances. Moreover, there are stark disparities in diagnosis, access to care, and treatment among persons of color and transgender/nonbinary identity, socioeconomically disadvantaged populations, and adolescents, and a disturbing low awareness among health care providers, policymakers, and the lay public about endometriosis, which, if left undiagnosed and under-treated can lead to significant fibrosis, infertility, depression, and markedly diminished quality of life. This review summarizes endometriosis epidemiology, compelling evidence for its pathogenesis, mechanisms underlying its pathophysiology in the age of precision medicine, recent biomarker discovery, novel therapeutic approaches, and issues around reproductive justice for marginalized populations with this disorder spanning the past 100 years. As we enter the next revolution in health care and biomedical research, with rich molecular and clinical datasets, single-cell omics, and population-level data, endometriosis is well positioned to benefit from data-driven research leveraging computational and artificial intelligence approaches integrating data and predicting disease risk, diagnosis, response to medical and surgical therapies, and prognosis for recurrence.
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Affiliation(s)
- Linda C. Giudice
- UCSF Stanford Endometriosis Center for Innovation, Training, and Community Outreach (ENACT)University of California, San FranciscoSan FranciscoCaliforniaUSA
- Center for Reproductive SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Tomiko T. Oskotsky
- UCSF Stanford Endometriosis Center for Innovation, Training, and Community Outreach (ENACT)University of California, San FranciscoSan FranciscoCaliforniaUSA
- Bakar Computational Health Sciences InstituteUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Simileoluwa Falako
- UCSF Stanford Endometriosis Center for Innovation, Training, and Community Outreach (ENACT)University of California, San FranciscoSan FranciscoCaliforniaUSA
- Columbia University Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Jessica Opoku‐Anane
- UCSF Stanford Endometriosis Center for Innovation, Training, and Community Outreach (ENACT)University of California, San FranciscoSan FranciscoCaliforniaUSA
- Division of Gynecologic Specialty SurgeryColumbia UniversityNew YorkNew YorkUSA
| | - Marina Sirota
- UCSF Stanford Endometriosis Center for Innovation, Training, and Community Outreach (ENACT)University of California, San FranciscoSan FranciscoCaliforniaUSA
- Bakar Computational Health Sciences InstituteUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of PediatricsUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
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10
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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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11
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Santin A, Spedicati B, Morgan A, Lenarduzzi S, Tesolin P, Nardone GG, Mazzà D, Di Lorenzo G, Romano F, Buonomo F, Mangogna A, Concas MP, Zito G, Ricci G, Girotto G. Puzzling Out the Genetic Architecture of Endometriosis: Whole-Exome Sequencing and Novel Candidate Gene Identification in a Deeply Clinically Characterised Cohort. Biomedicines 2023; 11:2122. [PMID: 37626618 PMCID: PMC10452899 DOI: 10.3390/biomedicines11082122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Endometriosis (EM) is a common multifactorial gynaecological disorder. Although Genome-Wide Association Studies have largely been employed, the current knowledge of the genetic mechanisms underlying EM is far from complete, and other approaches are needed. To this purpose, whole-exome sequencing (WES) was performed on a deeply characterised cohort of 80 EM patients aimed at the identification of rare and damaging variants within 46 EM-associated genes and novel candidates. WES analysis detected 63 rare, predicted, and damaging heterozygous variants within 24 genes in 63% of the EM patients. In particular, (1) a total of 43% of patients carried variants within 13 recurrent genes (FCRL3, LAMA5, SYNE1, SYNE2, GREB1, MAP3K4, C3, MMP3, MMP9, TYK2, VEGFA, VEZT, RHOJ); (2) a total of 8.8% carried private variants within eight genes (KAZN, IL18, WT1, CYP19A1, IL1A, IL2RB, LILRB2, ZNF366); (3) a total of 24% carried variants within three novel candidates (ABCA13, NEB, CSMD1). Finally, to deepen the polygenic architecture of EM, a comprehensive evaluation of the analysed genes was performed, revealing a higher burden (p < 0.05) of genes harbouring rare and damaging variants in the EM patients than in the controls. These results highlight new insights into EM genetics, allowing for the definition of novel genotype-phenotype correlations, thereby contributing, in a long-term perspective, to the development of personalised care for EM patients.
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Affiliation(s)
- Aurora Santin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (A.S.); (P.T.); (G.G.N.); (G.R.); (G.G.)
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (A.S.); (P.T.); (G.G.N.); (G.R.); (G.G.)
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Anna Morgan
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Stefania Lenarduzzi
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Paola Tesolin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (A.S.); (P.T.); (G.G.N.); (G.R.); (G.G.)
| | - Giuseppe Giovanni Nardone
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (A.S.); (P.T.); (G.G.N.); (G.R.); (G.G.)
| | - Daniela Mazzà
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Federico Romano
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Francesca Buonomo
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Alessandro Mangogna
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Maria Pina Concas
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Gabriella Zito
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Giuseppe Ricci
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (A.S.); (P.T.); (G.G.N.); (G.R.); (G.G.)
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (A.S.); (P.T.); (G.G.N.); (G.R.); (G.G.)
- Institute for Maternal and Child Health, I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy; (A.M.); (S.L.); (D.M.); (G.D.L.); (F.R.); (F.B.); (A.M.); (M.P.C.); (G.Z.)
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12
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Chiorean DM, Mitranovici MI, Toru HS, Cotoi TC, Tomuț AN, Turdean SG, Cotoi OS. New Insights into Genetics of Endometriosis-A Comprehensive Literature Review. Diagnostics (Basel) 2023; 13:2265. [PMID: 37443659 DOI: 10.3390/diagnostics13132265] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
This comprehensive review explores the genetic contributions to endometriosis and their potential impact on improving diagnostic techniques. The review begins by defining endometriosis and discussing its prevalence, emphasizing the need for a deeper understanding of the genetic basis of the condition. It highlights recent genome-wide association studies (GWAS) that have identified specific genetic variants associated with endometriosis, shedding light on the molecular pathways and mechanisms involved. The review addresses genetic heterogeneity across different populations and ethnicities, emphasizing the importance of considering population-specific markers in diagnostic approaches. It explores the diagnostic implications of genetic insights, including the potential use of genetic markers for precise and early detection, as well as risk prediction. The review also delves into the integration of genetic information with clinical parameters and imaging findings, and the exploration of multi-omics approaches for a comprehensive understanding of endometriosis. It discusses recent studies on genetic and epigenetic biomarkers, their potential as diagnostic tools, and the need for validation in independent cohorts. The review highlights the impact of new genomic technologies, such as next-generation sequencing, in improving diagnostic accuracy and personalized management. It identifies the challenges and future directions in translating genetic findings into diagnostic tools and emphasizes the transformative potential of genetic insights in endometriosis diagnosis. This review provides a roadmap for future research and underscores the significance of genetic insights in improving diagnostic precision and personalized care for individuals with endometriosis.
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Affiliation(s)
- Diana Maria Chiorean
- Department of Pathology, County Clinical Hospital of Targu Mures, 540072 Targu Mures, Romania
| | - Melinda-Ildiko Mitranovici
- Department of Obstetrics and Gynecology, Emergency County Hospital Hunedoara, 14 Victoriei Street, 331057 Hunedoara, Romania
| | - Havva Serap Toru
- Department of Pathology, Akdeniz University School of Medicine, Antalya Pinarbasi Konyaalti, 07070 Antalya, Turkey
| | - Titiana Cornelia Cotoi
- Department of Pharmaceutical Technology, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania
| | - Alexandru Nicușor Tomuț
- Faculty of Medicine, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania
| | - Sabin Gligore Turdean
- Department of Pathology, County Clinical Hospital of Targu Mures, 540072 Targu Mures, Romania
| | - Ovidiu Simion Cotoi
- Department of Pathology, County Clinical Hospital of Targu Mures, 540072 Targu Mures, Romania
- Department of Pathophysiology, "George Emil Palade" University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 38 Gheorghe Marinescu Street, 540142 Targu Mures, Romania
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13
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Yang SC, Park M, Hong KH, La H, Park C, Wang P, Li G, Chen Q, Choi Y, DeMayo FJ, Lydon JP, Skalnik DG, Lim HJ, Hong SH, Park SH, Kim YS, Kim HR, Song H. CFP1 governs uterine epigenetic landscapes to intervene in progesterone responses for uterine physiology and suppression of endometriosis. Nat Commun 2023; 14:3220. [PMID: 37270588 DOI: 10.1038/s41467-023-39008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/24/2023] [Indexed: 06/05/2023] Open
Abstract
Progesterone (P4) is required for the preparation of the endometrium for a successful pregnancy. P4 resistance is a leading cause of the pathogenesis of endometrial disorders like endometriosis, often leading to infertility; however, the underlying epigenetic cause remains unclear. Here we demonstrate that CFP1, a regulator of H3K4me3, is required for maintaining epigenetic landscapes of P4-progesterone receptor (PGR) signaling networks in the mouse uterus. Cfp1f/f;Pgr-Cre (Cfp1d/d) mice showed impaired P4 responses, leading to complete failure of embryo implantation. mRNA and chromatin immunoprecipitation sequencing analyses showed that CFP1 regulates uterine mRNA profiles not only in H3K4me3-dependent but also in H3K4me3-independent manners. CFP1 directly regulates important P4 response genes, including Gata2, Sox17, and Ihh, which activate smoothened signaling pathway in the uterus. In a mouse model of endometriosis, Cfp1d/d ectopic lesions showed P4 resistance, which was rescued by a smoothened agonist. In human endometriosis, CFP1 was significantly downregulated, and expression levels between CFP1 and these P4 targets are positively related regardless of PGR levels. In brief, our study provides that CFP1 intervenes in the P4-epigenome-transcriptome networks for uterine receptivity for embryo implantation and the pathogenesis of endometriosis.
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Affiliation(s)
- Seung Chel Yang
- Department of Biomedical Science, CHA University, Seongnam, Gyeonggi, 13488, Korea
| | - Mira Park
- Department of Biomedical Science, CHA University, Seongnam, Gyeonggi, 13488, Korea
| | - Kwon-Ho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Peike Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Gaizhen Li
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qionghua Chen
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea
| | - Francesco J DeMayo
- Department of Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 12233, USA
| | - John P Lydon
- Department of Molecular and Cellular Biology and Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David G Skalnik
- Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Hyunjung J Lim
- Department of Veterinary Science, Konkuk University, Seoul, 05029, Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24431, Korea
- KW-Bio Co., Ltd, Wonju, 26493, Korea
| | - So Hee Park
- Department of Biomedical Science, CHA University, Seongnam, Gyeonggi, 13488, Korea
| | - Yeon Sun Kim
- Department of Biomedical Science, CHA University, Seongnam, Gyeonggi, 13488, Korea
| | - Hye-Ryun Kim
- Department of Biomedical Science, CHA University, Seongnam, Gyeonggi, 13488, Korea
| | - Haengseok Song
- Department of Biomedical Science, CHA University, Seongnam, Gyeonggi, 13488, Korea.
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14
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Wei J, Huang B, Nong Y, Zhang Q, Liu W, Xie Y, Peng T, Wang W, Liang X, Li Q, Liu F. Identification of a Novel Cuproptosis-Related Gene Signature in Eutopic Endometrium of Women with Endometriosis. Reprod Sci 2023; 30:1841-1853. [PMID: 36474131 PMCID: PMC10229735 DOI: 10.1007/s43032-022-01130-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Endometriosis (EMs) is a life-long endocrine disorder and a common cause for female infertility and pelvic pain. The key characteristics of eutopic endometrium of EMs patients are high proliferative and migratory potentials. Cuproptosis is a recently identified copper- and-mitochondrial-dependent regulated cell death. Regretfully, its role in EMs remains unclear. In this study, Kyoto Encyclopedia of Genes and Genomes analyses of differentially expressed genes (DEGs) indicated strong activation of the PI3K-Akt-mTOR pathway and biological process analysis reported positive regulation of kinase activity. Next, we screened 11 cuproptosis-related DEGs and found all of them were downregulated in the EMs group, which indicated the suppression of cuproptosis in EMs. One key cuproptosis-related gene, PDHA1, was selected via support vector machine, random forest algorithm and lasso regularization to build a risk-scoring model, which was tested in both internal and external validations. In conclusion, the downregulation and kinase activity of PDHA1 may function with the PI3K-Akt-mTOR pathway in some way, which could suppress the cuproptosis level and account for the cancer-like pathology in EMs.
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Affiliation(s)
- Jiahui Wei
- Guangzhou Medical University, Guangzhou, 511495, China
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Baoyi Huang
- Guangzhou Medical University, Guangzhou, 511495, China
| | - Yingqi Nong
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Qianyu Zhang
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Wenjuan Liu
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Yanni Xie
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Tong Peng
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Wei Wang
- Guangzhou Medical University, Guangzhou, 511495, China
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Xiangping Liang
- Guangzhou Medical University, Guangzhou, 511495, China
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Qiuyun Li
- Guangzhou Medical University, Guangzhou, 511495, China
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Fenghua Liu
- Department of Reproductive Health and Infertility, Guangdong Women and Children Hospital, Guangzhou, 511442, China.
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15
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Zheng W, Xiang D, Wen D, Luo M, Liang X, Cao L. Identification of key modules and candidate genes associated with endometriosis based on transcriptome data via bioinformatics analysis. Pathol Res Pract 2023; 244:154404. [PMID: 36996608 DOI: 10.1016/j.prp.2023.154404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUNDS Endometriosis is a common disease in women, but the signaling pathways and genes involved remain unclear. This study screened genes that were differentially expressed in ectopic endometrium (EC) and eutopic endometrium (EU) in endometriosis and provided clues for subsequent experimental verification. METHODS Endometriosis samples were harvested from inpatients that underwent surgery from 2017 to 2019 with pathological evidence of endometriosis. We assessed the mRNA expression profiles in endometriosis and further conducted gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Set Enrichment Analysis (GSEA) and weighted gene co-expression network analysis (WGCNA) to identify potential biomarkers in endometriosis. Finally, we further validated hub genes using public databases and immunohistochemistry assays. RESULTS The upregulated DEGs of ectopic endometrium from endometriosis patients were mainly involved in cell adhesion, MAPK signaling, PI3K-Akt signaling pathways, cytokine receptor interactions, and epithelial-mesenchymal transformation (EMT)-associated signaling pathways. The downregulated DEGs between ectopic endometrium and eutopic endometrium were related to decidualization-associated genes in endometriosis. The correlated gene modules in eutopic endometrial cells were mainly enriched in cell adhesion, embryo implantation and inflammation. The eutopic and ectopic endometrial lesions in endometriosis were involved in the EMT process. Furthermore, we identified 18 co-expression modules during WGCNA analysis. Hub genes in the pale turquoise module were FOSB, JUNB, ATF3, CXCL2, FOS, etc. Significantly enriched KEGG pathways included the TNF, MAPK, foxO, oxytocin, and p53 signaling pathways. Enrichment pathways were directly related to immune surveillance, stem cell self-renewal, and epithelial-mesenchymal transformation. Several pathways and modules of endometriosis are related to cancer-associated pathways, which substantiates the correlation between endometriosis and various gynecological tumors. CONCLUSIONS Endometriosis was tightly correlated with EMT and fibrosis mediated by inflammatory immunity, cytokines, estrogen, kinases and protooncogene through transcriptomics. Overall, our findings lay the groundwork for understanding the pathogenesis of endometriosis and its relationship with malignant transformation.
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Affiliation(s)
- Weilin Zheng
- Traditional Chinese Medicine Department, Guangdong Second Provincial General Hospital, Guangdong Provincial Emergency Hospital, Guangzhou, China
| | - Dongfang Xiang
- Department of Gynecology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danting Wen
- Department of Gynecology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meicheng Luo
- Department of Gynecology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuefang Liang
- Department of Gynecology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Lixing Cao
- Department of Gynecology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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16
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Kwan B, Fuhrer T, Montemayor D, Fink JC, He J, Hsu CY, Messer K, Nelson RG, Pu M, Ricardo AC, Rincon-Choles H, Shah VO, Ye H, Zhang J, Sharma K, Natarajan L. A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study. BMC Bioinformatics 2023; 24:57. [PMID: 36803209 PMCID: PMC9942303 DOI: 10.1186/s12859-023-05171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND The growing amount of high dimensional biomolecular data has spawned new statistical and computational models for risk prediction and disease classification. Yet, many of these methods do not yield biologically interpretable models, despite offering high classification accuracy. An exception, the top-scoring pair (TSP) algorithm derives parameter-free, biologically interpretable single pair decision rules that are accurate and robust in disease classification. However, standard TSP methods do not accommodate covariates that could heavily influence feature selection for the top-scoring pair. Herein, we propose a covariate-adjusted TSP method, which uses residuals from a regression of features on the covariates for identifying top scoring pairs. We conduct simulations and a data application to investigate our method, and compare it to existing classifiers, LASSO and random forests. RESULTS Our simulations found that features that were highly correlated with clinical variables had high likelihood of being selected as top scoring pairs in the standard TSP setting. However, through residualization, our covariate-adjusted TSP was able to identify new top scoring pairs, that were largely uncorrelated with clinical variables. In the data application, using patients with diabetes (n = 977) selected for metabolomic profiling in the Chronic Renal Insufficiency Cohort (CRIC) study, the standard TSP algorithm identified (valine-betaine, dimethyl-arg) as the top-scoring metabolite pair for classifying diabetic kidney disease (DKD) severity, whereas the covariate-adjusted TSP method identified the pair (pipazethate, octaethylene glycol) as top-scoring. Valine-betaine and dimethyl-arg had, respectively, ≥ 0.4 absolute correlation with urine albumin and serum creatinine, known prognosticators of DKD. Thus without covariate-adjustment the top-scoring pair largely reflected known markers of disease severity, whereas covariate-adjusted TSP uncovered features liberated from confounding, and identified independent prognostic markers of DKD severity. Furthermore, TSP-based methods achieved competitive classification accuracy in DKD to LASSO and random forests, while providing more parsimonious models. CONCLUSIONS We extended TSP-based methods to account for covariates, via a simple, easy to implement residualizing process. Our covariate-adjusted TSP method identified metabolite features, uncorrelated from clinical covariates, that discriminate DKD severity stage based on the relative ordering between two features, and thus provide insights into future studies on the order reversals in early vs advanced disease states.
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Grants
- R01 DK110541 NIDDK NIH HHS
- U24 DK060990 NIDDK NIH HHS
- R01DK118736, 1R01DK110541-01A1, U01DK060990, U01DK060984, U01DK061022, U01DK061021, U01DK061028, U01DK060980, U01DK060963, U01DK060902, U24DK060990 NIDDK NIH HHS
- National Science Foundation Graduate Research Fellowship Program
- Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases
- National Institute of Diabetes and Digestive and Kidney Diseases
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Affiliation(s)
- Brian Kwan
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Montemayor
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jeffery C Fink
- Department of Medicine, University of Maryland, Baltimore School of Medicine, Baltimore, MD, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine and Tulane University Translational Science Institute,, New Orleans, LA, USA
| | - Chi-Yuan Hsu
- Division of Nephrology, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Karen Messer
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Minya Pu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Ana C Ricardo
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Hernan Rincon-Choles
- Department of Nephrology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Vallabh O Shah
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Hongping Ye
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jing Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Kumar Sharma
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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17
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Zhao X, Kong W, Zhou C, Deng B, Zhang H, Guo H, Chen S, Pan Z. Bioinformatics-based analysis of the roles of sex hormone receptors in endometriosis development. Int J Med Sci 2023; 20:415-428. [PMID: 36860677 PMCID: PMC9969500 DOI: 10.7150/ijms.79516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
Endometriosis is a hormone-dependent disease in women of reproductive age and seriously affects women's health. To analyze the involvement of sex hormone receptors in endometriosis development, we performed bioinformatics analysis using four datasets derived from the Gene Expression Omnibus (GEO) database, which may help us understand the mechanisms by which the sex hormones act in vivo in endometriosis patients. The enrichment analysis and protein-protein interaction (PPI) analysis of the differentially expressed genes (DEGs) revealed that there are different key genes and pathways involved in eutopic endometrium aberrations of endometriosis patients and endometriotic lesions, and sex hormone receptors, including androgen receptor (AR), progesterone receptor (PGR) and estrogen receptor 1 (ESR1), may play important roles in endometriosis development. Androgen receptor (AR), as the hub gene of endometrial aberrations in endometriotic patients, showed positive expression in the main cell types for endometriosis development, and its decreased expression in the endometrium of endometriotic patients was also confirmed by immunohistochemistry (IHC). The nomogram model established based on it displayed good predictive value.
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Affiliation(s)
- Xiaoling Zhao
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Weimin Kong
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Chunxiao Zhou
- Division of Gynecologic Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boer Deng
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China.,Division of Gynecologic Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - He Zhang
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Huimin Guo
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Shuning Chen
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Zhendong Pan
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
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18
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Xu Z, Zhao H, Yue C, Zhang L, Li M, Du Y, Zhang N, Yan L. Low STING expression promotes endometrial stromal cell invasion and migration via the STING/IRF-3/IFN-β1 pathway in eutopic endometrium of women with endometriosis. Gynecol Endocrinol 2022; 38:1129-1135. [PMID: 36509095 DOI: 10.1080/09513590.2022.2154338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aims: The primary aim of the current study was to elucidate the function of the stimulator of interferon genes (STING) in the eutopic endometrium of women with endometriosis. Materials and Methods: STING expression and signaling pathways were verified by western blot analysis and immunohistochemistry after si-STING treatment. Cell proliferation and invasion and migration were assessed using 5-ethynyl-2'-deoxyuridine and transwell assays, respectively. Results: Within endometriosis tissues, STING was primarily expressed in the stroma of the eutopic endometrium and glandular epithelium of the ectopic endometrium. However, STING expression was significantly lower in the eutopic endometrium of patients with endometriosis compared to controls (p < 0.05). Additionally, cell proliferation (0.2866 ± 0.01470 vs. 0.6911 ± 0.01796, ****p < 0.0001), invasion (130.0 ± 6.296 vs. 424.1 ± 22.31, ****p < 0.0001), and migration (82.93 ± 6.940 vs. 82.93 ± 6.940, ****p < 0.0001) were significantly increased in the si-STING groups. Moreover, following si-STING transfection, the expression of phosphorylated IRF-3 and TBK1 that are involved in STING/IRF3/IFNb1 signaling pathway decreased. The addition of exogenous IFN-β1 effectively increased stromal cell invasion (IFN-β1-NC vs. IFN-β1-si-STING 274.7 ± 7.767 vs. 135.7 ± 12.63, ***p < 0.0001) and migration (IFN-β1-NC and IFN-β1-si-STING 28.53 ± 3.625 vs. 28.53 ± 3.625, ***p < 0.0001) without significantly impacting cell proliferation (si-STING vs. IFN-1β-si-STING 0.6874 ± 0.02081 vs. 0.7187 ± 0.02638, p = 0.795). Conclusions: The STING signaling pathway plays an important role in endometrial stromal cell proliferation, invasion and migration associated with endometriosis.
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Affiliation(s)
- Zhen Xu
- Medical Genetic and Prenatal Diagnosis Center, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Key Laboratory for Improving Birth Outcome Technique, Maternal and Child Health Care Hospital of Shandong Province, Jinan, China
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, China
- Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, China
| | - Heng Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, China
- Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, China
| | - Caixin Yue
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, China
- Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, China
| | - Lixia Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, China
- Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, China
- Maternal and Child Health and Family Planning Service Center of Yanggu County, Liaocheng, China
| | - Muzi Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, China
- Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, China
| | - Yanbo Du
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, China
- Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, China
| | - Na Zhang
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Lei Yan
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, China
- Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, China
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19
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Bolton KL, Chen D, Corona de la Fuente R, Fu Z, Murali R, Köbel M, Tazi Y, Cunningham JM, Chan IC, Wiley BJ, Moukarzel LA, Winham SJ, Armasu SM, Lester J, Elishaev E, Laslavic A, Kennedy CJ, Piskorz A, Sekowska M, Brand AH, Chiew YE, Pharoah P, Elias KM, Drapkin R, Churchman M, Gourley C, DeFazio A, Karlan B, Brenton JD, Weigelt B, Anglesio MS, Huntsman D, Gayther S, Konner J, Modugno F, Lawrenson K, Goode EL, Papaemmanuil E. Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes. Clin Cancer Res 2022; 28:4947-4956. [PMID: 35816189 PMCID: PMC9777703 DOI: 10.1158/1078-0432.ccr-21-3817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/24/2022] [Accepted: 07/07/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE To identify molecular subclasses of clear cell ovarian carcinoma (CCOC) and assess their impact on clinical presentation and outcomes. EXPERIMENTAL DESIGN We profiled 421 primary CCOCs that passed quality control using a targeted deep sequencing panel of 163 putative CCOC driver genes and whole transcriptome sequencing of 211 of these tumors. Molecularly defined subgroups were identified and tested for association with clinical characteristics and overall survival. RESULTS We detected a putative somatic driver mutation in at least one candidate gene in 95% (401/421) of CCOC tumors including ARID1A (in 49% of tumors), PIK3CA (49%), TERT (20%), and TP53 (16%). Clustering of cancer driver mutations and RNA expression converged upon two distinct subclasses of CCOC. The first was dominated by ARID1A-mutated tumors with enriched expression of canonical CCOC genes and markers of platinum resistance; the second was largely comprised of tumors with TP53 mutations and enriched for the expression of genes involved in extracellular matrix organization and mesenchymal differentiation. Compared with the ARID1A-mutated group, women with TP53-mutated tumors were more likely to have advanced-stage disease, no antecedent history of endometriosis, and poorer survival, driven by their advanced stage at presentation. In women with ARID1A-mutated tumors, there was a trend toward a lower rate of response to first-line platinum-based therapy. CONCLUSIONS Our study suggests that CCOC consists of two distinct molecular subclasses with distinct clinical presentation and outcomes, with potential relevance to both traditional and experimental therapy responsiveness. See related commentary by Lheureux, p. 4838.
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Affiliation(s)
- Kelly L. Bolton
- Washington University School of Medicine, St. Louis, Missouri
| | - Denise Chen
- Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania
| | | | - Zhuxuan Fu
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | | | - Martin Köbel
- The University of Calgary, Calgary, Alberta, Canada
| | - Yanis Tazi
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | | | - Brian J. Wiley
- Washington University School of Medicine, St. Louis, Missouri
| | | | | | | | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Esther Elishaev
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Angela Laslavic
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Catherine J. Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Anna Piskorz
- University of Cambridge, Cambridge, United Kingdom
| | | | - Alison H. Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Paul Pharoah
- University of Cambridge, Cambridge, United Kingdom
| | | | - Ronny Drapkin
- University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Anna DeFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Beth Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | | | - Britta Weigelt
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | - David Huntsman
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon Gayther
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Jason Konner
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Francesmary Modugno
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
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20
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Sivajohan B, Elgendi M, Menon C, Allaire C, Yong P, Bedaiwy MA. Clinical use of artificial intelligence in endometriosis: a scoping review. NPJ Digit Med 2022; 5:109. [PMID: 35927426 PMCID: PMC9352729 DOI: 10.1038/s41746-022-00638-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/24/2022] [Indexed: 02/07/2023] Open
Abstract
Endometriosis is a chronic, debilitating, gynecologic condition with a non-specific clinical presentation. Globally, patients can experience diagnostic delays of ~6 to 12 years, which significantly hinders adequate management and places a significant financial burden on patients and the healthcare system. Through artificial intelligence (AI), it is possible to create models that can extract data patterns to act as inputs for developing interventions with predictive and diagnostic accuracies that are superior to conventional methods and current tools used in standards of care. This literature review explored the use of AI methods to address different clinical problems in endometriosis. Approximately 1309 unique records were found across four databases; among those, 36 studies met the inclusion criteria. Studies were eligible if they involved an AI approach or model to explore endometriosis pathology, diagnostics, prediction, or management and if they reported evaluation metrics (sensitivity and specificity) after validating their models. Only articles accessible in English were included in this review. Logistic regression was the most popular machine learning method, followed by decision tree algorithms, random forest, and support vector machines. Approximately 44.4% (n = 16) of the studies analyzed the predictive capabilities of AI approaches in patients with endometriosis, while 47.2% (n = 17) explored diagnostic capabilities, and 8.33% (n = 3) used AI to improve disease understanding. Models were built using different data types, including biomarkers, clinical variables, metabolite spectra, genetic variables, imaging data, mixed methods, and lesion characteristics. Regardless of the AI-based endometriosis application (either diagnostic or predictive), pooled sensitivities ranged from 81.7 to 96.7%, and pooled specificities ranged between 70.7 and 91.6%. Overall, AI models displayed good diagnostic and predictive capacity in detecting endometriosis using simple classification scenarios (i.e., differentiating between cases and controls), showing promising directions for AI in assessing endometriosis in the near future. This timely review highlighted an emerging area of interest in endometriosis and AI. It also provided recommendations for future research in this field to improve the reproducibility of results and comparability between models, and further test the capacity of these models to enhance diagnosis, prediction, and management in endometriosis patients.
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Affiliation(s)
- Brintha Sivajohan
- Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Obstetrics and Gynecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mohamed Elgendi
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Biomedical and Mobile Health Technology Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Carlo Menon
- Biomedical and Mobile Health Technology Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Catherine Allaire
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Women's Hospital, Vancouver, BC, Canada
| | - Paul Yong
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Women's Hospital, Vancouver, BC, Canada
| | - Mohamed A Bedaiwy
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada. .,British Columbia Women's Hospital, Vancouver, BC, Canada.
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21
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Rytkönen KT, Faux T, Mahmoudian M, Heinosalo T, Nnamani MC, Perheentupa A, Poutanen M, Elo LL, Wagner GP. Histone H3K4me3 breadth in hypoxia reveals endometrial core functions and stress adaptation linked to endometriosis. iScience 2022; 25:104235. [PMID: 35494227 PMCID: PMC9051620 DOI: 10.1016/j.isci.2022.104235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/11/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Trimethylation of histone H3 at lysine 4 (H3K4me3) is a marker of active promoters. Broad H3K4me3 promoter domains have been associated with cell type identity, but H3K4me3 dynamics upon cellular stress have not been well characterized. We assessed this by exposing endometrial stromal cells to hypoxia, which is a major cellular stress condition. We observed that hypoxia modifies the existing H3K4me3 marks and that promoter H3K4me3 breadth rather than height correlates with transcription. Broad H3K4me3 domains mark genes for endometrial core functions and are maintained or selectively extended upon hypoxia. Hypoxic extension of H3K4me3 breadth associates with stress adaptation genes relevant for the survival of endometrial cells including transcription factor KLF4, for which we found increased protein expression in the stroma of endometriosis lesions. These results substantiate the view on broad H3K4me3 as a marker of cell identity genes and reveal participation of H3K4me3 extension in cellular stress adaptation.
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Affiliation(s)
- Kalle T. Rytkönen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Yale Systems Biology Institute, West Haven, CT 06516, USA
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, 20014 Turku, Finland
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Corresponding author
| | - Thomas Faux
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Mehrad Mahmoudian
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, 20014 Turku, Finland
| | - Taija Heinosalo
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, 20014 Turku, Finland
| | - Mauris C. Nnamani
- Yale Systems Biology Institute, West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Antti Perheentupa
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, 20014 Turku, Finland
- Department of Obstetrics and Gynecology, Turku University Hospital, Kiinamyllynkatu 4-8, 20521 Turku, Finland
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, 20014 Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20014 Turku, Finland
| | - Günter P. Wagner
- Yale Systems Biology Institute, West Haven, CT 06516, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School, New Haven, CT 06510, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
- Corresponding author
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22
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Vargas E, García-Moreno E, Aghajanova L, Salumets A, Horcajadas JA, Esteban FJ, Altmäe S. The mid-secretory endometrial transcriptomic landscape in endometriosis: a meta-analysis. Hum Reprod Open 2022; 2022:hoac016. [PMID: 35464885 PMCID: PMC9022214 DOI: 10.1093/hropen/hoac016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/16/2022] [Indexed: 12/01/2022] Open
Abstract
STUDY QUESTION Do women with endometriosis have a different endometrial gene expression profile at the time of embryo implantation than women without endometriosis? SUMMARY ANSWER The endometrial gene expression profile of women with endometriosis differs from that of women without endometriosis at the mid-secretory phase, although the differences are small. WHAT IS KNOWN ALREADY About 50% of women with endometriosis suffer infertility. Several molecular studies have suggested impaired endometrial receptivity in women with endometriosis, while others have detected no dysregulation of endometrial receptivity. Nevertheless, the previous endometrial transcriptome studies comparing women with and without endometriosis have been performed in small sample size with limited statistical power. We set out to systematically search and compile data of endometrial gene expression signatures at the receptive phase in women with endometriosis versus control women. Based on the obtained data, we conducted a meta-analysis of differentially expressed genes in order to raise the power of the analysis for identifying the molecular profiles of receptive phase endometria in endometriosis. STUDY DESIGN, SIZE, DURATION A systematic literature search was conducted up to February 2022 following PRISMA criteria and included PubMed, Cochrane and Web of Science databases. For the systematic search, the term ‘endometriosis’ was paired with the terms ‘transcriptomics’, ‘transcriptome’, ‘gene expression’, ‘RNA-seq’, ‘sequencing’ and ‘array’, by using the Boolean operator ‘AND’ to connect them. Articles written in English were screened and interrogated for data extraction. PARTICIPANTS/MATERIALS, SETTING, METHODS A meta-analysis was performed on the selected studies to extract the differentially expressed genes described at the mid-secretory phase in women with endometriosis versus women without endometriosis in natural cycles, using the robust rank aggregation method. In total, transcriptome data of 125 women (78 patients and 47 controls) were meta-analysed, with a special focus on endometrial receptivity-specific genes based on commercial endometrial receptivity tests. MAIN RESULTS AND THE ROLE OF CHANCE In total, 8 studies were eligible for the quantitative meta-analysis, gathering transcriptome data from the mid-secretory phase endometria of 125 women. A total of 7779 differentially expressed transcripts between the study groups were retrieved (3496 up-regulated and 4283 down-regulated) and were meta-analysed. After stringent multiple correction, there was no differential expression of any single molecule in the endometrium of women with endometriosis versus controls, while enrichment analysis detected that the pathways of chemotaxis and locomotion are dysregulated in endometriosis. Further analysis of endometrial receptivity-specific genes highlighted dysregulation of C4BPA, MAOA and PAEP and enrichment of immune and defence pathways in women with endometriosis. LIMITATIONS, REASONS FOR CAUTION Most of the studies included into the meta-analysis were relatively small and had different study designs, which might have contributed to a bias. WIDER IMPLICATIONS OF THE FINDINGS The current meta-analysis supports the hypothesis that endometrial receptivity is altered in women with endometriosis, although the changes are small. The molecules and pathways identified could serve as future biomarkers and therapeutical targets in detecting and treating endometriosis-associated infertility. STUDY FUNDING/COMPETING INTEREST(S) The authors declare no competing interests. This work was supported by the Spanish Ministry of Education, Culture and Sport [grant FPU15/01193] and the Margarita Salas program for the Requalification of the Spanish University system [grant UJAR01MS]; Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; Programa Operativo FEDER Andalucía (B-CTS-500-UGR18; A-CTS-614-UGR20); the Junta de Andalucía [BIO-302; and PAIDI P20_00158]; the University of Jaén [PAIUJA-EI_CTS02_2017]; the University of Granada, Plan Propio de Investigación 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES), and by the Junta de Andalucía, Consejería de Conocimiento, Investigación y Universidades and European Regional Development Fund (ERDF), ref. SOMM17/6107/UGR; the Estonian Research Council (grant PRG1076); Horizon 2020 innovation (ERIN, grant no. EU952516) of the European Commission and Enterprise Estonia (grant EU48695). TRIAL REGISTRATION NUMBER The systematic review was registered at PROSPERO (identifier: CRD42020122054).
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Affiliation(s)
- E Vargas
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Jaén, 23003, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, 18071, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, 18014, Spain
| | - E García-Moreno
- Immunology Unit,Hospital Universitario Puerta del Mar, Cádiz, Cádiz, 11009, Spain
| | - L Aghajanova
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford School of Medicine, Sunnyvale, CA, 94305, USA
| | - A Salumets
- Competence Centre on Health Technologies, Tartu, 50410, Estonia
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, 17177, Sweden
- Department of Obstetrics and Gyneaecology, Institute of Clinical Medicine, University of Tartu, Tartu, 50406, Estonia
| | - J A Horcajadas
- University Pablo de Olavide, Sevilla, Sevilla, 41013, Spain
| | - F J Esteban
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Jaén, 23003, Spain
| | - S Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, 18071, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, 18014, Spain
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford School of Medicine, Sunnyvale, CA, 94305, USA
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23
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MacLean JA, Hayashi K. Progesterone Actions and Resistance in Gynecological Disorders. Cells 2022; 11:647. [PMID: 35203298 PMCID: PMC8870180 DOI: 10.3390/cells11040647] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 02/06/2023] Open
Abstract
Estrogen and progesterone and their signaling mechanisms are tightly regulated to maintain a normal menstrual cycle and to support a successful pregnancy. The imbalance of estrogen and progesterone disrupts their complex regulatory mechanisms, leading to estrogen dominance and progesterone resistance. Gynecological diseases are heavily associated with dysregulated steroid hormones and can induce chronic pelvic pain, dysmenorrhea, dyspareunia, heavy bleeding, and infertility, which substantially impact the quality of women's lives. Because the menstrual cycle repeatably occurs during reproductive ages with dynamic changes and remodeling of reproductive-related tissues, these alterations can accumulate and induce chronic and recurrent conditions. This review focuses on faulty progesterone signaling mechanisms and cellular responses to progesterone in endometriosis, adenomyosis, leiomyoma (uterine fibroids), polycystic ovary syndrome (PCOS), and endometrial hyperplasia. We also summarize the association with gene mutations and steroid hormone regulation in disease progression as well as current hormonal therapies and the clinical consequences of progesterone resistance.
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Affiliation(s)
- James A. MacLean
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, 1770 NE Stadium Way, Pullman, WA 99164, USA
| | - Kanako Hayashi
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, 1770 NE Stadium Way, Pullman, WA 99164, USA
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24
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Endometrial cytokines in patients with and without endometriosis evaluated for infertility. Fertil Steril 2022; 117:629-640. [DOI: 10.1016/j.fertnstert.2021.11.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022]
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25
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Bunis DG, Wang W, Vallvé-Juanico J, Houshdaran S, Sen S, Ben Soltane I, Kosti I, Vo KC, Irwin JC, Giudice LC, Sirota M. Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis. Front Immunol 2022; 12:788315. [PMID: 35069565 PMCID: PMC8766492 DOI: 10.3389/fimmu.2021.788315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
The uterine lining (endometrium) exhibits a pro-inflammatory phenotype in women with endometriosis, resulting in pain, infertility, and poor pregnancy outcomes. The full complement of cell types contributing to this phenotype has yet to be identified, as most studies have focused on bulk tissue or select cell populations. Herein, through integrating whole-tissue deconvolution and single-cell RNAseq, we comprehensively characterized immune and nonimmune cell types in the endometrium of women with or without disease and their dynamic changes across the menstrual cycle. We designed metrics to evaluate specificity of deconvolution signatures that resulted in single-cell identification of 13 novel signatures for immune cell subtypes in healthy endometrium. Guided by statistical metrics, we identified contributions of endometrial epithelial, endothelial, plasmacytoid dendritic cells, classical dendritic cells, monocytes, macrophages, and granulocytes to the endometrial pro-inflammatory phenotype, underscoring roles for nonimmune as well as immune cells to the dysfunctionality of this tissue.
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Affiliation(s)
- Daniel G. Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
| | - Wanxin Wang
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Júlia Vallvé-Juanico
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Sahar Houshdaran
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Sushmita Sen
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Isam Ben Soltane
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
| | - Kim Chi Vo
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Juan C. Irwin
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Linda C. Giudice
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Department of Pediatrics, Division of Neonatology, University of California, San Francisco, San Francisco, CA, United States
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26
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Huang Y, Li Q, Hu R, Li R, Yang Y. Five immune-related genes as diagnostic markers for endometriosis and their correlation with immune infiltration. Front Endocrinol (Lausanne) 2022; 13:1011742. [PMID: 36277723 PMCID: PMC9582281 DOI: 10.3389/fendo.2022.1011742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Endometriosis (EMS) is a chronic disease that can cause dysmenorrhea, chronic pelvic pain, and infertility, among other symptoms. EMS diagnosis is often delayed compared to other chronic diseases, and there are currently no accurate, easily accessible, and non-invasive diagnostic tools. Therefore, it is important to elucidate the mechanism of EMS and explore potential biomarkers and diagnostic tools for its accurate diagnosis and treatment. In the present study, we comprehensively analyzed the differential expression, immune infiltration, and interactions of EMS-related genes in three Homo sapiens datasets. Our results identified 332 differentially expressed genes (DEGs) associated with EMS. Gene ontology analysis showed that these changes mainly focused on the positive regulation of endometrial cell proliferation, cell metabolism, and extracellular space, and EMS involved the integrin, complement activation, folic acid metabolism, interleukin, and lipid signaling pathways. The LASSO regression model was established using immune DEGs with an area under the curve of 0.783 for the internal dataset and 0.656 for the external dataset. Five genes with diagnostic value, ACKR1, LMNB1, MFAP4, NMU, and SEMA3C, were screened from M1 and M2 macrophages, activated mast cells, neutrophils, natural killer cells, follicular T helper cells, CD8+, and CD4+ cells. A protein-protein interaction network based on the immune DEGs was constructed, and ten hub genes with the highest scores were identified. Our results may provide a framework for the development of pathological molecular networks in EMS.
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Affiliation(s)
- Yi Huang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Qiong Li
- Department of Obstetrics and Gynecology, Minqin People’s Hospital, Minqin, China
| | - Rui Hu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Ruiyun Li
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Yuan Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- The Reproductive Medicine Center, The 1st Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Yuan Yang,
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27
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Pei T, Luo B, Huang W, Liu D, Li Y, Xiao L, Huang X, Ouyang Y, Zhu H. Increased Expression of YAP Inhibited the Autophagy Level by Upregulating mTOR Signal in the Eutopic ESCs of Endometriosis. Front Endocrinol (Lausanne) 2022; 13:813165. [PMID: 35173685 PMCID: PMC8842667 DOI: 10.3389/fendo.2022.813165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/03/2022] [Indexed: 01/18/2023] Open
Abstract
We first reported that the Hippo-YAP signaling pathway plays a critical role in the pathogenesis of endometriosis (EMS). Autophagy is also related to the invasion ability of endometrial cells and is involved in the pathogenesis of EMS through multi-levels. However, the precise regulatory mechanism of YAP on autophagy in the eutopic endometrial stromal cells (ESCs) is still unclear. Primary eutopic ESCs of EMS patients (n = 12) and control patients without EMS (n = 9) were isolated and cultured to investigate the expressions of YAP and mTOR, the role of YAP in autophagy, and the effect of the YAP-autophagy signal on the decidualization of the eutopic ESCs. Endometriosis-related sequencing data (GSE51981) in the GEO database were used to find the genes significantly correlated with YAP. We found 155 genes with significant differences in the interaction with YAP in EMS from the dataset, and the autophagy pathway was significantly enriched. Following on from our previous studies of YAP knockdown, overexpression of YAP resulted in an increased expression of mTOR and decreased ratio of LC3-II/LC3-I and autophagy markers, in the eutopic ESCs; transmission electron microscope observation also showed fewer autophagosomes compared with the control cells. Furthermore, ESCs of the Rapamycin-treated group showed significant decidual-like changes with significantly increased decidual prolactin level at 72 h after in vitro decidualization. These results demonstrate that the increased YAP inhibited the level of autophagy by upregulating the mTOR signal in the eutopic ESCs of endometriosis. The YAP-autophagy signal plays an important role in the pathogenesis of endometriosis-associated infertility.
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Affiliation(s)
- Tianjiao Pei
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Bin Luo
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Wei Huang
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Dong Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
- Department of Reproductive Endocrinology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Yujing Li
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Li Xiao
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Xin Huang
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Yunwei Ouyang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
- Department of Reproductive Endocrinology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Huili Zhu
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
- *Correspondence: Huili Zhu,
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28
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Lin LL, Makwana S, Chen M, Wang CM, Gillette LH, Huang TH, Burney RO, Nicholson BJ, Kirma NB. Cellular junction and mesenchymal factors delineate an endometriosis-specific response of endometrial stromal cells to the mesothelium. Mol Cell Endocrinol 2022; 539:111481. [PMID: 34624439 DOI: 10.1016/j.mce.2021.111481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Endometriosis is a debilitating gynecologic disorder that affects ∼10% of women of reproductive age. Endometriosis is characterized by growth of endometriosis lesions within the abdominal cavity, generally thought to arise from retrograde menstruation of shed endometrial tissue. While the pathophysiology underlying peritoneal endometriosis lesion formation is still unclear, the interaction between invading endometrial tissue and the peritoneal mesothelial lining is an essential step in lesion formation. In this study, we assessed proteomic differences between eutopic endometrial stromal cells (ESCs) from women with and without endometriosis in response to peritoneal mesothelial cell (PMC) exposure, using single-cell cytometry by time-of-flight (CyTOF). Co-cultured primary eutopic ESCs from women with and without endometriosis with an established PMC line were subjected to immunostaining with a panel of Maxpar CyTOF metal-conjugated antibodies (n = 28) targeting cell junction and mesenchymal markers, which are involved in cell-cell adhesions and epithelial-mesenchymal transition. Exposure of the ESCs to PMCs resulted in a drastic shift in cellular expression profiles in ESCs derived from endometriosis, whereas little effect by PMCs was observed in ESCs from non-endometriosis subjects. The transcription factor SNAI1 was consistently repressed by PMC interactions. ESCs from endometriosis patients are unique in that they respond to PMCs by undergoing changes in adhesive properties and mesenchymal characteristics that would facilitate lesion formation.
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Affiliation(s)
- Li-Ling Lin
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Simran Makwana
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | | | - Tim H Huang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | | | - Bruce J Nicholson
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, Texas, USA.
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA.
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29
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Wu XG, Chen JJ, Zhou HL, Wu Y, Lin F, Shi J, Wu HZ, Xiao HQ, Wang W. Identification and Validation of the Signatures of Infiltrating Immune Cells in the Eutopic Endometrium Endometria of Women With Endometriosis. Front Immunol 2021; 12:671201. [PMID: 34539624 PMCID: PMC8446207 DOI: 10.3389/fimmu.2021.671201] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/09/2021] [Indexed: 12/21/2022] Open
Abstract
Endometriosis is an oestrogen-dependent chronic inflammatory process with primary symptoms including dysmenorrhea, chronic pelvic pain, and infertility. The immune environment of the endometrium is essential for successful embryo implantation and ongoing pregnancy. In this study, we assessed the composition, density, and distribution of infiltrating immune cells in the endometria of women with endometriosis. Gene expression profiles of endometrial samples were downloaded from the Gene Expression Omnibus (GEO) database. We found that the TNF signalling pathway, the IL-17 signalling pathway, and the MAPK signalling pathway were significantly enriched in the eutopic endometria of women with endometriosis. The fractions and proportion of infiltrating immune cells were estimated by the CIBERSORT, MCP-counter, and ImmuCellAI methods. We found that the proportions of CD8+ T cells, activated NK cells, and follicular helper T cells were significantly higher in the endometria of women with endometriosis than in the endometria of normal controls, while the proportions of M2 macrophages and resting mast cells were significantly lower in the eutopic endometria. In GSE120103 (n = 36), we found that elevated CD8+ T cells in endometriosis increased the risk of infertility (P = 0.0019). The area under the receiver operating characteristic (ROC) curve (AUC) of CD8+ T cells to distinguish fertile and infertile endometriosis was 0.914. In clinical samples (n = 40), we found that the proportions of CD8+ T cells and CD56+ NK cells were significantly higher in the eutopic endometria of women with endometriosis than in the endometria of normal controls, while the proportion of CD163+ macrophages were lower in the eutopic endometria. The AUCs of CD8+ T cells and CD163+ macrophages were 0.727 and 0.833, respectively, which indicated that CD8 and CD163 were potential diagnostic markers for endometriosis. In conclusion, our results demonstrated that increased CD8+ T cells and CD56+ NK cells and decreased CD163+ macrophages within the eutopic endometria of women with endometriosis reveal a proinflammatory feature in the endometrial immune environment and that elevated CD8+ T cells increase the risk of infertility in women with the disease.
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Affiliation(s)
- Xiang-Guang Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jin-Jiao Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui-Ling Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fei Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jing Shi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hong-Zhen Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hai-Qun Xiao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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30
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Romero R. Giants in Obstetrics and Gynecology Series: a profile of Linda C. Giudice, MD, PhD, MSc. Am J Obstet Gynecol 2021; 225:113-119. [PMID: 34332715 PMCID: PMC10568801 DOI: 10.1016/j.ajog.2021.04.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI.
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31
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Bane K, Desouza J, Shetty D, Choudhary P, Kadam S, Katkam RR, Fernandes G, Sawant R, Dudhedia U, Warty N, Chauhan A, Chaudhari U, Gajbhiye R, Sachdeva G. Endometrial DNA damage response is modulated in endometriosis. Hum Reprod 2021; 36:160-174. [PMID: 33246341 DOI: 10.1093/humrep/deaa255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
STUDY QUESTION Is the DNA damage response (DDR) dysregulated in the eutopic endometrium of women with endometriosis? SUMMARY ANSWER Endometrial expression of genes involved in DDR is modulated in women with endometriosis, compared to those without the disease. WHAT IS KNOWN ALREADY Ectopic endometriotic lesions are reported to harbour somatic mutations, thereby hinting at dysregulation of DDR and DNA repair pathways. However, it remains inconclusive whether the eutopic endometrium also manifests dysregulated DDR in endometriosis. STUDY DESIGN, SIZE, DURATION For this case-control study conducted between 2015 and 2019, eutopic endometrial (E) samples (EE- from women with endometriosis, CE- from women without endometriosis) were collected in either mid-proliferative (EE-MP, n = 23; CE-MP, n = 17) or mid-secretory (EE-MS, n = 17; CE-MS, n = 9) phases of the menstrual cycle. This study compares: (i) DNA damage marker localization, (ii) expression of DDR genes and (iii) expression of DNA repair genes in eutopic endometrial samples from women with and without endometriosis. PARTICIPANTS/MATERIALS, SETTING, METHODS The study included (i) 40 women (aged 31.9 ± 0.81 years) with endometriosis and (ii) 26 control women (aged 31.4 ± 1.02 years) without endometriosis. Eutopic endometrial samples from the two groups were divided into different parts for histological analysis, immunohistochemistry, RNA extraction, protein extraction and comet assays. Eighty-four genes of relevance in the DNA damage signalling pathway were evaluated for their expression in eutopic endometrial samples, using RT2 Profiler PCR arrays. Validations of the expression of two GADD (Growth Arrest DNA Damage Inducible) proteins - GADD45A and GADD45G were carried out by immunoblotting. DNA damage was assessed by immunohistochemical localization of γ-H2AFX (a phosphorylated variant of histone H2AX) and 8-OHdG (8-hydroxy-2'-deoxyguanosine). RNA sequencing data from mid-proliferative (EE-MP, n = 4; CE-MP, n = 3) and mid-secretory phase (EE-MS and CE-MS, n = 4 each) endometrial samples were scanned to compare the expression status of all the genes implicated in human DNA repair. PCNA (Proliferating Cell Nuclear Antigen) expression was determined to assess endometrial proliferation. Residual DNA damage in primary endometrial cells was checked by comet assays. Public datasets were also scanned for the expression of DDR and DNA repair genes as our RNASeq data were limited by small sample size. All the comparisons were made between phase-matched endometrial samples from women with and without endometriosis. MAIN RESULTS AND THE ROLE OF CHANCE Endometrial expression of DDR genes and intensity of immunolocalized γ-H2AFX were significantly (P < 0.05) higher in EE, compared to CE samples. DDR proteins, especially those belonging to the GADD family, were found to be differentially abundant in EE, as compared to CE. These patterns were evident in both mid-proliferative and mid-secretory phases. Intriguingly, higher DDR was associated with increased cell proliferation in EE-MP, compared to CE-MP. Furthermore, among the differentially expressed transcripts (DETs) encoded by DNA repair genes, the majority showed up-regulation in EE-MP, compared to CE-MP. Interestingly, CE-MP and EE-MP had a comparable percentage (P > 0.05) of cells with residual DNA damage. However, unlike the mid-proliferative phase data, many DETs encoded by DNA repair genes were down-regulated in EE-MS, compared to CE-MS. An analysis of the phase-matched control and endometriosis samples included in the GSE51981 dataset available in the Gene Expression Omnibus database also revealed significant (P < 0.05) alterations in the expression of DDR and DNA repair genes in EE, compared to CE. LARGE-SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION The study was conducted on a limited number of endometrial samples. Also, the study does not reveal the causes underlying dysregulated DDR in the eutopic endometrium of women with endometriosis. WIDER IMPLICATIONS OF THE FINDINGS Alterations in the expression of DDR and DNA repair genes indirectly suggest that eutopic endometrium, as compared to its healthy counterpart, encounters DNA damage-inducing stimuli, either of higher strength or for longer duration in endometriosis. It will be worthwhile to identify the nature of such stimuli and also explore the role of higher genomic insults and dysregulated DDR/DNA repair in the origin and/or progression of endometriosis. STUDY FUNDING/COMPETING INTEREST(S) The study was supported by the Department of Biotechnology and Indian Council of Medical Research, Government of India. No conflict of interest is declared.
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Affiliation(s)
- Kashmira Bane
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Junita Desouza
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Diksha Shetty
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Prakash Choudhary
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Shalaka Kadam
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - R R Katkam
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Gwendolyn Fernandes
- Department of Pathology, Seth G.S. Medical College and King Edward Memorial Hospital, Mumbai, India
| | - Raj Sawant
- Sanjeevani Diagnostic Centre and General Maternity Home, Mumbai, India.,Jaslok Hospital and Research Centre, Mumbai, India
| | - Uddhavraj Dudhedia
- Advanced Multi Specialty Hospitals and Criticare Multispecialty Hospital and Research Center, Mumbai, India
| | - Neeta Warty
- Sanjeevani Diagnostic Centre and General Maternity Home, Mumbai, India.,Jaslok Hospital and Research Centre, Mumbai, India
| | - Anahita Chauhan
- Department of Obstetrics and Gynecology, Seth G. S. Medical College and King Edward Memorial Hospital, Mumbai, India
| | - Uddhav Chaudhari
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Rahul Gajbhiye
- Department of Clinical Research, ICMR-NIRRH, Mumbai, India
| | - Geetanjali Sachdeva
- Primate Biology Laboratory, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
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Devesa-Peiro A, Sebastian-Leon P, Pellicer A, Diaz-Gimeno P. Guidelines for biomarker discovery in endometrium: correcting for menstrual cycle bias reveals new genes associated with uterine disorders. Mol Hum Reprod 2021; 27:gaab011. [PMID: 33576824 PMCID: PMC8063681 DOI: 10.1093/molehr/gaab011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/27/2021] [Indexed: 12/11/2022] Open
Abstract
Transcriptomic approaches are increasingly used in reproductive medicine to identify candidate endometrial biomarkers. However, it is known that endometrial progression in the molecular biology of the menstrual cycle is a main factor that could affect the discovery of disorder-related genes. Therefore, the aim of this study was to systematically review current practices for considering the menstrual cycle effect and to demonstrate its bias in the identification of potential biomarkers. From the 35 studies meeting the criteria, 31.43% did not register the menstrual cycle phase. We analysed the menstrual cycle effect in 11 papers (including 12 studies) from Gene Expression Omnibus: three evaluating endometriosis, two evaluating recurrent implantation failure, one evaluating recurrent pregnancy loss, one evaluating uterine fibroids and five control studies, which collected endometrial samples throughout menstrual cycle. An average of 44.2% more genes were identified after removing menstrual cycle bias using linear models. This effect was observed even if studies were balanced in the proportion of samples collected at different endometrial stages or only in the mid-secretory phase. Our bias correction method increased the statistical power by retrieving more candidate genes than per-phase independent analyses. Thanks to this practice, we discovered 544 novel candidate genes for eutopic endometriosis, 158 genes for ectopic ovarian endometriosis and 27 genes for recurrent implantation failure. In conclusion, we demonstrate that menstrual cycle progression masks molecular biomarkers, provides new guidelines to unmask them and proposes a new classification that distinguishes between biomarkers of disorder or/and menstrual cycle progression.
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Affiliation(s)
- Almudena Devesa-Peiro
- Department of Genomic & Systems Reproductive Medicine, IVI-RMA IVI Foundation, Valencia, Spain—Instituto de Investigación Sanitaria Hospital Universitario y Politécnico La Fe, Valencia 46026, Spain
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia 46010, Spain
| | - Patricia Sebastian-Leon
- Department of Genomic & Systems Reproductive Medicine, IVI-RMA IVI Foundation, Valencia, Spain—Instituto de Investigación Sanitaria Hospital Universitario y Politécnico La Fe, Valencia 46026, Spain
| | - Antonio Pellicer
- Department of Genomic & Systems Reproductive Medicine, IVI-RMA IVI Foundation, Valencia, Spain—Instituto de Investigación Sanitaria Hospital Universitario y Politécnico La Fe, Valencia 46026, Spain
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia 46010, Spain
- IVI-RMA IVI Rome, Reproductive medicine clinic, Largo Ildebrando Pizzetti, 1, Rome 00197, Italy
| | - Patricia Diaz-Gimeno
- Department of Genomic & Systems Reproductive Medicine, IVI-RMA IVI Foundation, Valencia, Spain—Instituto de Investigación Sanitaria Hospital Universitario y Politécnico La Fe, Valencia 46026, Spain
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Poli-Neto OB, Carlos D, Favaretto A, Rosa-E-Silva JC, Meola J, Tiezzi D. Eutopic endometrium from women with endometriosis and chlamydial endometritis share immunological cell types and DNA repair imbalance: A transcriptome meta-analytical perspective. J Reprod Immunol 2021; 145:103307. [PMID: 33725527 DOI: 10.1016/j.jri.2021.103307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/03/2021] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
The aim of this study was to identify the key similarities between the eutopic endometrium of women with endometriosis and chlamydia-induced endometritis taking into account tissue microenvironment heterogeneity, transcript gene profile, and enriched pathways. A meta-analysis of whole transcriptome microarrays was performed using publicly available data, including samples containing both glandular and stromal endometrial components. Control samples were obtained from women without any reported pathological condition. Only samples obtained during the proliferative menstrual phase were included. Cellular tissue heterogeneity was predicted using a method that integrates gene set enrichment and deconvolution approaches. The batch effect was estimated by principal variant component analysis and removed using an empirical Bayes method. Differentially expressed genes were identified using an adjusted p-value < 0.05 and fold change = 1.5. The protein-protein interaction network was built using the STRING database and interaction score over 400. The Molecular Signatures Database was used to analyse the functional enrichment analysis. Both conditions showed similarities in cell types in the microenvironment, particularly CD4+ and CD8+ Tem cells, NKT cells, Th2 cells, basophils, and eosinophils. With regards to the regulation of cellular senescence and DNA integrity/damage checkpoint, which are commonly enriched pathways, 21 genes were down-regulated and directly related to DNA repair. Compared to the endometriosis samples, some chlamydial endometritis samples presented a lack of enriched immune pathways. Our results suggest that both conditions show similar distributions of microenvironment cell types, the downregulation of genes involved in DNA repair and cell cycle control, and pathways involved in immune response evasion.
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Affiliation(s)
- Omero Benedicto Poli-Neto
- Gynecological and Obstetrics Department, Ribeirão Preto Medical School of the University of São Paulo, Ribeirão Preto, 14049-900, SP, Brazil.
| | - Daniela Carlos
- Biochemistry and Immunology Department, Ribeirão Preto Medical School of the University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Aureo Favaretto
- Gynecological and Obstetrics Department, Ribeirão Preto Medical School of the University of São Paulo, Ribeirão Preto, 14049-900, SP, Brazil
| | - Julio Cesar Rosa-E-Silva
- Gynecological and Obstetrics Department, Ribeirão Preto Medical School of the University of São Paulo, Ribeirão Preto, 14049-900, SP, Brazil
| | - Juliana Meola
- Gynecological and Obstetrics Department, Ribeirão Preto Medical School of the University of São Paulo, Ribeirão Preto, 14049-900, SP, Brazil
| | - Daniel Tiezzi
- Gynecological and Obstetrics Department, Ribeirão Preto Medical School of the University of São Paulo, Ribeirão Preto, 14049-900, SP, Brazil
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Identification of candidate microRNA markers of endometriosis with the use of next-generation sequencing and quantitative real-time polymerase chain reaction. Fertil Steril 2021; 113:1232-1241. [PMID: 32482255 DOI: 10.1016/j.fertnstert.2020.01.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To identify novel candidate diagnostic microRNA (miRNA) markers of endometriosis by means of an unbiased search with confirmation by means of targeted polymerase chain reaction (PCR). DESIGN Retrospective cohort. SETTING University teaching hospitals. PATIENT(S) Women with endometriosis and control women, confirmed with the use of laparoscopy. INTERVENTIONS(S) Diagnostic laparoscopy and blood sample. MAIN OUTCOME MEASURE(S) Next-generation sequencing (NGS) and quantitative real-time PCR (qRT-PCR). RESULT(S) Candidate miRNAs differentially expressed in women with endometriosis compared with control women were identified by means of NGS and selected for qRT-PCR. Plasma samples from another cohort of women with surgically confirmed endometriosis (n = 53) and disease-free control women (n = 53) were checked for hemolysis using spectrophotometry and the ratio of miR-23a and miR-451 by means of qRT-PCR. MicroRNA signatures were quantified by means of qRT-PCR in hemolysis-free plasma samples of case subjects (n = 25) and control subjects (n = 28) with the use of miRcury LNA miRNA. Circulating levels of eight miRNAs (miR-199a-3p, miR-143-3p, miR-340-5p, let-7b-5p, miR-21-5p, miR-17-5p, miR-20a-5p, and miR-103a-3p) were significantly lower in case subjects compared to control subjects. The sensitivity and specificity for individual miRNAs ranged from 0.36 to 1.00 and from 0.43 to 1.00, respectively, but when combined produced sensitivity and specificity of 0.92 and 0.86 with positive (PPV) and (NPV) predictive values of 0.85 and 0.92, respectively. However, combination of five miRNAs (miR-17-5p, miR-20a-5p, miR-199a-3p, miR-143-3p, and let-7b-5p) produced sensitivity and specificity of 0.96 and 0.79 with PPV and NPV of 0.80 and 0.96, respectively. CONCLUSION(S) We conclude that a panel of candidate miRNAs was comparable to laparoscopy in distinguishing between women with endometriosis and control women.
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Wu YT, Ma SY, Sun WQ, Shen WW, Zhu HT, Zhang Q, Chen HF. TRIM65 Promotes Invasion of Endometrial Stromal Cells by Activating ERK1/2/C-myc Signaling via Ubiquitination of DUSP6. J Clin Endocrinol Metab 2021; 106:526-538. [PMID: 33146694 DOI: 10.1210/clinem/dgaa804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Endometriosis (EM) is a benign gynecological disease that shares some characteristics with malignancy, such as proliferation and invasion. So far, the pathogenesis of EM is still unclear. In this study, we investigated whether TRIM65 can play a role in the development of EM. METHODS TRIM65 expression levels in eutopic, ectopic, and normal endometrium were detected by quantitative real-time PCR and Western blot. Cell proliferation and invasion of primary endometrial stromal (EMS) cells were detected by CCK-8 and Transwell analysis. The interaction between TRIM65 and DUSP6 or C-myc was measured by coimmunoprecipitation, ubiquitylation, dual luciferase, and chromatin immunoprecipitation analysis. RESULTS We found that TRIM65 was identified as an up-regulated gene in ectopic endometrial tissues and EMS cells compared with control groups without EM. TRIM65 expression was positively correlated with the levels of p-ERK1/2, C-myc, matrix metalloproteinase-2, and integrin β1 in ectopic endometrial tissues in patients and mice. TRIM65 promoted the cell proliferation and invasion of EMS cells via the ERK1/2/C-myc pathway through ubiquitination of DUSP6. C-myc promoted TRIM65 expression through inducing TRIM65 promoter activity. Additionally, the increased expression of TRIM65, C-myc, matrix metalloproteinase-2, integrin β1, and p-ERK1/2 and the decreased expression of DUSP6 in ectopic endometrial tissues were significantly suppressed by inhibition of ERK1/2 signaling pathway in ectopic endometrial tissues in experimental mice model. CONCLUSION In conclusion, TRIM65 promotes invasion of ectopic EMS cells by activating a feedback loop with the ERK1/2/C-myc signaling pathway and may be a potential therapeutic target for EM.
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Affiliation(s)
- Ying-Ting Wu
- Department of Laboratory Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Si-Yu Ma
- Department of Laboratory Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wen-Qin Sun
- Department of Laboratory Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei-Wei Shen
- Department of Laboratory Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hui-Ting Zhu
- Department of Pathology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qin Zhang
- Department of Infectious Disease of Tongren Hospital, Jiao Tong University School of Medicine, Shanghai, China
| | - Hui-Fen Chen
- Department of Laboratory Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
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Clinical utility of the endometrial receptivity analysis in women with prior failed transfers. J Assist Reprod Genet 2021; 38:645-650. [PMID: 33454901 DOI: 10.1007/s10815-020-02041-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023] Open
Abstract
PURPOSE To determine the utility of the endometrial receptivity analysis (ERA) in women with prior failed embryo transfers (ET). METHODS This was a retrospective study of patients who underwent an ERA test with a subsequent frozen ET. Women were classified based on their indication for an ERA test: (1) ≥ 1 prior failed ET (cases), or (2) as a prophylactic measure (controls). A subset analysis of women with ≥ 3 prior failed transfers was performed. Pregnancy outcomes of the subsequent cycle were examined, including conception, clinical pregnancy, and ongoing pregnancy/live birth. RESULTS A total of 222 women were included, 131 (59%) women with ≥ 1 prior failed ET and 91 (41%) controls. Among the 131 women with ≥ 1 prior failed ET, 20 women (9%) had ≥ 3 prior failed ETs. The proportion of non-receptive ERA tests in the three groups were the following: 45% (≥ 1 prior failed ET), 40% (≥ 3 prior failed ETs), and 52% (controls). The results did not differ between cases and controls. The pregnancy outcomes did not differ between women with ≥ 1 prior failed ET and controls. In women with ≥ 3 prior failed ETs, there was a lower ongoing pregnancy/live birth rate (28% vs 54%, P = 0.046). CONCLUSION Women with ≥ 1 prior failed ET and ≥ 3 prior failed ETs had a similar prevalence of non-receptive endometrium compared to controls. Women with ≥ 3 prior failed ETs had a lower ongoing pregnancy/live birth rate despite a personalized FET, suggesting that there are additional factors in implantation failure beyond an adjustment in progesterone exposure.
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mHealth for research. Digit Health 2021. [DOI: 10.1016/b978-0-12-820077-3.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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McAllister SL, Sinharoy P, Vasu M, Gross ER. Aberrant reactive aldehyde detoxification by aldehyde dehydrogenase-2 influences endometriosis development and pain-associated behaviors. Pain 2021; 162:71-83. [PMID: 32541390 PMCID: PMC7718385 DOI: 10.1097/j.pain.0000000000001949] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 01/15/2023]
Abstract
Endometriosis affects ∼176 million women worldwide, yet on average, women experience pain ∼10 years from symptom onset before being properly diagnosed. Standard treatments (drugs or surgery) often fail to provide long-term pain relief. Elevated levels of reactive aldehydes such as 4-hydroxynonenal (4-HNE) have been implicated in the peritoneal fluid of women with endometriosis and upon accumulation, reactive aldehydes can form protein-adducts and/or generate pain. A key enzyme in detoxifying reactive aldehydes to less reactive forms is the mitochondrial enzyme aldehyde dehydrogenase-2 (ALDH2). Here, we tested the hypothesis that aberrant reactive aldehyde detoxification by ALDH2 underlies endometriosis and its associated pain. We determined, in the eutopic and ectopic endometrium of women with severe (stage IV) peritoneal endometriosis, that ALDH2 enzyme activity was decreased, which was associated with decreased ALDH2 expression and increased 4-HNE adduct formation compared to the eutopic endometrium of controls in the proliferative phase. Using a rodent model of endometriosis and an ALDH2*2 knock-in mouse with decreased ALDH2 activity, we determined that increasing ALDH2 activity with the enzyme activator Alda-1 could prevent endometriosis lesion development as well as alleviate pain-associated behaviors in proestrus. Overall, our findings suggest that targeting the ALDH2 enzyme in endometriosis may lead to better treatment strategies and in the proliferative phase, that increased 4-HNE adduct formation within the endometrium may serve as a less invasive diagnostic biomarker to reduce years of suffering in women.
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Affiliation(s)
- Stacy L. McAllister
- Department of Obstetrics and Gynecology, School of Medicine, Emory University, Atlanta, GA, United States
- Department of Anesthesiology, Perioperative, and Pain Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | - Pritam Sinharoy
- Department of Anesthesiology, Perioperative, and Pain Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | - Megana Vasu
- Department of Anesthesiology, Perioperative, and Pain Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | - Eric R. Gross
- Department of Anesthesiology, Perioperative, and Pain Medicine, School of Medicine, Stanford University, Stanford, CA, United States
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Endometriosis Is Associated with a Significant Increase in hTERC and Altered Telomere/Telomerase Associated Genes in the Eutopic Endometrium, an Ex-Vivo and In Silico Study. Biomedicines 2020; 8:biomedicines8120588. [PMID: 33317189 PMCID: PMC7764055 DOI: 10.3390/biomedicines8120588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Telomeres protect chromosomal ends and they are maintained by the specialised enzyme, telomerase. Endometriosis is a common gynaecological disease and high telomerase activity and higher hTERT levels associated with longer endometrial telomere lengths are characteristics of eutopic secretory endometrial aberrations of women with endometriosis. Our ex-vivo study examined the levels of hTERC and DKC1 RNA and dyskerin protein levels in the endometrium from healthy women and those with endometriosis (n = 117). The in silico study examined endometriosis-specific telomere- and telomerase-associated gene (TTAG) transcriptional aberrations of secretory phase eutopic endometrium utilising publicly available microarray datasets. Eutopic secretory endometrial hTERC levels were significantly increased in women with endometriosis compared to healthy endometrium, yet dyskerin mRNA and protein levels were unperturbed. Our in silico study identified 10 TTAGs (CDKN2A, PML, ZNHIT2, UBE3A, MCCC2, HSPC159, FGFR2, PIK3C2A, RALGAPA1, and HNRNPA2B1) to be altered in mid-secretory endometrium of women with endometriosis. High levels of hTERC and the identified other TTAGs might be part of the established alteration in the eutopic endometrial telomerase biology in women with endometriosis in the secretory phase of the endometrium and our data informs future research to unravel the fundamental involvement of telomerase in the pathogenesis of endometriosis.
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Jiang L, Zhang M, Wu J, Wang S, Yang X, Yi M, Zhang X, Fang X. Exploring diagnostic m6A regulators in endometriosis. Aging (Albany NY) 2020; 12:25916-25938. [PMID: 33232273 PMCID: PMC7803542 DOI: 10.18632/aging.202163] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022]
Abstract
Endometriosis is an estrogen-dependent inflammatory disorder, usually causing infertility, pelvic pain, and ovarian masses. This study intended to investigate the implication of N6-methyladenosine (m6A) regulators in endometriosis. We acquired 34 normal, 127 eutopic, and 46 ectopic, samples of endometrium from the Gene Expression Omnibus (GSE7305, GSE7307, GSE51981) database and the Array-express (E-MTAB-694) database. These samples were then used to profile the expression of 20 m6A regulators in endometriosis. The results indicated that most dysregulated (19/20) m6A regulators were significantly downregulated in eutopic vs. normal endometrium and also significantly downregulated in ectopic vs. eutopic endometrium. Several dysregulated m6A regulators were common to both contrast matrices: METTL3, YTHDF2, YTHDF3, HNRNPA2B1, HNRNPC, and FTO. Both HNRNPA2B1 and HNRNPC were associated with the severity of endometriosis in eutopic samples, and also exhibited diagnostic potential for endometriosis. HNRNPA2B1 and HNRNPC may influence immune pathways and the infiltration of immune cells in endometriosis. Abnormalities in the gene transcription factors network associated with endometriosis might affect the expression of HNRNPA2B1 and HNRNPC. In conclusion, we observed significant dysregulation of m6A regulators in endometriosis, and found that HNRNPA2B1 and HNRNPC might correlate with the immune response and serve as useful diagnostic biomarkers for endometriosis.
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Affiliation(s)
- Li Jiang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mengmeng Zhang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingni Wu
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Sixue Wang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiang Yang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Yi
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinyue Zhang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoling Fang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Poli-Neto OB, Meola J, Rosa-E-Silva JC. What the Transcriptome of the Eutopic Endometrium from Women with Endometriosis tells us about the Disease Pathophysiology: A Brief Reflection. REVISTA BRASILEIRA DE GINECOLOGIA E OBSTETRÍCIA 2020; 42:593-596. [PMID: 33129215 DOI: 10.1055/s-0040-1713807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Omero Benedicto Poli-Neto
- Department of Gynecology and Obstetrics, Division of Gynecological Surgery, Faculty of Medicine, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Juliana Meola
- Department of Gynecology and Obstetrics, Division of Gynecological Surgery, Faculty of Medicine, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Julio Cesar Rosa-E-Silva
- Department of Gynecology and Obstetrics, Division of Gynecological Surgery, Faculty of Medicine, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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Critchley HOD, Babayev E, Bulun SE, Clark S, Garcia-Grau I, Gregersen PK, Kilcoyne A, Kim JYJ, Lavender M, Marsh EE, Matteson KA, Maybin JA, Metz CN, Moreno I, Silk K, Sommer M, Simon C, Tariyal R, Taylor HS, Wagner GP, Griffith LG. Menstruation: science and society. Am J Obstet Gynecol 2020; 223:624-664. [PMID: 32707266 PMCID: PMC7661839 DOI: 10.1016/j.ajog.2020.06.004] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/13/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022]
Abstract
Women's health concerns are generally underrepresented in basic and translational research, but reproductive health in particular has been hampered by a lack of understanding of basic uterine and menstrual physiology. Menstrual health is an integral part of overall health because between menarche and menopause, most women menstruate. Yet for tens of millions of women around the world, menstruation regularly and often catastrophically disrupts their physical, mental, and social well-being. Enhancing our understanding of the underlying phenomena involved in menstruation, abnormal uterine bleeding, and other menstruation-related disorders will move us closer to the goal of personalized care. Furthermore, a deeper mechanistic understanding of menstruation-a fast, scarless healing process in healthy individuals-will likely yield insights into a myriad of other diseases involving regulation of vascular function locally and systemically. We also recognize that many women now delay pregnancy and that there is an increasing desire for fertility and uterine preservation. In September 2018, the Gynecologic Health and Disease Branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development convened a 2-day meeting, "Menstruation: Science and Society" with an aim to "identify gaps and opportunities in menstruation science and to raise awareness of the need for more research in this field." Experts in fields ranging from the evolutionary role of menstruation to basic endometrial biology (including omic analysis of the endometrium, stem cells and tissue engineering of the endometrium, endometrial microbiome, and abnormal uterine bleeding and fibroids) and translational medicine (imaging and sampling modalities, patient-focused analysis of menstrual disorders including abnormal uterine bleeding, smart technologies or applications and mobile health platforms) to societal challenges in health literacy and dissemination frameworks across different economic and cultural landscapes shared current state-of-the-art and future vision, incorporating the patient voice at the launch of the meeting. Here, we provide an enhanced meeting report with extensive up-to-date (as of submission) context, capturing the spectrum from how the basic processes of menstruation commence in response to progesterone withdrawal, through the role of tissue-resident and circulating stem and progenitor cells in monthly regeneration-and current gaps in knowledge on how dysregulation leads to abnormal uterine bleeding and other menstruation-related disorders such as adenomyosis, endometriosis, and fibroids-to the clinical challenges in diagnostics, treatment, and patient and societal education. We conclude with an overview of how the global agenda concerning menstruation, and specifically menstrual health and hygiene, are gaining momentum, ranging from increasing investment in addressing menstruation-related barriers facing girls in schools in low- to middle-income countries to the more recent "menstrual equity" and "period poverty" movements spreading across high-income countries.
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Affiliation(s)
- Hilary O D Critchley
- Medical Research Council Centre for Reproductive Health, The University of Edinburgh, United Kingdom.
| | - Elnur Babayev
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Serdar E Bulun
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Iolanda Garcia-Grau
- Igenomix Foundation-Instituto de Investigación Sanitaria Hospital Clínico, INCLIVA, Valencia, Spain; Department of Pediatrics, Obstetrics and Gynecology, School of Medicine, University of Valencia, Valencia, Spain
| | - Peter K Gregersen
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
| | | | | | | | - Erica E Marsh
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI
| | - Kristen A Matteson
- Division of Research, Department of Obstetrics and Gynecology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI
| | - Jacqueline A Maybin
- Medical Research Council Centre for Reproductive Health, The University of Edinburgh, United Kingdom
| | - Christine N Metz
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
| | - Inmaculada Moreno
- Igenomix Foundation-Instituto de Investigación Sanitaria Hospital Clínico, INCLIVA, Valencia, Spain
| | - Kami Silk
- Department of Communication, University of Delaware, Newark, DE
| | - Marni Sommer
- Department of Sociomedical Sciences, Columbia University Mailman School of Public Health, New York, NY
| | - Carlos Simon
- Igenomix Foundation-Instituto de Investigación Sanitaria Hospital Clínico, INCLIVA, Valencia, Spain; Department of Pediatrics, Obstetrics and Gynecology, School of Medicine, University of Valencia, Valencia, Spain; Beth Israel Deaconess Medical Center, Harvard University, Boston, MA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | | | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Department of Obstetrics, Gynecology and Reproductive Sciences, Systems Biology Institute, Yale University, New Haven, CT; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI
| | - Linda G Griffith
- Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA
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The Diagnostic Accuracy of Combined Enolase/Cr, CA125, and CA19-9 in the Detection of Endometriosis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5208279. [PMID: 33062681 PMCID: PMC7545435 DOI: 10.1155/2020/5208279] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 07/28/2020] [Indexed: 01/01/2023]
Abstract
Background The present study was designed to verify the accuracy of the noninvasive biomarkers enolase/Cr, CA125, and CA19-9 as a clinical diagnostic tool for the detection of endometriosis. Methods A cross-sectional study was performed at Rasool-e-Akram Hospital affiliated to Iran University of Medical Sciences, Tehran, Iran, from April 2015 to April 2018. Eighty-six women were scheduled to undergo laparoscopy due to chronic pelvic pain, infertility, pelvic mass, and abnormal uterine bleeding. Serum and urine samples of all patients were collected preoperatively. Serum levels of CA125 and CA19-9, and urine levels of enolase-1 were measured. Serum levels of CA125 and CA19-9 were determined by the electrochemiluminescence method (ECL). Urinary enolase-1 was measured by the ELISA method. Result Serum levels of CA125 and CA19-9 were significantly higher in the endometriosis group than in controls (p < 0.001, p = 0.004, respectively). Levels of enolase I and enolase/Cr were higher in patients with endometriosis, but the differences were not statistically significant. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of combined enolase/Cr, CA125, and CA19-9 were 65%, 66.6%, 71%, and 60.1%, respectively. The positive likelihood ratio (PLR) and negative likelihood ratio (NLR) of combined enolase/Cr, CA125, and CA19-9 was 1.94 and 0.52, respectively. The area under the ROC curve for enolase/Cr + CA125 + CA19 - 9 was 0.675 (95% confidence interval 0.573-0.710). Conclusion The present study revealed that concurrent measurement of enolase-1, CA125, and CA19-9 might be a valuable noninvasive test for the identification of endometriosis.
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Vallvé-Juanico J, López-Gil C, Ponomarenko J, Melnychuk T, Castellví J, Ballesteros A, Colás E, Gil-Moreno A, Santamaria Costa X. External validation of putative biomarkers in eutopic endometrium of women with endometriosis using NanoString technology. J Assist Reprod Genet 2020; 37:2981-2987. [PMID: 33033989 DOI: 10.1007/s10815-020-01965-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/04/2020] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To combine different independent endometrial markers to classify the presence of endometriosis. METHODS Endometrial biopsies were obtained from 109 women with endometriosis as well as 110 control women. Nine candidate biomarkers independent of cycle phase were selected from the literature and NanoString was performed. We compared differentially expressed genes between groups and generated generalized linear models to find a classifier for the disease. RESULTS Generalized linear models correctly detected 68% of women with endometriosis (combining deep infiltrating and ovarian endometriosis). However, we were not able to distinguish between individual types of endometriosis compared to controls. From the 9 tested genes, FOS, MMP7, and MMP11 seem to be important for disease classification, and FOS was the most over-expressed gene in endometriosis. CONCLUSION(S) Although generalized linear models may allow identification of endometriosis, we did not obtain perfect classification with the selected gene candidates.
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Affiliation(s)
- Júlia Vallvé-Juanico
- Department of Gynecology, IVIRMA Barcelona S.L., Ronda del General Mitre, 14, 08017, Barcelona, Spain.,Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain.,Centre for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carlos López-Gil
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Gynecology, Vall d'Hebron Hospital, Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Taisiia Melnychuk
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Gynecology, Vall d'Hebron Hospital, Barcelona, Spain
| | - Josep Castellví
- Department of Pathology, Vall d'Hebron Hospital, Barcelona, Spain
| | - Agustín Ballesteros
- Department of Gynecology, IVIRMA Barcelona S.L., Ronda del General Mitre, 14, 08017, Barcelona, Spain
| | - Eva Colás
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Antonio Gil-Moreno
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Gynecology, Vall d'Hebron Hospital, Barcelona, Spain
| | - Xavier Santamaria Costa
- Department of Gynecology, IVIRMA Barcelona S.L., Ronda del General Mitre, 14, 08017, Barcelona, Spain. .,Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain. .,Igenomix, Paterna, Valencia, Spain.
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Ensari I, Pichon A, Lipsky-Gorman S, Bakken S, Elhadad N. Augmenting the Clinical Data Sources for Enigmatic Diseases: A Cross-Sectional Study of Self-Tracking Data and Clinical Documentation in Endometriosis. Appl Clin Inform 2020; 11:769-784. [PMID: 33207385 PMCID: PMC7673957 DOI: 10.1055/s-0040-1718755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Self-tracking through mobile health technology can augment the electronic health record (EHR) as an additional data source by providing direct patient input. This can be particularly useful in the context of enigmatic diseases and further promote patient engagement. OBJECTIVES This study aimed to investigate the additional information that can be gained through direct patient input on poorly understood diseases, beyond what is already documented in the EHR. METHODS This was an observational study including two samples with a clinically confirmed endometriosis diagnosis. We analyzed data from 6,925 women with endometriosis using a research app for tracking endometriosis to assess prevalence of self-reported pain problems, between- and within-person variability in pain over time, endometriosis-affected tasks of daily function, and self-management strategies. We analyzed data from 4,389 patients identified through a large metropolitan hospital EHR to compare pain problems with the self-tracking app and to identify unique data elements that can be contributed via patient self-tracking. RESULTS Pelvic pain was the most prevalent problem in the self-tracking sample (57.3%), followed by gastrointestinal-related (55.9%) and lower back (49.2%) pain. Unique problems that were captured by self-tracking included pain in ovaries (43.7%) and uterus (37.2%). Pain experience was highly variable both across and within participants over time. Within-person variation accounted for 58% of the total variance in pain scores, and was large in magnitude, based on the ratio of within- to between-person variability (0.92) and the intraclass correlation (0.42). Work was the most affected daily function task (49%), and there was significant within- and between-person variability in self-management effectiveness. Prevalence rates in the EHR were significantly lower, with abdominal pain being the most prevalent (36.5%). CONCLUSION For enigmatic diseases, patient self-tracking as an additional data source complementary to EHR can enable learning from the patient to more accurately and comprehensively evaluate patient health history and status.
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Affiliation(s)
- Ipek Ensari
- Data Science Institute, Columbia University, New York, New York, United States
| | - Adrienne Pichon
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, United States
| | - Sharon Lipsky-Gorman
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, United States
| | - Suzanne Bakken
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, United States
- Columbia School of Nursing, Columbia University, New York, New York, United States
| | - Noémie Elhadad
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, United States
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Impaired pathogen-induced autophagy and increased IL-1β and TNFα release in response to pathogenic triggers in secretory phase endometrial stromal cells of endometriosis patients. Reprod Biomed Online 2020; 41:767-781. [PMID: 32978075 DOI: 10.1016/j.rbmo.2020.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/25/2020] [Accepted: 06/17/2020] [Indexed: 11/20/2022]
Abstract
RESEARCH QUESTION It is not clear whether innate immunity along with autophagy is altered in endometrial cells of patients with endometriosis. DESIGN This study evaluated the effects of lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid (poly I:C) stimulation on autophagy induction, pro-IL-1β expression, and secretion of interleukin-1β (IL-1β) and tumour necrosis factor-α (TNFα) in endometrial epithelial and/or stromal cells of patients with endometriosis (EE-endo, ES-endo, respectively), those of patients with hydrosalpinx (EE-hydro, ES-hydro, respectively) and those of healthy fertile women (EE-healthy, ES-healthy, respectively), with and without inhibition of autophagy by autophagy-related (ATG)13 gene small interfering RNA (siRNA). RESULTS Stimulation with either LPS or poly I:C triggered autophagy in EE/ES-healthy, whereas no significant induction was observed in either EE/ES-endo or EE/ES-hydro. In EE- and/or ES-healthy, IL-1β and/or TNFα secretion after stimulation with LPS or poly I:C was significantly higher in cells with ATG13 knockdown compared with those with siRNA control (P < 0.03), whereas no significant difference was observed in either EE/ES-endo or EE/ES-hydro. In the secretory phase ES-endo without autophagy inhibition, IL-1β and TNFα secretion were significantly higher compared with those of ES-healthy after stimulation with either LPS or poly I:C for 4 h (P < 0.001) and for 24 h (P < 0.01). CONCLUSION Pathogen-induced autophagy was impaired in EE/ES-endo. Increased IL-1β and TNFα release in response to pathogenic triggers in the secretory phase ES-endo may result in the development of an inflammatory uterine microenvironment detrimental to successful embryo implantation.
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47
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Determining the Molecular Background of Endometrial Receptivity in Adenomyosis. Biomolecules 2020; 10:biom10091311. [PMID: 32933042 PMCID: PMC7563201 DOI: 10.3390/biom10091311] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022] Open
Abstract
Background: Adenomyosis is a gynaecological condition with limited evidence of negative impact to endometrial receptivity. It is commonly associated with endometriosis, which has been shown to alter endometrial expression patterns. Therefore, the candidate genes identified in endometriosis could serve as a source to study endometrial function in adenomyosis. Methods: Transcripts/proteins associated with endometrial receptivity in women with adenomyosis or endometriosis and healthy women were obtained from publications and their nomenclature was adopted according to the HUGO Gene Nomenclature Committee (HGNC). Retrieved genes were analysed for enriched pathways using Cytoscape/Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Reactome tools to prioritise candidates for endometrial receptivity. These were used for validation on women with (n = 9) and without (n = 13) adenomyosis. Results: Functional enrichment analysis of 173, 42 and 151 genes associated with endometriosis, adenomyosis and healthy women, respectively, revealed signalling by interleukins and interleukin-4 and interleukin-13 signalling pathways, from which annotated LIF, JUNB, IL6, FOS, IL10 and SOCS3 were prioritised. Selected genes showed downregulated expression levels in adenomyosis compared to the control group, but without statistical significance. Conclusion: This is the first integrative study providing putative candidate genes and pathways characterising endometrial receptivity in women with adenomyosis in comparison to healthy women and women with endometriosis.
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van Weelden WJ, van der Putten LJM, Inda MA, van Brussel A, Snijders MPLM, Schriever LMM, Bulten J, Massuger LFAG, van de Stolpe A, Pijnenborg JMA. Oestrogen receptor pathway activity is associated with outcome in endometrial cancer. Br J Cancer 2020; 123:785-792. [PMID: 32507853 PMCID: PMC7463017 DOI: 10.1038/s41416-020-0925-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/22/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Oestrogen receptor (ER) expression is a prognostic biomarker in endometrial cancer (EC). However, expression does not provide information about the functional activity of the ER pathway. We evaluated a model to quantify ER pathway activity in EC, and determined the prognostic relevance of ER pathway activity. METHODS ER pathway activity was measured in two publicly available datasets with endometrial and EC tissue, and one clinical cohort with 107 samples from proliferative and hyperplastic endometrium and endometrioid-type EC (EEC) and uterine serous cancer (USC). ER pathway activity scores were inferred from ER target gene mRNA levels from Affymetrix microarray data (public datasets), or measured by qPCR on formalin-fixed paraffin-embedded samples (clinical cohort) and related to ER expression and outcome. RESULTS ER pathway activity scores differed significantly throughout the menstrual cycle supporting the validity of the pathway test. The highest ER pathway scores were found in proliferative and hyperplastic endometrium and stage I EEC, whereas stage II-IV EEC and USCs had significantly lower levels. Low ER pathway activity was associated with recurrent disease, and added prognostic value in patients with low ER expression. CONCLUSION The ER pathway test reflects activity of the ER pathway, and may improve prediction of outcome in EC patients.
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Affiliation(s)
- Willem Jan van Weelden
- Department of Obstetrics and Gynaecology, Radboud Institute for Health Science, Radboud university medical center, Nijmegen, the Netherlands.
| | - Louis J M van der Putten
- Department of Obstetrics and Gynaecology, Radboud Institute for Health Science, Radboud university medical center, Nijmegen, the Netherlands
| | | | | | - Marc P L M Snijders
- Department of Obstetrics and Gynaecology, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Lisanne M M Schriever
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Johan Bulten
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Leon F A G Massuger
- Department of Obstetrics and Gynaecology, Radboud Institute for Health Science, Radboud university medical center, Nijmegen, the Netherlands
| | | | - Johanna M A Pijnenborg
- Department of Obstetrics and Gynaecology, Radboud Institute for Health Science, Radboud university medical center, Nijmegen, the Netherlands
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Gabriel M, Fey V, Heinosalo T, Adhikari P, Rytkönen K, Komulainen T, Huhtinen K, Laajala TD, Siitari H, Virkki A, Suvitie P, Kujari H, Aittokallio T, Perheentupa A, Poutanen M. A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions. Sci Data 2020; 7:284. [PMID: 32859947 PMCID: PMC7455745 DOI: 10.1038/s41597-020-00623-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/03/2020] [Indexed: 01/06/2023] Open
Abstract
Endometriosis is a common inflammatory estrogen-dependent gynecological disorder, associated with pelvic pain and reduced fertility in women. Several aspects of this disorder and its cellular and molecular etiology remain unresolved. We have analyzed the global gene expression patterns in the endometrium, peritoneum and in endometriosis lesions of endometriosis patients and in the endometrium and peritoneum of healthy women. In this report, we present the EndometDB, an interactive web-based user interface for browsing the gene expression database of collected samples without the need for computational skills. The EndometDB incorporates the expression data from 115 patients and 53 controls, with over 24000 genes and clinical features, such as their age, disease stages, hormonal medication, menstrual cycle phase, and the different endometriosis lesion types. Using the web-tool, the end-user can easily generate various plot outputs and projections, including boxplots, and heatmaps and the generated outputs can be downloaded in pdf-format. Availability and implementationThe web-based user interface is implemented using HTML5, JavaScript, CSS, Plotly and R. It is freely available from https://endometdb.utu.fi/. Measurement(s) | RNA • differential expression analysis data • endometriosis | Technology Type(s) | Microarray Analysis • digital curation | Factor Type(s) | age • disease stage • menstrual cycle phase • hormonal medication • endometriosis lesion type • endometrium | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12800642
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Affiliation(s)
- Michael Gabriel
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland.,Department of Obstetrics and Gynecology, University of Turku, and Turku University Hospital, 20014, Turku, Finland
| | - Vidal Fey
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland
| | - Taija Heinosalo
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland
| | - Prem Adhikari
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland
| | - Kalle Rytkönen
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi, Turku, Finland
| | - Tuomo Komulainen
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland
| | - Kaisa Huhtinen
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, 20520, Turku, Finland.,Department of Pathology, Turku University Hospital, 20521, Turku, Finland
| | - Teemu Daniel Laajala
- Department of Mathematics and Statistics, University of Turku, 20014, Turku, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Harri Siitari
- Department of Neurology, Faculty of Medicine, University of Turku, 20014, Turku, Finland
| | - Arho Virkki
- Department of Mathematics and Statistics, University of Turku, 20014, Turku, Finland
| | - Pia Suvitie
- Department of Obstetrics and Gynecology, University of Turku, and Turku University Hospital, 20014, Turku, Finland
| | - Harry Kujari
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, 20520, Turku, Finland.,Department of Pathology, Turku University Hospital, 20521, Turku, Finland
| | - Tero Aittokallio
- Department of Mathematics and Statistics, University of Turku, 20014, Turku, Finland. .,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland.
| | - Antti Perheentupa
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland. .,Department of Obstetrics and Gynecology, University of Turku, and Turku University Hospital, 20014, Turku, Finland.
| | - Matti Poutanen
- Institute of Biomedicine, Research Center for Integrative Physiology and Pharmacology, University of Turku, 20520, Turku, Finland. .,Institute of Medicine, Sahlgrenska Academy, 405 30 Gothenburg University, Gothenburg, Sweden.
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50
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Malvezzi H, Marengo EB, Podgaec S, Piccinato CDA. Endometriosis: current challenges in modeling a multifactorial disease of unknown etiology. J Transl Med 2020; 18:311. [PMID: 32787880 PMCID: PMC7425005 DOI: 10.1186/s12967-020-02471-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Endometriosis is a chronic inflammatory hormone-dependent condition associated with pelvic pain and infertility, characterized by the growth of ectopic endometrium outside the uterus. Given its still unknown etiology, treatments usually aim at diminishing pain and/or achieving pregnancy. Despite some progress in defining mode-of-action for drug development, the lack of reliable animal models indicates that novel approaches are required. The difficulties inherent to modeling endometriosis are related to its multifactorial nature, a condition that hinders the recreation of its pathology and the identification of clinically relevant metrics to assess drug efficacy. In this review, we report and comment endometriosis models and how they have led to new therapies. We envision a roadmap for endometriosis research, integrating Artificial Intelligence, three-dimensional cultures and organ-on-chip models as ways to achieve better understanding of physiopathological features and better tailored effective treatments.
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Affiliation(s)
- Helena Malvezzi
- Hospital Israelita Albert Einstein, São Paulo, SP 05652-900 Brazil
| | - Eliana Blini Marengo
- Instituto Butanta- EstabilidadeBiotech Quality Control, São Paulo, SP 05503-900 Brazil
| | - Sérgio Podgaec
- Hospital Israelita Albert Einstein, São Paulo, SP 05652-900 Brazil
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