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Mirza Z, Abdel-dayem UA. Uncovering Potential Roles of Differentially Expressed Genes, Upstream Regulators, and Canonical Pathways in Endometriosis Using an In Silico Genomics Approach. Diagnostics (Basel) 2020; 10:diagnostics10060416. [PMID: 32575462 PMCID: PMC7344784 DOI: 10.3390/diagnostics10060416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Endometriosis is characterized by ectopic endometrial tissue implantation, mostly within the peritoneum, and affects women in their reproductive age. Studies have been done to clarify its etiology, but the precise molecular mechanisms and pathophysiology remain unclear. We downloaded genome-wide mRNA expression and clinicopathological data of endometriosis patients and controls from NCBI’s Gene Expression Omnibus, after a systematic search of multiple independent studies comprising 156 endometriosis patients and 118 controls to identify causative genes, risk factors, and potential diagnostic/therapeutic biomarkers. Comprehensive gene expression meta-analysis, pathway analysis, and gene ontology analysis was done using a bioinformatics-based approach. We identified 1590 unique differentially expressed genes (129 upregulated and 1461 downregulated) mapped by IPA as biologically relevant. The top upregulated genes were FOS, EGR1, ZFP36, JUNB, APOD, CST1, GPX3, and PER1, and the top downregulated ones were DIO2, CPM, OLFM4, PALLD, BAG5, TOP2A, PKP4, CDC20B, and SNTN. The most perturbed canonical pathways were mitotic roles of Polo-like kinase, role of Checkpoint kinase proteins in cell cycle checkpoint control, and ATM signaling. Protein–protein interaction analysis showed a strong network association among FOS, EGR1, ZFP36, and JUNB. These findings provide a thorough understanding of the molecular mechanism of endometriosis, identified biomarkers, and represent a step towards the future development of novel diagnostic and therapeutic options.
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Affiliation(s)
- Zeenat Mirza
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence:
| | - Umama A. Abdel-dayem
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Zhao L, Gu C, Ye M, Zhang Z, Han W, Fan W, Meng Y. Identification of global transcriptome abnormalities and potential biomarkers in eutopic endometria of women with endometriosis: A preliminary study. Biomed Rep 2017; 6:654-662. [PMID: 28584637 PMCID: PMC5449958 DOI: 10.3892/br.2017.902] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/13/2017] [Indexed: 12/11/2022] Open
Abstract
The etiology and pathophysiology of endometriosis remain unclear. The aim of the current study was to identify a candidate pathogenic gene, as well as potential biomarkers of endometriosis using messenger RNA (mRNA) sequencing (mRNA-seq). Twenty-three eutopic endometria from women with endometriosis and 20 endometria from control subjects were investigated. Eight eutopic endometria and five normal endometria were selected for mRNA-seq. Differentially expressed genes (DEGs) were identified and functional analysis was conducted. Validation of certain DEGs was performed in the remaining cases and control subjects by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 72 DEGs (66 upregulated and 6 downregulated) were identified in samples from women with endometriosis and compared with the control subjects. High DEGs included those involved in various functions, such as extracellular matrix (ECM) remodeling, angiogenesis, cell proliferation and differentiation. Enriched by these DEGs, 100 Gene Ontology terms were identified as significantly important, particularly ‘ECM’ and ‘endogenous stimulus’. Validation using RT-qPCR indicated that matrix metallopeptidase 11, dual specificity phosphatase 1, Fos proto-oncogeneand serpin family E member 1 were significantly upregulated and adenosine deaminase 2 was significantly downregulated in the eutopic endometrium of patients with endometriosis. The identified DEGs may be involved in the pathogenesis of endometriosis and may be potential biomarkers in the eutopic endometrium. The current study provides a comprehensive, but preliminary insight for elucidating the mechanisms of endometriosis, which require further in-depth studies for confirmation.
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Affiliation(s)
- Luyang Zhao
- Department of Gynecology and Obstetrics, People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China.,Department of Gynecology and Obstetrics, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Chenglei Gu
- Department of Gynecology and Obstetrics, People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China.,Department of Gynecology and Obstetrics, the 309th Hospital of Chinese People's Liberation Army, Beijing 100853, P.R. China
| | - Mingxia Ye
- Department of Gynecology and Obstetrics, People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Zhe Zhang
- Department of Gynecology and Obstetrics, People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Weidong Han
- Department of Molecular Biology, Institute of Basic Medicine, People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Wensheng Fan
- Department of Gynecology and Obstetrics, People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Yuanguang Meng
- Department of Gynecology and Obstetrics, People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
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Ke H, Suzuki A, Miyamoto T, Kashima H, Shiozawa T. 4-hydroxy estrogen induces DNA damage on codon 130/131 of PTEN in endometrial carcinoma cells. Mol Cell Endocrinol 2015; 400:71-7. [PMID: 25449419 DOI: 10.1016/j.mce.2014.10.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
Abstract
Catechol estrogens, such as 4-hydroxyestradiol (4-OHE2), are estrogen metabolites that form DNA adducts and may induce mutations and subsequent cell transformation in mammary cells; however, little is known about their roles in endometrial carcinogenesis. Furthermore, it remains unclear whether 4-OHE2 is able to induce DNA damage on specific genes involved in carcinogenesis or a 'pro'-mutation status such as microsatellite instability (MSI). Therefore, we modified terminal transferase-dependent PCR by the application of a capillary sequencer to detect DNA damage at the single base level. Using this method, we demonstrated that 4-OHE2 directly induced DNA damage on codon 130/131 in exon 5 of PTEN, which is a mutation hot spot for PTEN in endometrial carcinoma. Whereas, both estradiol and 4-OHE2 treatment did not affect MSI status in immortalized endometrial glandular cells. 4-OHE2 might contribute to endometrial carcinogenesis by inducing PTEN mutation on codon 130/131.
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Affiliation(s)
- He Ke
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, 1 Zhongshan 2nd Road, Yuexiu, Guangzhou, Guangdong, China
| | - Akihisa Suzuki
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan; Department of Obstetrics and Gynecology, Iida Municipal Hospital, 438 Yawatamachi, Iida 395-8502, Japan.
| | - Tsutomu Miyamoto
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan
| | - Hiroyasu Kashima
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan
| | - Tanri Shiozawa
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan
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Pernodet N, Hermetet F, Adami P, Vejux A, Descotes F, Borg C, Adams M, Pallandre JR, Viennet G, Esnard F, Jouvenot M, Despouy G. High expression of QSOX1 reduces tumorogenesis, and is associated with a better outcome for breast cancer patients. Breast Cancer Res 2012; 14:R136. [PMID: 23098186 PMCID: PMC4053115 DOI: 10.1186/bcr3341] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022] Open
Abstract
Introduction The gene quiescin/sulfhydryl oxidase 1, QSOX1, encodes an enzyme directed to the secretory pathway and excreted into the extracellular space. QSOX1 participates in the folding and stability of proteins and thus could regulate the biological activity of its substrates in the secretory pathway and/or outside the cell. The involvement of QSOX1 in oncogenesis has been studied primarily in terms of its differential expression in systemic studies. QSOX1 is overexpressed in prostate cancers and in pancreatic adenocarcinoma. In contrast, QSOX1 gene expression is repressed in endothelial tumors. In the present study, we investigated the role of QSOX1 in breast cancer. Methods We analyzed QSOX1 mRNA expression in a cohort of 217 invasive ductal carcinomas of the breast. Moreover, we investigated QSOX1's potential role in regulating tumor growth and metastasis using cellular models in which we overexpressed or extinguished QSOX1 and xenograft experiments. Results We showed that the QSOX1 expression level is inversely correlated to the aggressiveness of breast tumors. Our results show that QSOX1 leads to a decrease in cell proliferation, clonogenic capacities and promotes adhesion to the extracellular matrix. QSOX1 also reduces the invasive potential of cells by reducing cell migration and decreases the activity of the matrix metalloproteinase, MMP-2, involved in these mechanisms. Moreover, in vivo experiments show that QSOX1 drastically reduces the tumor development. Conclusions Together, these results suggest that QSOX1 could be posited as a new biomarker of good prognosis in breast cancer and demonstrate that QSOX1 inhibits human breast cancer tumorogenesis.
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Yamaguchi S, Asanoma K, Takao T, Kato K, Wake N. Homeobox gene HOPX is epigenetically silenced in human uterine endometrial cancer and suppresses estrogen-stimulated proliferation of cancer cells by inhibiting serum response factor. Int J Cancer 2009; 124:2577-88. [PMID: 19173292 DOI: 10.1002/ijc.24217] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
HOPX (homeodomain only protein X) is a newly identified homeobox gene whose loss of expression has been reported for several types of neoplasm. Although we found most human uterine endometrial cancers (HEC) defective in HOPX expression, genetic mutations in the HOPX gene were undetectable. As is the case with several tumor suppressor genes, the promoter region of HOPX is densely methylated in HEC tissue samples obtained by laser capture microdissection. HOPX mRNA and protein levels were reduced in the majority of samples, and this correlated with hypermethylation of the HOPX promoter. Forced expression of HOPX resulted in a partial block in cell proliferation, in vivo tumorigenicity and c-fos gene expression in HEC and MCF7 cells in response to 17beta-estradiol (E(2)) stimulation. Analysis of the serum response element (SRE) of c-fos gene promoter showed that the effect of HOPX expression is associated with inhibition of E(2)-induced c-fos activation through the serum response factor (SRF) motif. Knockdown of HOPX in immortalized human endometrial cells resulted in accelerated proliferation. Our study indicates that transcriptional silencing of HOPX results from hypermethylation of the HOPpromoter, which leads to HEC development.
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Affiliation(s)
- Shinichiro Yamaguchi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
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Hastings JM, Jackson KS, Mavrogianis PA, Fazleabas AT. The Estrogen Early Response Gene FOS Is Altered in a Baboon Model of Endometriosis1. Biol Reprod 2006; 75:176-82. [PMID: 16672717 DOI: 10.1095/biolreprod.106.052852] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Endometriosis, the presence of a functional endometrium outside of the uterine cavity, is associated with infertility. In our simulated model of pregnancy in baboons with experimental endometriosis, hCG infusion fails to induce expression of the immunoregulatory protein glycodelin. To test the hypothesis that the development of endometriosis is associated with an aberrant endometrial immunological environment, we examined the expression of a series of immunoregulatory genes in endometrium from baboons with and without endometriosis. Six months following intraperitoneal inoculation with menstrual endometrium, eutopic endometrium was surgically collected between Days 9 and 11 postovulation. Control endometrium was similarly collected from disease-free animals. Total RNA was extracted, and biotinylated cDNA probes were hybridized to the SuperArray GEArray Q series Th1/Th2/Th3 cDNA array, representing 96 genes. Gene expression levels were determined using ScanAlyze and GEArray Analyzer software. Seven genes were upregulated, including JUND, FOS, CCL11, NFKB1 and others, in the endometrium from baboons with endometriosis compared with the endometrium from disease-free animals; one gene, IL1R1, was downregulated. Quantitative RT-PCR confirmed upregulation of FOS and CCL11 in endometriotic eutopic endometrium. Immunohistochemical analysis revealed altered levels and distribution of FOS protein in the eutopic endometrium of baboons with induced endometriosis. These data suggest that in an induced model of endometriosis an aberrant eutopic immunological environment results in a decreased apoptotic potential and in rapid alterations in endometrial gene expression. We propose that the reduced fecundity associated with endometriosis has a multifold etiology in spontaneous and induced disease.
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Affiliation(s)
- Julie M Hastings
- Department of Obstetrics and Gynecology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, USA
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Abstract
Endometriosis is one of the most common causes of chronic pelvic pain and infertility in women in the reproductive age group. Although the existence of this disease has been known for over 100 years our current knowledge of its pathogenesis and the pathophysiology of its related infertility remains unclear. Several reasons contribute to our lack of knowledge, the most critical being the difficulty in carrying out objective long-term studies in women. Thus, we and others have developed a model of this disease in the non-human primate, the baboon (Papio anubis). Intraperitoneal inoculation of autologous menstrual endometrium results in the development of endometriotic lesions with gross morphological characteristics similar to those seen in the human. Multiple factors have been implicated in endometriosis-associated infertility. We have described aberrant levels of factors involved in multiple pathways important in the establishment of pregnancy, in the endometrium of baboons induced with endometriosis. Specifically, we have observed dysregulation of proteins involved in invasion, angiogenesis, methylation, cell growth, immunomodulation, and steroid hormone action. These data suggest that, in an induced model of endometriosis in the baboon, an increased angiogenic capacity, decreased apoptotic potential, progesterone resistance, estrogen hyper-responsiveness, and an inability to respond appropriately to embryonic signals contribute to the reduced fecundity associated with this disease.
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Affiliation(s)
- Julie M Hastings
- Department of Obstetrics and Gynecology (MC808), College of Medicine, University of Illinois at Chicago, 820 S Wood Street, Chicago, Illinois, 60612, USA
| | - Asgerally T Fazleabas
- Department of Obstetrics and Gynecology (MC808), College of Medicine, University of Illinois at Chicago, 820 S Wood Street, Chicago, Illinois, 60612, USA
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Vernier-Magnin S, Nemos C, Mansuy V, Tolle F, Guichard L, Delage-Mourroux R, Jouvenot M, Fraichard A. Analysis of the guinea-pig estrogen-regulated gec1/GABARAPL1 gene promoter and identification of a functional ERE in the first exon. ACTA ACUST UNITED AC 2005; 1731:23-31. [PMID: 16153720 DOI: 10.1016/j.bbaexp.2005.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Revised: 05/06/2005] [Accepted: 05/11/2005] [Indexed: 11/19/2022]
Abstract
The gec1/GABARAPL1 (GABA(A)-receptor-associated protein like-1) gene has been identified as an early estrogen-regulated gene in guinea-pig cultured endometrial glandular epithelial cells (GEC). Guinea-pig and human gec1/GABARAPL1 proteins share 87% identity with GABARAP, which acts as a protein linker between microtubules and the GABA(A) receptor. To investigate the molecular mechanisms regulating gec1/GABARAPL1 gene expression, the 1.5-kbp region upstream of the translation initiation codon of the guinea-pig gec1/GABARAPL1 gene was cloned. A 300-bp fragment encompassing a pyrimidine-rich initiator element (INR) and the transcription start site (+1) was sufficient to initiate transcription. Transfection and gel shift experiments showed that a sequence located at +36/+50 in the first exon permitted induction of expression of this gene by estradiol acting via ERalpha. This sequence (GGGTCAACGTGACGT) differs only by one base pair from the consensus estrogen response element ERE (GGGTCAACGTGACCT). It can be concluded that the ERE located in the first exon encoding the 5'-untranslated region is sufficient for E2 activation of gec1/GABARAPL1 transcription.
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Affiliation(s)
- Sandrine Vernier-Magnin
- Laboratoire de Biochimie Biologie Moléculaire, EA3922 Estrogènes, Expression Génique et Pathologies du Système Nerveux Central, IFR 133, Université de Franche-Comté, U.F.R. Sciences et Techniques, 16 route de Gray, 25030 Besançon cedex, France
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Mansuy V, Boireau W, Fraichard A, Schlick JL, Jouvenot M, Delage-Mourroux R. GEC1, a protein related to GABARAP, interacts with tubulin and GABA(A) receptor. Biochem Biophys Res Commun 2005; 325:639-48. [PMID: 15530441 DOI: 10.1016/j.bbrc.2004.10.072] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Indexed: 10/26/2022]
Abstract
We have previously identified in uterine cells a novel estrogen-regulated gene called gec1. GEC1 presents 87% identity with GABARAP which, so far, was the only protein found to associate with tubulin and GABA(A) receptor. We demonstrated then that GEC1 interacts in vitro with tubulin and GABA(A) receptor, and promotes tubulin assembly and microtubule bundling. Since all polyclonal antibodies failed in discrimination of both proteins GEC1 and GABARAP, a GEC1-GFP fusion protein was used to specifically localize GEC1. GEC1-GFP was distributed over the cytoplasm in perinuclear vesicles with a scattered pattern. Overall, our data show that GEC1 could be a new member of the GABARAP family involved in the transport of GABA(A) receptor.
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Affiliation(s)
- Virginie Mansuy
- Equipe Estrogènes, Expression Génique et Pathologies du Système Nerveux Central, Université de Franche-Comté, U.F.R. Sciences et Techniques, IFR 133, 16 route de Gray, 25030 Besançon Cedex, France
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Hennessy BA, Harvey BJ, Healy V. 17beta-Estradiol rapidly stimulates c-fos expression via the MAPK pathway in T84 cells. Mol Cell Endocrinol 2005; 229:39-47. [PMID: 15607527 DOI: 10.1016/j.mce.2004.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 09/30/2004] [Accepted: 10/06/2004] [Indexed: 10/26/2022]
Abstract
In this study, we show that 17beta-Estradiol (E2) induced the proliferation of T84 colonic carcinoma cells. We, further, investigated the mechanisms underlying this proliferation and show that E2 induced c-fos protooncogene expression in T84 cells in a timescale consistent with a rapid non-genomic action of the hormone. Furthermore, E2 rapidly phosphorylated both CREB and ELK1, transcription factors that bind to the c-fos promoter and stimulate transcription. Pretreatment with PD98059 and H89, mitogen-activated protein kinase (MAPK) pathway and protein kinase A (PKA) inhibitors, respectively showed that phosphorylation of CREB and ELK1 and subsequent c-fos induction was mediated by the MAPK pathway only. Finally, the estrogen receptor (ER) antagonist, ICI 182,780, blocked the activation of MAPK pathway, subsequent CREB and ELK1 phosphorylation and c-fos induction in T84 cells suggesting an ER dependent mechanism. Consistent with this finding, ICI 182,780 caused a substantial reduction in the proliferative effects of E2 on T84 cells.
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