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Oliveira FG, Rosa-e-Silva JC, Gomes AG, Grzesiuk JD, Vidotto T, Squire JA, Panepucci RA, Meola J, Martelli L. Identification of a rare copy number polymorphic gain at 3q12.2 with candidate genes for familial endometriosis. REVISTA BRASILEIRA DE GINECOLOGIA E OBSTETRÍCIA 2024; 46:e-rbgo12. [PMID: 38765507 PMCID: PMC11075382 DOI: 10.61622/rbgo/2024cr12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 10/10/2023] [Indexed: 05/22/2024] Open
Abstract
Endometriosis is a complex disease that affects 10-15% of women of reproductive age. Familial studies show that relatives of affected patients have a higher risk of developing the disease, implicating a genetic role for this disorder. Little is known about the impact of germline genomic copy number variant (CNV) polymorphisms on the heredity of the disease. In this study, we describe a rare CNV identified in two sisters with familial endometriosis, which contain genes that may increase the susceptibility and progression of this disease. We investigated the presence of CNVs from the endometrium and blood of the sisters with endometriosis and normal endometrium of five women as controls without the disease using array-CGH through the Agilent 2x400K platform. We excluded common CNVs that were present in the database of genomic variation. We identified, in both sisters, a rare CNV gain affecting 113kb at band 3q12.2 involving two candidate genes: ADGRG7 and TFG. The CNV gain was validated by qPCR. ADGRG7 is located at 3q12.2 and encodes a G protein-coupled receptor influencing the NF-kappaβ pathway. TFG participates in chromosomal translocations associated with hematologic tumor and soft tissue sarcomas, and is also involved in the NF-kappa B pathway. The CNV gain in this family provides a new candidate genetic marker for future familial endometriosis studies. Additional longitudinal studies of affected families must confirm any associations between this rare CNV gain and genes involved in the NF-kappaβ pathway in predisposition to endometriosis.
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Affiliation(s)
- Flávia Gaona Oliveira
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Júlio Cesar Rosa-e-Silva
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of Gynecology and ObstetricsRibeirão PretoSPBrazilDepartment of Gynecology and Obstetrics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Alexandra Galvão Gomes
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Juliana Dourado Grzesiuk
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Thiago Vidotto
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Jeremy Andrew Squire
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Rodrigo Alexandre Panepucci
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
- Universidade de São PauloBlood CenterCenter for Cell TherapyRibeirão PretoSPBrazilCenter for Cell Therapy, Blood Center, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Juliana Meola
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of Gynecology and ObstetricsRibeirão PretoSPBrazilDepartment of Gynecology and Obstetrics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Lúcia Martelli
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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Zachaki S, Kalomoiraki M, Kouvidi E, Promponas E, Syrkos S, Panopoulou B, Pantou A, Mavrou A, Kanavakis E, Manola KN. Cytogenetic findings of ectopic endometriotic tissue in women with endometriosis and review of the literature. Eur J Obstet Gynecol Reprod Biol 2021; 264:212-218. [PMID: 34332218 DOI: 10.1016/j.ejogrb.2021.07.028] [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: 06/04/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To determine chromosome and gene alterations in ectopic endometrial (EM) tissue which may be implicated in the clinical course or the progression of endometriosis and to review the literature concerning the cytogenetic findings of women with endometriosis. STUDY DESIGN 15 women who underwent laparoscopic endometriosis surgery at the Athens Genesis Clinic were enrolled in the study. Ectopic endometrial tissue was surgically removed and further analyzed by conventional and molecular cytogenetic techniques. Fluoresent in situ hibridization (FISH) with probes for p53, ATM, MYC, MLL1 and IGH genes, the centromeres of chromosomes 7 and 8 and 7q22/7q31 chromosomal regions was carried out. RESULTS Karyotypic analysis revealed no clonal chromosomal abnormalities. However, an increased frequency of polyploidy (55.6%) and sporadic chromosomal abnormalities (40.0%) concerning chromosomes 9, 11, 17 and X were noticed involving mainly deletions, trisomies or monosomies. FISH analysis showed IGH gene rearrangements in 54% of the EM cases and MLL gene rearrangements in 73% of the examined samples. Normal hybridization patterns were observed for p53, ATM and MYC. The increased frequency of polyploidy shown by conventional karyotyping was also confirmed by FISH. CONCLUSION Polyploidy, sporadic chromosomal abnormalities, as well as IGH and MLL gene rearrangements, may provoke genetic instability and play a potential role in the development of endometriosis. IGH and MLL gene rearrangements indicate a genetic relation between endometriosis and carcinogenesis. Confirmation of the above gene rearrangements in a large series of women may allow the determination of their possible involvement in the pathogenesis of this complex disease and their possible contribution in the early identification of women in danger for malignant transformation.
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Affiliation(s)
- Sophia Zachaki
- Laboratory of Health Physics, Radiobiology & Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", Athens, Greece; Genesis Athens Clinic, Athens, Greece.
| | - Marina Kalomoiraki
- Laboratory of Health Physics, Radiobiology & Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", Athens, Greece
| | - Elisavet Kouvidi
- Genesis Genoma Lab, Genetic Diagnosis, Clinical Genetics & Research, Athens, Greece
| | | | | | | | - Amelia Pantou
- Genesis Athens Clinic, Athens, Greece; Genesis Genoma Lab, Genetic Diagnosis, Clinical Genetics & Research, Athens, Greece
| | - Ariadni Mavrou
- Genesis Genoma Lab, Genetic Diagnosis, Clinical Genetics & Research, Athens, Greece
| | | | - Kalliopi N Manola
- Laboratory of Health Physics, Radiobiology & Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", Athens, Greece
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Yong PJ, Talhouk A, Anglesio MS. Somatic Genomic Events in Endometriosis: Review of the Literature and Approach to Phenotyping. Reprod Sci 2021; 28:2743-2757. [PMID: 33469880 DOI: 10.1007/s43032-020-00451-9] [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: 10/09/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
In this review, we provide a survey and appraisal of research into somatic genomic events in endometriosis. Methodologies have evolved from conventional cytogenetics to next-generation sequencing, with findings ranging from chromosome imbalances to recurrent somatic cancer driver mutations. Somatic cancer driver mutations have been described in a range of endometriosis lesions, dominated by recurrent mutations in KRAS and PIK3CA as well as loss of PTEN and BAF250a (ARID1A). These somatic events appear to be largely restricted to the endometriosis glandular epithelium. Somatic mutations, particularly PTEN loss, have also been observed in eutopic (uterine) endometrium, although at lower mutant allele frequencies compared with ectopic lesions. Systematic studies of the potential clinical phenotype of these somatic genomic events have yet to be performed. Thus, we propose a framework to investigate the potential clinical phenotype associated with somatic genomic events in endometriosis. Technical requirements include pathology review of histological endometriosis, microdissection for tissue enrichment, orthogonal validation of whole genome/exome sequencing, and a germline sample for confirmation of somatic origin. Clinical requirements include annotation of surgical findings; patient demographics; cross-sectional and prospective data on pain and fertility; consideration of sampling multiple lesions in each patient, mutant allele frequency, and somatic events in the eutopic endometrium; and confirmation of any associations with mechanistic studies. Given the multifactorial nature of endometriosis-associated symptoms, it is likely that somatic events have small (or at most, moderate) effect sizes, and thus careful consideration will have to be given to future study design.
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Affiliation(s)
- Paul J Yong
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada. .,BC Women's Centre for Pelvic Pain and Endometriosis, F2 - 4500 Oak Street, Vancouver, British Columbia, V6H3N1, Canada.
| | - Aline Talhouk
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
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Guo SW. Cancer-associated mutations in endometriosis: shedding light on the pathogenesis and pathophysiology. Hum Reprod Update 2020; 26:423-449. [PMID: 32154564 DOI: 10.1093/humupd/dmz047] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/22/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Endometriosis is a benign gynaecological disease. Thus, it came as a complete surprise when it was reported recently that the majority of deep endometriosis lesions harbour somatic mutations and a sizeable portion of them contain known cancer-associated mutations (CAMs). Four more studies have since been published, all demonstrating the existence of CAMs in different subtypes of endometriosis. While the field is still evolving, the confirmation of CAMs has raised many questions that were previously overlooked. OBJECTIVE AND RATIONALE A comprehensive overview of CAMs in endometriosis has been produced. In addition, with the recently emerged understanding of the natural history of endometriotic lesions as well as CAMs in normal and apparently healthy tissues, this review attempts to address the following questions: Why has there been such a wild discrepancy in reported mutation frequencies? Why does ectopic endometrium have a higher mutation rate than that of eutopic endometrium? Would the presence of CAMs in endometriotic lesions increase the risk of cancer to the bearers? Why do endometriotic epithelial cells have much higher mutation frequencies than their stromal counterpart? What clinical implications, if any, do the CAMs have for the bearers? Do these CAMs tell us anything about the pathogenesis and/or pathophysiology of endometriosis? SEARCH METHODS The PubMed database was searched, from its inception to September 2019, for all papers in English using the term 'endometriosis and CAM', 'endometriosis and cancer-driver mutation', 'somatic mutations', 'fibrosis', 'fibrosis and epigenetic', 'CAMs and tumorigenesis', 'somatic mutation and normal tissues', 'oestrogen receptor and fibrosis', 'oxidative stress and fibrosis', 'ARID1A mutation', and 'Kirsten rat sarcoma mutation and therapeutics'. All retrieved papers were read and, when relevant, incorporated into the review results. OUTCOMES Seven papers that identified CAMs in endometriosis using various sequencing methods were retrieved, and their results were somewhat different. Yet, it is apparent that those using microdissection techniques and more accurate sequencing methods found more CAMs, echoing recent discoveries that apparently healthy tissues also harbour CAMs as a result of the replicative aging process. Hence endometriotic lesions, irrespective of subtype, if left intact, would generate CAMs as part of replicative aging, oxidative stress and perhaps other factors yet to be identified and, in some rare cases, develop cancer. The published data still are unable to paint a clear picture on pathogenesis of endometriosis. However, since endometriotic epithelial cells have a higher turnover than their stromal counterpart due to cyclic bleeding, and since the endometriotic stromal component can be formed by refresh influx of mesenchymal cells through epithelial-mesenchymal transition, endothelial-mesenchymal transition, mesothelial-mesenchymal transition and other processes as well as recruitment of bone-marrow-derived stem cells and outflow due to smooth muscle metaplasia, endometriotic epithelial cells have much higher mutation frequencies than their stromal counterpart. The epithelial and stromal cellular components develop in a dependent and co-evolving manner. Genes involved in CAMs are likely to be active players in lesional fibrogenesis, and hyperestrogenism and oxidative stress are likely drivers of both CAMs and fibrogenesis. Finally, endometriotic lesions harbouring CAMs would conceivably be more refractory to medical treatment, due, in no small part, to their high fibrotic content and reduced vascularity and cellularity. WIDER IMPLICATIONS The accumulating data on CAMs in endometriosis have shed new light on the pathogenesis and pathophysiology of endometriosis. They also suggest new challenges in management. The distinct yet co-evolving developmental trajectories of endometriotic stroma and epithelium underscore the importance of the lesional microenvironment and ever-changing cellular identity. Mutational profiling of normal endometrium from women of different ages and reproductive history is needed in order to gain a deeper understanding of the pathogenesis. Moreover, one area that has conspicuously received scant attention is the epigenetic landscape of ectopic, eutopic and normal endometrium.
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Affiliation(s)
- Sun-Wei Guo
- Shanghai Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai 200011, China
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Suda K, Cruz Diaz LA, Yoshihara K, Nakaoka H, Yachida N, Motoyama T, Inoue I, Enomoto T. Clonal lineage from normal endometrium to ovarian clear cell carcinoma through ovarian endometriosis. Cancer Sci 2020; 111:3000-3009. [PMID: 32473611 PMCID: PMC7419022 DOI: 10.1111/cas.14507] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/14/2020] [Accepted: 05/25/2020] [Indexed: 12/20/2022] Open
Abstract
Clear cell carcinoma of the ovary is thought to arise from endometriosis. In addition, retrograde menstruation of shed endometrium is considered the origin of endometriosis. However, little evidence supports cellular continuity from uterine endometrium to clear cell carcinoma through endometriosis at the genomic level. Here, we performed multiregional whole-exome sequencing to clarify clonal relationships among uterine endometrium, ovarian endometriosis and ovarian clear cell carcinoma in a 56-year-old patient. Many somatic mutations including cancer-associated gene mutations in ARID1A, ATM, CDH4, NRAS and PIK3CA were shared among epithelium samples from uterine endometrium, endometriotic lesions distant from and adjacent to the carcinoma, and the carcinoma. The mutant allele frequencies of shared mutations increased from uterine endometrium to distant endometriosis, adjacent endometriosis, and carcinoma. Although a splice site mutation of ARID1A was shared among the four epithelium samples, a frameshift insertion in ARID1A was shared by adjacent endometriosis and carcinoma samples, suggesting that the biallelic mutations triggered malignant transformation. Somatic copy number alterations, including loss of heterozygosity events at PIK3CA and ATM, were identified only in adjacent endometriosis and carcinoma, suggesting that mutant allele-specific imbalance is another key factor driving malignant transformation. By reconstructing a clonal evolution tree based on the somatic mutations, we showed that the epithelium samples were derived from a single ancestral clone. Although the study was limited to a single patient, the results from this illustrative case could suggest the possibility that epithelial cells of ovarian endometriosis and clear cell carcinoma were descendants of uterine endometrial epithelium.
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Affiliation(s)
- Kazuaki Suda
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Luis Antonio Cruz Diaz
- Department of GeneticsSchool of Life SciencesSOKENDAI (Graduate University for Advanced Studies)MishimaJapan
- Human Genetics LaboratoryNational Institute of GeneticsMishimaJapan
| | - Kosuke Yoshihara
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Hirofumi Nakaoka
- Department of GeneticsSchool of Life SciencesSOKENDAI (Graduate University for Advanced Studies)MishimaJapan
- Human Genetics LaboratoryNational Institute of GeneticsMishimaJapan
- Department of Cancer Genome ResearchSasaki InstituteSasaki FoundationChiyoda‐kuJapan
| | - Nozomi Yachida
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic PathologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Ituro Inoue
- Department of GeneticsSchool of Life SciencesSOKENDAI (Graduate University for Advanced Studies)MishimaJapan
- Human Genetics LaboratoryNational Institute of GeneticsMishimaJapan
| | - Takayuki Enomoto
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
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Duplications in 19p13.3 are associated with male infertility. J Assist Reprod Genet 2019; 36:2171-2179. [PMID: 31418107 DOI: 10.1007/s10815-019-01547-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023] Open
Abstract
PURPOSE To identify genomic imbalances and candidate loci in idiopathic male infertility. METHODS Affymetrix CytoScan 750K Array was used to analyze genomic imbalances and candidate loci in 34 idiopathic infertile cases of different phenotypes (hypo-spermatogenesis, n = 8; maturation arrest, n = 7; and Sertoli cell-only syndrome, n = 13, severe oligozoospermia, n = 6, and 10 normozoospermic fertile men). Ten ethnically matched controls were screened for comparison. RESULTS The cytogenetic array analysis detected a genomic gain at the 19p13.3 region in 9 (26.47%) cases, with the highest frequency in patients with Sertoli cell-only syndrome (SCOS) (38%). Its complete absence in the control group suggests its likely pathogenic nature. In addition to Y-classical, micro, and partial deletions, the duplication in 19p13.3 could serve as a unique biomarker for evaluation of infertility risk. The common region across the individuals harboring the duplication identified STK11, ATP5D, MIDN, CIRBP, and EFNA2 genes which make them strong candidates for further investigations. The largest duplicated region identified in this study displayed a major network of 7 genes, viz., CIRBP, FSTL3, GPX4, GAMT, KISS1R, STK11, and PCSK4, associated with reproductive system development and function. The role of chance was ruled out by screening of ethnically matched controls. CONCLUSION The result clearly indicates the significance of 19p13.3 duplication in infertile men with severe testicular phenotypes. The present study underlines the utility and significance of whole genomic analysis in the cases of male infertility which goes undiagnosed due to limitations in the conventional cytogenetic techniques and for identifying genes that are essential for spermatogenesis.
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Challenges in endometriosis miRNA studies — From tissue heterogeneity to disease specific miRNAs. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2282-2292. [DOI: 10.1016/j.bbadis.2017.06.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/06/2017] [Accepted: 06/22/2017] [Indexed: 12/31/2022]
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Zhao L, Gu C, Huang K, Han W, Fu M, Meng Y. Endometriosis research using capture microdissection techniques: Progress and future applications. Biomed Rep 2016; 5:531-540. [PMID: 27882213 DOI: 10.3892/br.2016.758] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/07/2016] [Indexed: 12/26/2022] Open
Abstract
Endometriosis is a common gynecological disease with high prevalence, while its etiology and pathophysiology have remained to be fully elucidated. Previous evidence suggested that this disorder may be in part or completely of somatic origin. However, traditional endometrial samples may not be ideal for investigation, as target cells, including epithelial and stromal cells, in endometriotic lesions are too sparse to be analyzed. Recently, capture microdissection techniques have been used to overcome these limitations and eliminate tissue heterogeneity in endometriosis research. Therefore, the present review summarized the alterations in epithelial and stromal cells in endometriosis tissues isolated through capture microdissection, outlined recent progress and provided directions for future investigation of the pathogenesis of endometriosis.
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Affiliation(s)
- Luyang Zhao
- Department of Gynecology and Obstetrics, Chinese People's Liberation Army (PLA) Medical School, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Chenglei Gu
- Department of Gynecology and Obstetrics, Chinese People's Liberation Army (PLA) Medical School, Chinese PLA General Hospital, Beijing 100853, P.R. China; Department of Gynecology and Obstetrics, the 309th Hospital of the PLA, Beijing 100091, P.R. China
| | - Ke Huang
- Department of Gynecology and Obstetrics, Chinese People's Liberation Army (PLA) Medical School, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Weidong Han
- Department of Molecular Biology, Institute of Basic Medicine, PLA Medical School, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Meng Fu
- Department of Gynecology and Obstetrics, Chinese People's Liberation Army (PLA) Medical School, Chinese PLA General Hospital, Beijing 100853, P.R. China; Department of Gynecology and Obstetrics, Haidian Maternal and Child Health Hospital, Beijing 100080, P.R. China
| | - Yuanguang Meng
- Department of Gynecology and Obstetrics, Chinese People's Liberation Army (PLA) Medical School, Chinese PLA General Hospital, Beijing 100853, P.R. China
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Endometriosis is associated with rare copy number variants. PLoS One 2014; 9:e103968. [PMID: 25083881 PMCID: PMC4118997 DOI: 10.1371/journal.pone.0103968] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/09/2014] [Indexed: 12/22/2022] Open
Abstract
Endometriosis is a complex gynecological condition that affects 6-10% of women in their reproductive years and is defined by the presence of endometrial glands and stroma outside the uterus. Twin, family, and genome-wide association (GWA) studies have confirmed a genetic role, yet only a small part of the genetic risk can be explained by SNP variation. Copy number variants (CNVs) account for a greater portion of human genetic variation than SNPs and include more recent mutations of large effect. CNVs, likely to be prominent in conditions with decreased reproductive fitness, have not previously been examined as a genetic contributor to endometriosis. Here we employ a high-density genotyping microarray in a genome-wide survey of CNVs in a case-control population that includes 2,126 surgically confirmed endometriosis cases and 17,974 population controls of European ancestry. We apply stringent quality filters to reduce the false positive rate common to many CNV-detection algorithms from 77.7% to 7.3% without noticeable reduction in the true positive rate. We detected no differences in the CNV landscape between cases and controls on the global level which showed an average of 1.92 CNVs per individual with an average size of 142.3 kb. On the local level we identify 22 CNV-regions at the nominal significance threshold (P<0.05), which is greater than the 8.15 CNV-regions expected based on permutation analysis (P<0.001). Three CNV's passed a genome-wide P-value threshold of 9.3 × 10(-4); a deletion at SGCZ on 8p22 (P = 7.3 × 10(-4), OR = 8.5, Cl = 2.3-31.7), a deletion in MALRD1 on 10p12.31 (P = 5.6 × 10(-4), OR = 14.1, Cl = 2.7-90.9), and a deletion at 11q14.1 (P = 5.7 × 10(-4), OR = 33.8, Cl = 3.3-1651). Two SNPs within the 22 CNVRs show significant genotypic association with endometriosis after adjusting for multiple testing; rs758316 in DPP6 on 7q36.2 (P = 0.0045) and rs4837864 in ASTN2 on 9q33.1 (P = 0.0002). Together, the CNV-loci are detected in 6.9% of affected women compared to 2.1% in the general population.
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Li X, Zhang Y, Zhao L, Wang L, Wu Z, Mei Q, Nie J, Li X, Li Y, Fu X, Wang X, Meng Y, Han W. Whole-exome sequencing of endometriosis identifies frequent alterations in genes involved in cell adhesion and chromatin-remodeling complexes. Hum Mol Genet 2014; 23:6008-21. [PMID: 24969084 DOI: 10.1093/hmg/ddu330] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Endometriosis is a complex and enigmatic disease that arises from the interplay among multiple genetic and environmental factors. The defining feature of endometriosis is the deposition and growth of endometrial tissues at sites outside of the uterine cavity. Studies to date have established that endometriosis is heritable but have not addressed the causal genetic variants for this disease. Here, we conducted whole-exome sequencing to comprehensively search for somatic mutations in both eutopic and ectopic endometrium from 16 endometriosis patients and five normal control patients using laser capture microdissection. We compared the mutational landscape of ectopic endometrium with the corresponding eutopic sample from endometriosis patients compared with endometrium from normal women and identified previously unreported mutated genes and pathway alternations. Statistical analysis of exome data identified that most genes were specifically mutated in both eutopic and ectopic endometrium cells. In particular, genes that are involved in biological adhesion, cell-cell junctions, and chromatin-remodeling complex(es) were identified, which partially supports the retrograde menstruation theory that proposes that endometrial cells are refluxed through the fallopian tubes during menstruation and implanted onto the peritoneum or pelvic organs. Conspicuously, when we compared exomic mutation data for paired eutopic and ectopic endometrium, we identified a mutational signature in both endometrial types for which no overlap in somatic single nucleotide variants were observed. These mutations occurred in a mutually exclusive manner, likely because of the discrepancy in endometriosis pathology and physiology, as eutopic endometrium rapidly regrows, and ectopic endometrial growth is inert. Our findings provide, to our knowledge, an unbiased view of the landscape of genetic alterations in endometriosis and vital information for indicating that genetic alterations in cytoskeletal and chromatin-remodeling proteins could be involved in the pathogenesis of endometriosis, thus implicating a novel therapeutic possibility for endometriosis.
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Affiliation(s)
- Xiaolei Li
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Yan Zhang
- Department of Bio-therapeutic, Chinese PLA General Hospital, Beijing, China
| | - Luyang Zhao
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing, China
| | - Lingxiong Wang
- Department of Cancer Center, Chinese PLA General Hospital, Beijing, China and
| | - Zhiqiang Wu
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Qian Mei
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Jing Nie
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Xiang Li
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Yali Li
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing, China
| | - Xiaobing Fu
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China, Department of Bio-therapeutic, Chinese PLA General Hospital, Beijing, China, Key Laboratory of Wound Healing and Cell Biology, Institute of Burns, the First Affiliated Hospital to the Chinese PLA General Hospital, Trauma Center of Postgraduate Medical School, Beijing, China
| | - Xiaoning Wang
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Yuanguang Meng
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing, China,
| | - Weidong Han
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China, Department of Bio-therapeutic, Chinese PLA General Hospital, Beijing, China,
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KOBAYASHI HIROSHI, IMANAKA SHOGO, NAKAMURA HARUKI, TSUJI AYUMI. Understanding the role of epigenomic, genomic and genetic alterations in the development of endometriosis (Review). Mol Med Rep 2014; 9:1483-505. [DOI: 10.3892/mmr.2014.2057] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/03/2014] [Indexed: 11/05/2022] Open
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Altmäe S, Esteban FJ, Stavreus-Evers A, Simón C, Giudice L, Lessey BA, Horcajadas JA, Macklon NS, D'Hooghe T, Campoy C, Fauser BC, Salamonsen LA, Salumets A. Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. Hum Reprod Update 2014; 20:12-28. [PMID: 24082038 PMCID: PMC3845681 DOI: 10.1093/humupd/dmt048] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 08/04/2013] [Accepted: 08/19/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data. METHODS Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013. RESULTS The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies. CONCLUSION A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
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Affiliation(s)
- Signe Altmäe
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | | | - Anneli Stavreus-Evers
- Department of Women's and Children's Health, Uppsala University, Akademiska Sjukhuset, 75185 Uppsala, Sweden
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad (FIVI) and Instituto Universitario IVI/INCLIVA, Valencia University, 46021 Valencia, Spain
| | - Linda Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143-0132, USA
| | - Bruce A. Lessey
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, University Medical Group, Greenville Hospital System, Greenville, South Carolina, SC 29605, USA
| | - Jose A. Horcajadas
- Araid-Hospital Miguel Servet, 50004 Zaragoza, Spain
- Department of Genetics, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Nick S. Macklon
- Department of Obstetrics and Gynaecology, Division of Developmental Origins of Adult Disease, University of Southampton, Princess Anne Hospital, SO16 5YA Southampton, UK
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Thomas D'Hooghe
- Leuven University Fertility Center, Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven (Leuven University), 3000 Leuven, Belgium
| | - Cristina Campoy
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | - Bart C. Fauser
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Lois A. Salamonsen
- Prince Henry's Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Andres Salumets
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- Department of Obstetrics and Gynaecology, University of Tartu, 51014 Tartu, Estonia
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Genetic, epigenetic and stem cell alterations in endometriosis: new insights and potential therapeutic perspectives. Clin Sci (Lond) 2013; 126:123-38. [PMID: 24059589 DOI: 10.1042/cs20130099] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human endometrium is a highly dynamic tissue, undergoing periodic growth and regression at each menstrual cycle. Endometriosis is a frequent chronic pathological status characterized by endometrial tissue with an ectopic localization, causing pelvic pain and infertility and a variable clinical presentation. In addition, there is well-established evidence that, although endometriosis is considered benign, it is associated with an increased risk of malignant transformation in approximately 1.0% of affected women, with the involvement of multiple pathways of development. Increasing evidence supports a key contribution of different stem/progenitor cell populations not only in the cyclic regeneration of eutopic endometrium, but also in the pathogenesis of at least some types of endometriosis. Evidence has arisen from experiments in animal models of disease through different kinds of assays (including clonogenicity, the label-retaining cell approach, the analysis of undifferentiation markers), as well as from descriptive studies on ectopic and eutopic tissue samples harvested from affected women. Changes in stem cell populations in endometriotic lesions are associated with genetic and epigenetic alterations, including imbalance of miRNA expression, histone and DNA modifications and chromosomal aberrations. The present short review mainly summarizes the latest observations contributing to the current knowledge regarding the presence and the potential contribution of stem/progenitor cells in eutopic endometrium and the aetiology of endometriosis, together with a report of the most recently identified genetic and epigenetic alterations in endometriosis. We also describe the potential advantages of single cell molecular profiling in endometrium and in endometriotic lesions. All these data can have clinical implications and provide a basis for new potential therapeutic applications.
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