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Cho SB. Molecular Mechanisms of Endometriosis Revealed Using Omics Data. Biomedicines 2023; 11:2210. [PMID: 37626707 PMCID: PMC10452455 DOI: 10.3390/biomedicines11082210] [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: 06/06/2023] [Revised: 07/22/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Endometriosis is a gynecological disorder prevalent in women of reproductive age. The primary symptoms include dysmenorrhea, irregular menstruation, and infertility. However, the pathogenesis of endometriosis remains unclear. With the advent of high-throughput technologies, various omics experiments have been conducted to identify genes related to the pathophysiology of endometriosis. This review highlights the molecular mechanisms underlying endometriosis using omics. When genes identified in omics experiments were compared with endometriosis disease genes identified in independent studies, the number of overlapping genes was moderate. However, the characteristics of these genes were found to be equivalent when functional gene set enrichment analysis was performed using gene ontology and biological pathway information. These findings indicate that omics technology provides invaluable information regarding the pathophysiology of endometriosis. Moreover, the functional characteristics revealed using enrichment analysis provide important clues for discovering endometriosis disease genes in future research.
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Affiliation(s)
- Seong Beom Cho
- Department of Biomedical Informatics, College of Medicine, Gachon University, 38-13, Dokgeom-ro 3 Street Namdon-gu, Incheon 21565, Republic of Korea
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2
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Zhu Y, Pan H, Han Y, Li T, Liu K, Wang B. Novel missense variant of CIITA contributing to endometriosis. Reprod Biomed Online 2022; 45:544-551. [DOI: 10.1016/j.rbmo.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/28/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
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3
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Genomics of Endometriosis: From Genome Wide Association Studies to Exome Sequencing. Int J Mol Sci 2021; 22:ijms22147297. [PMID: 34298916 PMCID: PMC8304276 DOI: 10.3390/ijms22147297] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
This review aims at better understanding the genetics of endometriosis. Endometriosis is a frequent feminine disease, affecting up to 10% of women, and characterized by pain and infertility. In the most accepted hypothesis, endometriosis is caused by the implantation of uterine tissue at ectopic abdominal places, originating from retrograde menses. Despite the obvious genetic complexity of the disease, analysis of sibs has allowed heritability estimation of endometriosis at ~50%. From 2010, large Genome Wide Association Studies (GWAS), aimed at identifying the genes and loci underlying this genetic determinism. Some of these loci were confirmed in other populations and replication studies, some new loci were also found through meta-analyses using pooled samples. For two loci on chromosomes 1 (near CCD42) and chromosome 9 (near CDKN2A), functional explanations of the SNP (Single Nucleotide Polymorphism) effects have been more thoroughly studied. While a handful of chromosome regions and genes have clearly been identified and statistically demonstrated as at-risk for the disease, only a small part of the heritability is explained (missing heritability). Some attempts of exome sequencing started to identify additional genes from families or populations, but are still scarce. The solution may reside inside a combined effort: increasing the size of the GWAS designs, better categorize the clinical forms of the disease before analyzing genome-wide polymorphisms, and generalizing exome sequencing ventures. We try here to provide a vision of what we have and what we should obtain to completely elucidate the genetics of this complex disease.
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4
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Chang CYY, Tseng CC, Lai MT, Chiang AJ, Lo LC, Chen CM, Yen MJ, Sun L, Yang L, Hwang T, Tsai FJ, Sheu JJC. Genetic impacts on thermostability of onco-lncRNA HOTAIR during the development and progression of endometriosis. PLoS One 2021; 16:e0248168. [PMID: 33667269 PMCID: PMC7935326 DOI: 10.1371/journal.pone.0248168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 02/20/2021] [Indexed: 02/07/2023] Open
Abstract
HOTAIR is a well-known long non-coding RNA (lncRNA) involved in various cellular signaling, whereas its functional impacts on endometriosis development are still largely unknown. To this end, six potential functional single nucleotide polymorphisms (SNPs) in HOTAIR, with minor allele frequencies more than 10% in Han population and altered net energy of RNA structures larger than 0.5 kcal/mol, were selected for genotyping study. The study included 207 endometriosis patients and 200 healthy women. Genetic substitutions at rs1838169 and rs17720428 were frequently found in endometriosis patients, and rs1838169 showed statistical significance (p = 0.0174). The G-G (rs1838169-rs17720428) haplotype showed the most significant association with endometriosis (p < 0.0001) with enhanced HOTAIR stability, and patients who harbor such haplotype tended to show higher CA125. Data mining further revealed higher mRNA HOTAIR levels in the endometria of patients with severe endometriosis which consistently showed reduced HOXD10 and HOXA5 levels. HOTAIR knockdown with specific shRNAs down-regulated cell proliferation and migration with the induction of HOXD10 and HOXA5 expression in human ovarian clear cancer cells. Our study therefore provided evidence to indicate a prominent role of HOTAIR in promoting endometriosis, which could be used as a potential target for clinical applications.
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Affiliation(s)
- Cherry Yin-Yi Chang
- Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung, Taiwan.,School of Medicine, China Medical University, Taichung, Taiwan
| | - Chung-Chen Tseng
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare, Taichung, Taiwan
| | - An-Jen Chiang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Obstetrics and Gynecology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Lun-Chien Lo
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Chih-Mei Chen
- Human Genetic Center, China Medical University Hospital, Taichung, Taiwan
| | - Man-Ju Yen
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Li Sun
- Department of Gynecological Oncology, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, People's Republic of China.,Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Li Yang
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tritium Hwang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Fuu-Jen Tsai
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Human Genetic Center, China Medical University Hospital, Taichung, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
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Chou YC, Chen MJ, Chen PH, Chang CW, Yu MH, Chen YJ, Tsai EM, Tsai SF, Kuo WS, Tzeng CR. Integration of genome-wide association study and expression quantitative trait locus mapping for identification of endometriosis-associated genes. Sci Rep 2021; 11:478. [PMID: 33436679 PMCID: PMC7803948 DOI: 10.1038/s41598-020-79515-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
To determine whether genetic predisposition to endometriosis varies depending on ethnicity and in association with expression quantitative trait loci (eQTL) in a Taiwanese population. We conducted a genome-wide association study (GWAS) and replicated it in 259 individuals with laparoscopy-confirmed stage III or IV endometriosis (cases) and 171 women without endometriosis (controls). Their genomic DNA was extracted from blood and evaluated by the GWAS of Taiwan Biobank Array. Novel genetic variants that predispose individuals to endometriosis were identified using GWAS and replication, including rs10739199 (P = 6.75 × 10-5) and rs2025392 (P = 8.01 × 10-5) at chromosome 9, rs1998998 (P = 6.5 × 10-6) at chromosome 14, and rs6576560 (P = 9.7 × 10-6) at chromosome 15. After imputation, strong signals were exhibited by rs10822312 (P = 1.80 × 10-7) at chromosome 10, rs58991632 (P = 1.92 × 10-6) and rs2273422 (P = 2.42 × 10-6) at chromosome 20, and rs12566078 (P = 2.5 × 10-6) at chromosome 1. We used the Genotype-Tissue Expression (GTEx) database to observe eQTL. Among these SNPs, the cis-eQTL rs13126673 of inturned planar cell polarity protein (INTU) showed significant association with INTU expression (P = 5.1 × 10-33). Moreover, the eQTL analysis was performed on endometriotic tissues from women with endometriosis. The expression of INTU in 78 endometriotic tissue of women with endometriosis is associated with rs13126673 genotype (P = 0.034). To our knowledge, this is the first GWAS to link endometriosis and eQTL in a Taiwanese population.
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Affiliation(s)
- Ya-Ching Chou
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan.,Center for Reproductive Medicine and Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ming-Jer Chen
- Department of Obstetrics and Gynecology and Women's Health, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Pi-Hua Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ching-Wen Chang
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Mu-Hsien Yu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Jen Chen
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Eing-Mei Tsai
- General Research Centers of R&D Office, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Wun-Syuan Kuo
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chii-Ruey Tzeng
- Center for Reproductive Medicine and Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan. .,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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6
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Candidate genes for age at menarche are associated with endometriosis. Reprod Biomed Online 2020; 41:943-956. [PMID: 33051137 DOI: 10.1016/j.rbmo.2020.04.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/25/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023]
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7
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Cardoso JV, Perini JA, Machado DE, Pinto R, Medeiros R. Systematic review of genome-wide association studies on susceptibility to endometriosis. Eur J Obstet Gynecol Reprod Biol 2020; 255:74-82. [PMID: 33113402 DOI: 10.1016/j.ejogrb.2020.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
Endometriosis is a complex and heterogeneous disease in which extrinsic and intrinsic factors, such as genetics, provide to the disease development. Genome-wide association (GWA) studies may be essential to recognize genetic variants associated with the endometriosis risk. However, in the current literature there are some conflicting results between these studies. The aim of the present study was to undertake a systematic review about endometriosis GWA studies, to describe the disease-associated genes and single nucleotide polymorphisms (SNPs) to try to understand the endometriosis etiopathogenesis, besides to discuss possible bias of conflicting results among these studies. This study is a systematic review of GWA studies in endometriosis published until December 31th, 2019 by PubMed database, considering the following descriptors: endometriosis and ("polymorphism" or "SNP" or "genetic polymorphism" or "variants" or "locus") and ("GWA" or "Genome-wide" or "Genome wide" or "Genetic association study"). The included studies were analyzed with methodological rigor (STROBE and PRISMA) to enable better quality of case-control and meta-analysis studies, respectively. Of the 88 articles found, only 15 were eligible. All articles had appropriate quality evaluated by STROBE and PRISMA checklists (77% and 81%, respectively). Overall, 35,022 endometriosis cases and 181,760 controls were analyzed. The number of participants in each study was quite different (171 to 17,045 for the cases and 308 to 150,021 for the controls), with a predominance of European ethnicity. Most endometriosis cases (86%) were diagnosed by surgery, while selection of the control group was different among studies. About 47% performed only one stage (discovery stage) and 53% performed both the discovery and replication analyses. Eleven genes/SNPs were associated with endometriosis risk in more than one article (chromosome 1, 2, 6, 7, 9 and 12; WNT4, GREB1, FN1, IL1A, ETAA1, RND3, ID4, NFE2L3, CDKN2B-AS1 and VEZT). SNPs were localized in intergenic and intronic regions, their risk allele frequencies varied among the studies and their results were conflicting. In summary, WNT4 rs7521902, GREB1 rs13394619, FN1 rs1250248, IL1A rs6542095 and VEZT rs10859871 variants are highlighted due to high frequency and pathways and function that each gene influences in the development of endometriosis. However, the replication and validation of these variants in different populations are necessary for a better understanding of the endometriosis etiopathogenesis, in order to optimize the diagnosis and improve the efficiency of clinical treatment of the disease.
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Affiliation(s)
- Jéssica Vilarinho Cardoso
- Research Laboratory of Pharmaceutical Sciences, State University Centre of the West Zone, Rio de Janeiro, Brazil; Program of Post-graduation in Public Health and Environment, National School of Public Health, Oswald Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Jamila Alessandra Perini
- Research Laboratory of Pharmaceutical Sciences, State University Centre of the West Zone, Rio de Janeiro, Brazil; Program of Post-graduation in Public Health and Environment, National School of Public Health, Oswald Cruz Foundation, Rio de Janeiro, RJ, Brazil.
| | - Daniel Escorsim Machado
- Research Laboratory of Pharmaceutical Sciences, State University Centre of the West Zone, Rio de Janeiro, Brazil
| | - Ricardo Pinto
- Molecular Oncology Group-CI, Portuguese Institute of Oncology, Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology Group-CI, Portuguese Institute of Oncology, Porto, Portugal
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Saadat M, Qasemian-Talgard A, Darvishi FZ, Taghipour N, Saadat I. A new simple method for estimation of allelic frequencies using pooled samples. Gene 2019; 703:13-16. [PMID: 30951855 DOI: 10.1016/j.gene.2019.04.003] [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: 12/21/2018] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/15/2022]
Abstract
Today several millions polymorphic sites in human genome are well described. Many investigators are studying the association between these polymorphisms and susceptibility to multifactorial traits. These polymorphisms are also used for studying the population's genetic structures. Here, we introduce a new simple one step method for estimating the allelic frequency of polymorphic sites in pooled samples. The method is based on measurement of the intensity of polymorphic bands on agarose gel electrophoresis. This method is very simple, rapid, inexpensive, and is more sensitive compared to the chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry method.
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Affiliation(s)
- Mostafa Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
| | | | | | - Nahid Taghipour
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Iraj Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
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Hirata T, Koga K, Johnson TA, Morino R, Nakazono K, Kamitsuji S, Akita M, Kawajiri M, Kami A, Hoshi Y, Tada A, Ishikawa K, Hine M, Kobayashi M, Kurume N, Fujii T, Kamatani N, Osuga Y. Japanese GWAS identifies variants for bust-size, dysmenorrhea, and menstrual fever that are eQTLs for relevant protein-coding or long non-coding RNAs. Sci Rep 2018; 8:8502. [PMID: 29855537 PMCID: PMC5981393 DOI: 10.1038/s41598-018-25065-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/13/2018] [Indexed: 02/05/2023] Open
Abstract
Traits related to primary and secondary sexual characteristics greatly impact females during puberty and day-to-day adult life. Therefore, we performed a GWAS analysis of 11,348 Japanese female volunteers and 22 gynecology-related phenotypic variables, and identified significant associations for bust-size, menstrual pain (dysmenorrhea) severity, and menstrual fever. Bust-size analysis identified significant association signals in CCDC170-ESR1 (rs6557160; P = 1.7 × 10-16) and KCNU1-ZNF703 (rs146992477; P = 6.2 × 10-9) and found that one-third of known European-ancestry associations were also present in Japanese. eQTL data points to CCDC170 and ZNF703 as those signals' functional targets. For menstrual fever, we identified a novel association in OPRM1 (rs17181171; P = 2.0 × 10-8), for which top variants were eQTLs in multiple tissues. A known dysmenorrhea signal near NGF replicated in our data (rs12030576; P = 1.1 × 10-19) and was associated with RP4-663N10.1 expression, a putative lncRNA enhancer of NGF, while a novel dysmenorrhea signal in the IL1 locus (rs80111889; P = 1.9 × 10-16) contained SNPs previously associated with endometriosis, and GWAS SNPs were most significantly associated with IL1A expression. By combining regional imputation with colocalization analysis of GWAS/eQTL signals along with integrated annotation with epigenomic data, this study further refines the sets of candidate causal variants and target genes for these known and novel gynecology-related trait loci.
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Affiliation(s)
- Tetsuya Hirata
- Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kaori Koga
- Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | | | - Ryoko Morino
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | | | | | | | - Azusa Kami
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Yuria Hoshi
- Life Science Group, Healthcare Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Asami Tada
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | - Maaya Hine
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Miki Kobayashi
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Nami Kurume
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Tomoyuki Fujii
- Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | | | - Yutaka Osuga
- Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan.
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