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Wallace AD, Blue NR, Morgan T, Workalemahu T, Silver RM, Quinlan AR. Placental somatic mutation in human stillbirth and live birth: A pilot case-control study of paired placental, fetal, and maternal whole genomes. Placenta 2024; 154:137-144. [PMID: 38972082 DOI: 10.1016/j.placenta.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION A high frequency of single nucleotide somatic mutations in the placenta has been recently described, but its relationship to placental dysfunction is unknown. METHODS We performed a pilot case-control study using paired fetal, maternal, and placental samples collected from healthy live birth controls (n = 10), live births with fetal growth restriction (FGR) due to placental insufficiency (n = 7), and stillbirths with FGR and placental insufficiency (n = 11). We quantified single nucleotide and structural somatic variants using bulk whole genome sequencing (30-60X coverage) in four biopsies from each placenta. We also assessed their association with clinical and histological evidence of placental dysfunction. RESULTS Seventeen pregnancies had sufficiently high-quality placental, fetal, and maternal DNA for analysis. Each placenta had a median of 473 variants (range 111-870), with 95 % arising in just one biopsy within each placenta. In controls, live births with FGR, and stillbirths, the median variant counts per placenta were 514 (IQR 381-779), 582 (450-735), and 338 (245-441), respectively. After adjusting for depth of sequencing coverage and gestational age at birth, the somatic mutation burden was similar between groups (FGR live births vs. controls, adjusted diff. 59, 95 % CI -218 to +336; stillbirths vs controls, adjusted diff. -34, -351 to +419), and with no association with placental dysfunction (p = 0.7). DISCUSSION We confirmed the high prevalence of somatic mutation in the human placenta and conclude that the placenta is highly clonal. We were not able to identify any relationship between somatic mutation burden and clinical or histologic placental insufficiency.
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Affiliation(s)
- Amelia D Wallace
- University of Utah Health, Department of Human Genetics, 15 N 2030 E, Eccles Institute of Human Genetics Rm 7160B, Salt Lake City, UT, 84112, USA; Utah Center for Genetic Discovery, 15 N 2030 E, #2100, Salt Lake City, UT, 4112, USA
| | - Nathan R Blue
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA
| | - Terry Morgan
- Oregon Health & Science University, Departments of Pathology and Obstetrics and Gynecology, 3181 SW Sam Jackson Park Rd, L-113, Portland, OR, 97239, USA
| | - Tsegaselassie Workalemahu
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA
| | - Robert M Silver
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA.
| | - Aaron R Quinlan
- University of Utah Health, Department of Human Genetics, 15 N 2030 E, Eccles Institute of Human Genetics Rm 7160B, Salt Lake City, UT, 84112, USA; Utah Center for Genetic Discovery, 15 N 2030 E, #2100, Salt Lake City, UT, 4112, USA.
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Jahangir M, Li L, Zhou JS, Lang B, Wang XP. L1 Retrotransposons: A Potential Endogenous Regulator for Schizophrenia. Front Genet 2022; 13:878508. [PMID: 35832186 PMCID: PMC9271560 DOI: 10.3389/fgene.2022.878508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
The long interspersed nuclear elements 1 (LINE-1/L1s) are the only active autonomous retrotransposons found in humans which can integrate anywhere in the human genome. They can expand the genome and thus bring good or bad effects to the host cells which really depends on their integration site and associated polymorphism. LINE-1 retrotransposition has been found participating in various neurological disorders such as autism spectrum disorder, Alzheimer’s disease, major depression disorder, post-traumatic stress disorder and schizophrenia. Despite the recent progress, the roles and pathological mechanism of LINE-1 retrotransposition in schizophrenia and its heritable risks, particularly, contribution to “missing heritability” are yet to be determined. Therefore, this review focuses on the potentially etiological roles of L1s in the development of schizophrenia, possible therapeutic choices and unaddressed questions in order to shed lights on the future research.
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Affiliation(s)
| | | | | | - Bing Lang
- *Correspondence: Bing Lang, ; Xiao-Ping Wang,
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Li S, Yang Q, Hou Y, Jiang T, Zong L, Wang Z, Luo X, Liang W, Zhao H, Ning Y, Zhao C. Hypomethylation of LINE-1 elements in schizophrenia and bipolar disorder. J Psychiatr Res 2018; 107:68-72. [PMID: 30326341 DOI: 10.1016/j.jpsychires.2018.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 01/08/2023]
Abstract
Schizophrenia (SCZ) and bipolar disorder (BPD) are severe mental illnesses with evidence of significant genetic and environmental etiological elements in their complex etiologies. 5'-Methylcytosine is the main epigenetic DNA modification that mediates the interplay between genetic and environmental components. In humans, most 5'-methylcytosine modifications are observed in CpG-rich regions within the long interspersed nuclear element (LINE-1). LINE-1 is a mobile retrotransposon that comprises ∼17% of the human genome, and its methylation levels are highly correlated with global DNA methylation levels. LINE-1 insertions are also reported to be mental illnesses-associated genomic risk factors. To examine the LINE-1 methylation levels in SCZ and BPD, this study employed a bisulfite conversion-specific one-label extension (BS-OLE) method to detect the methylation levels at three CpG sites (S1, S2 and S3) of LINE-1 in peripheral blood DNA from a Han Chinese cohort composed of 92 SCZ patients, 99 BPD patients and 92 controls (CON). The results showed a decreased S1 methylation level in SCZ, decreased S2 methylation level in BPD and decreased S3 methylation levels in both SCZ and BPD relative to those of the CON. A female-dependent positive correlation of the S3 methylation level with age in CON became non-significant in both SCZ and BPD. These findings demonstrated that LINE-1 methylation varied with development and disease status. The roles of LINE-1 methylation in the pathogenesis of SCZ and BPD remain to be elucidated.
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Affiliation(s)
- Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Yang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Yu Hou
- Department of Pediatric Neurology, Affiliated BaYi Children's Hospital, PLA Army General Hospital, Beijing, China
| | - Tingyun Jiang
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Lu Zong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xia Luo
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wenquan Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Hu Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Yuping Ning
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China.
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, Guangdong, China.
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Kerachian MA, Kerachian M. Long interspersed nucleotide element-1 (LINE-1) methylation in colorectal cancer. Clin Chim Acta 2018; 488:209-214. [PMID: 30445031 DOI: 10.1016/j.cca.2018.11.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) represents a group of molecularly heterogeneous diseases characterized by genetic and epigenetic alterations. Long interspersed nuclear elements (LINEs) are a form of retrotransposable element found in many eukaryotic genomes. These LINEs, when active, can mobilize in the cell and steadily cause genomic rearrangement. Active LINE reorganization is a source of endogenous mutagenesis and polymorphism in the cell that brings about individual genomic variation. In normal somatic cells, these elements are heavily methylated and thus mostly suppressed, in turn, preventing their potential for bringing about genomic instability. When LINEs are inadequately controlled, they can play a role in the pathogenesis of several genetic diseases, such as cancer. In tumor cells, LINE hypomethylation can reactivate the mobilization of these elements and is associated with both an advanced stage and a poor prognosis. In this article, we summarize the current knowledge surrounding LINE methylation, its correlation to CRC and its application as a diagnostic, prognostic and predictive biomarker in colon cancer.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Matin Kerachian
- Faculty of Medicine, McGill University, Montreal, Canada; Research Institute at McGill University Health Center, Montreal, Canada
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Erichsen L, Beermann A, Arauzo-Bravo MJ, Hassan M, Dkhil MA, Al-Quraishy S, Hafiz TA, Fischer JC, Santourlidis S. Genome-wide hypomethylation of LINE-1 and Alu retroelements in cell-free DNA of blood is an epigenetic biomarker of human aging. Saudi J Biol Sci 2018; 25:1220-1226. [PMID: 30174526 PMCID: PMC6117241 DOI: 10.1016/j.sjbs.2018.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/31/2018] [Accepted: 02/11/2018] [Indexed: 11/26/2022] Open
Abstract
Aging associated DNA hypomethylation of LINE-1 and Alu retroelements may be a crucial determinant of loss of genomic integrity, deterioration and cancer. In peripheral blood LINE-1 hypomethylation has been reported to increase during aging, but other studies did not observe significant changes. We hypothesized that these apparently inconsistent reports might relate to differences between cellular and cell-free DNA. Using the technique of idiolocal normalization of real-time methylation-specific PCR (IDLN-MSP) for genetic imbalanced DNA specimens we obtained evidence that LINE-1 hypomethylation in cell-free DNA, but not cellular DNA from peripheral blood is an epigenetic biomarker for human aging. Furthermore, hypomethylation of cell-free DNA is more extensive in smokers, suggesting that it might be used as a surrogate marker for monitoring the improvement of smoking-induced adverse effects after cancelling smoking.
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Affiliation(s)
- Lars Erichsen
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
| | - Agnes Beermann
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
| | - Marcos J Arauzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Mohamed Hassan
- Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA.,Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France
| | - Mohamed A Dkhil
- Department of Zoology, College of Science, King Saud University, Saudi Arabia.,Department of Zoology and Entomology, Faculty of Science, Helwan University, Cairo, Egypt
| | - Saleh Al-Quraishy
- Department of Zoology, College of Science, King Saud University, Saudi Arabia
| | - Taghreed A Hafiz
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Saudi Arabia
| | - Johannes C Fischer
- Institute of Transplantation Diagnostics and Cell Therapeutics, University Hospital and Medical Faculty of the Heinrich-Heine-University Duesseldorf, Moorenstr. 5, Duesseldorf 40225, Germany
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
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Kabanov IN, Mavropulo-Stolyarenko GR, Tishchenko LI. Changes in Gene Expression and DNA Methylation of Evolutionarily Young AluY Repeats during Apoptosis of Human K562 Erythro-Myeloblastic Leukemia Cells. J EVOL BIOCHEM PHYS+ 2018. [DOI: 10.1134/s0022093018010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vafadar-Isfahani N, Parr C, McMillan LE, Sanner J, Yeo Z, Saddington S, Peacock O, Cruickshanks HA, Meehan RR, Lund JN, Tufarelli C. Decoupling of DNA methylation and activity of intergenic LINE-1 promoters in colorectal cancer. Epigenetics 2017; 12:465-475. [PMID: 28300471 PMCID: PMC5501206 DOI: 10.1080/15592294.2017.1300729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/23/2017] [Indexed: 01/02/2023] Open
Abstract
Hypomethylation of LINE-1 repeats in cancer has been proposed as the main mechanism behind their activation; this assumption, however, was based on findings from early studies that were biased toward young and transpositionally active elements. Here, we investigate the relationship between methylation of 2 intergenic, transpositionally inactive LINE-1 elements and expression of the LINE-1 chimeric transcript (LCT) 13 and LCT14 driven by their antisense promoters (L1-ASP). Our data from DNA modification, expression, and 5'RACE analyses suggest that colorectal cancer methylation in the regions analyzed is not always associated with LCT repression. Consistent with this, in HCT116 colorectal cancer cells lacking DNA methyltransferases DNMT1 or DNMT3B, LCT13 expression decreases, while cells lacking both DNMTs or treated with the DNMT inhibitor 5-azacytidine (5-aza) show no change in LCT13 expression. Interestingly, levels of the H4K20me3 histone modification are inversely associated with LCT13 and LCT14 expression. Moreover, at these LINE-1s, H4K20me3 levels rather than DNA methylation seem to be good predictor of their sensitivity to 5-aza treatment. Therefore, by studying individual LINE-1 promoters we have shown that in some cases these promoters can be active without losing methylation; in addition, we provide evidence that other factors (e.g., H4K20me3 levels) play prominent roles in their regulation.
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Affiliation(s)
| | - Christina Parr
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Lara E. McMillan
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Juliane Sanner
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Zhao Yeo
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Stephen Saddington
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Oliver Peacock
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | | | - Richard R. Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan N. Lund
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Cristina Tufarelli
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
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Ye D, Jiang D, Li Y, Jin M, Chen K. The role of LINE-1 methylation in predicting survival among colorectal cancer patients: a meta-analysis. Int J Clin Oncol 2017; 22:749-757. [PMID: 28343299 DOI: 10.1007/s10147-017-1106-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/23/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND The prognostic value of long interspersed nucleotide element-1 (LINE-1) methylation in patients with colorectal cancer (CRC) remains uncertain. We have therefore performed a meta-analysis to elucidate this issue. METHODS The PubMed and Web of Science databases were searched for studies published up to 30 June 2016 which reported on an association between LINE-1 methylation and overall survival (OS), disease-free survival (DFS), or cancer-specific survival (CSS) among CRC patients. The reference lists of the identified studies were also analyzed to identify additional eligible studies. Hazard ratios (HRs) with 95% confidence intervals (CIs) were pooled using the fixed-effects or the random-effects model. Stratification analysis and meta-regression analysis were performed to detect the source of heterogeneity. Analyses of sensitivity and publication bias were also carried out. RESULTS Thirteen independent studies involving 3620 CRC patients were recruited to the meta-analysis. LINE-1 hypomethylation was found to be significantly associated with shorter OS (HR 2.92, 95% CI 2.20-3.88, p < 0.001) and DFS (HR 2.18, 95% CI 1.46-3.27, p < 0.001), as well as unfavorable CSS (HR 1.96, 95% CI 1.35-2.85, p < 0.001). No heterogeneity was found among the studies evaluating the associations between LINE-1 hypomethylation and OS or DFS, with the exception being CSS. Moreover, meta-regression analysis suggested that one of the contributors to between-study heterogeneity on the association between LINE-1 methylation and CSS was statistical methodology. The subgroup analysis suggested that the association in studies using the Cox model statistical method (HR 2.76, 95% CI 1.90-4.01, p < 0.001) was stronger than that in studies using the Log-rank test (HR 1.41, 95% CI 1.07-1.87, p = 0.015). CONCLUSIONS The results of this meta-analysis suggest that LINE-1 methylation is significantly associated with the survival of CRC patients and that it could be a predictive factor for CRC prognosis.
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Affiliation(s)
- Ding Ye
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Danjie Jiang
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yingjun Li
- Department of Public Health, Hangzhou Medical School, Hangzhou, China
| | - Mingjuan Jin
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kun Chen
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, 866 Yuhangtang Road, Hangzhou, 310058, China.
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Marino D, Perković M, Hain A, Jaguva Vasudevan AA, Hofmann H, Hanschmann KM, Mühlebach MD, Schumann GG, König R, Cichutek K, Häussinger D, Münk C. APOBEC4 Enhances the Replication of HIV-1. PLoS One 2016; 11:e0155422. [PMID: 27249646 PMCID: PMC4889046 DOI: 10.1371/journal.pone.0155422] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 04/28/2016] [Indexed: 12/24/2022] Open
Abstract
APOBEC4 (A4) is a member of the AID/APOBEC family of cytidine deaminases. In this study we found a high mRNA expression of A4 in human testis. In contrast, there were only low levels of A4 mRNA detectable in 293T, HeLa, Jurkat or A3.01 cells. Ectopic expression of A4 in HeLa cells resulted in mostly cytoplasmic localization of the protein. To test whether A4 has antiviral activity similar to that of proteins of the APOBEC3 (A3) subfamily, A4 was co-expressed in 293T cells with wild type HIV-1 and HIV-1 luciferase reporter viruses. We found that A4 did not inhibit the replication of HIV-1 but instead enhanced the production of HIV-1 in a dose-dependent manner and seemed to act on the viral LTR. A4 did not show detectable cytidine deamination activity in vitro and weakly interacted with single-stranded DNA. The presence of A4 in virus producer cells enhanced HIV-1 replication by transiently transfected A4 or stably expressed A4 in HIV-susceptible cells. APOBEC4 was capable of similarly enhancing transcription from a broad spectrum of promoters, regardless of whether they were viral or mammalian. We hypothesize that A4 may have a natural role in modulating host promoters or endogenous LTR promoters.
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Affiliation(s)
- Daniela Marino
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Mario Perković
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Anika Hain
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Ananda A. Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Henning Hofmann
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | | | - Michael D. Mühlebach
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
- Product Testing of Immunological Medicinal Products for Veterinary Uses, Paul-Ehrlich-Institute, Langen, Germany
| | - Gerald G. Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, Langen, Germany
- Sanford Burnham Prebys Medical Discovery Institute, Immunity and Pathogenesis Program, La Jolla, California, United States of America
| | - Klaus Cichutek
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
- * E-mail:
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He ZM, Li J, Hwa YL, Brost B, Fang Q, Jiang SW. Transition of LINE-1 DNA methylation status and altered expression in first and third trimester placentas. PLoS One 2014; 9:e96994. [PMID: 24821186 PMCID: PMC4018393 DOI: 10.1371/journal.pone.0096994] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/14/2014] [Indexed: 12/30/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of gene expression, genomic DNA stability, cell proliferation, and malignant transformation. Common cellular features including fast tissue expansion, invasive growth, and active angiogenesis, have been noticed between placental development and tumorigenesis by many investigators. While the DNA hypomethylation and transcriptional activation of LINE-1 has been found to be a feature of tumorigenesis, it is not clear if similar changes could be involved in placental development. In this study, we assessed LINE-1 methylation in human placentas from different gestational ages and observed a significant decrease of LINE-1 methylation levels in third trimester placentas compared to first trimester placentas. Accompanying with this change is the significantly increased LINE-1 mRNA levels in third trimester placentas. Since no global DNA methylation change was detected between first and third trimesters, LINE-1 methylation changes appeared to be a specific epigenetic entity contributing to placental development. Indeed, further analyses showed that LINE-1 upregulation was correlated with higher levels of PCNA, suggesting a link between LINE-1 activation and fast proliferation of certain cellular components in third trimester placentas. Measurement of the DNMT1, DNMT3A, and DNMT3B expression found a significant reduction of DNMT3B between third and first trimesters, pointing to the possible involvement of this enzyme in the regulation of LINE-1 methylation. Taken together these results provided evidence for a dynamic temporal regulation of LINE-1 methylation and activation during placental development. These studies have laid a foundation for future investigation on the function of LINE-1 expression in human placenta under different patho-physiological conditions.
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Affiliation(s)
- Zhi-ming He
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Department of Biological Science, Mercer University School of Medicine, Savannah, Georgia, United States of America
| | - Jinping Li
- Department of Biological Science, Mercer University School of Medicine, Savannah, Georgia, United States of America
- Department of Obstetrics and Gynecology, Mayo Clinic and Mayo College of Medicine, Rochester, Minnesota, United States of America
- Department of Obstetrics and Gynecology, Memorial Health University Medical Center, Savannah, Georgia, United States of America
| | - Yi Lisa Hwa
- Department of Medicine, Mayo Clinic and Mayo College of Medicine, Rochester, Minnesota, United States of America
| | - Brian Brost
- Department of Obstetrics and Gynecology, Mayo Clinic and Mayo College of Medicine, Rochester, Minnesota, United States of America
| | - Qun Fang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- * E-mail: (S-WJ); (QF)
| | - Shi-Wen Jiang
- Department of Biological Science, Mercer University School of Medicine, Savannah, Georgia, United States of America
- Department of Obstetrics and Gynecology, Mayo Clinic and Mayo College of Medicine, Rochester, Minnesota, United States of America
- Department of Obstetrics and Gynecology, Memorial Health University Medical Center, Savannah, Georgia, United States of America
- * E-mail: (S-WJ); (QF)
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Clinical implications of the LINE-1 methylation levels in patients with gastrointestinal cancer. Surg Today 2013; 44:1807-16. [DOI: 10.1007/s00595-013-0763-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/30/2013] [Indexed: 12/17/2022]
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12
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Stembalska A, Leszczyński P, Gil J, Ramsey D, Pitala G, Maciejczyk A, Frączek M. Global DNA methylation status in laryngeal cancer. Head Neck 2013; 36:419-24. [DOI: 10.1002/hed.23315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2013] [Indexed: 01/25/2023] Open
Affiliation(s)
| | - Przemysław Leszczyński
- Department of Genetics; Wroclaw Medical University; Wroclaw Poland
- Department of Biology and Medical Parasitology; Wroclaw Medical University; Wroclaw Poland
| | - Justyna Gil
- Department of Genetics; Wroclaw Medical University; Wroclaw Poland
| | - David Ramsey
- Department of Mathematics and Statistics; University of Limerick; Limerick Ireland
| | - Grzegorz Pitala
- Department of Clinical Otolaryngology; 4th Military Hospital; Wroclaw Wroclaw Poland
| | | | - Marcin Frączek
- Department of Otolaryngology; Wroclaw Medical University; Wroclaw Poland
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13
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Jung YD, Ahn K, Kim YJ, Bae JH, Lee JR, Kim HS. Retroelements: molecular features and implications for disease. Genes Genet Syst 2013; 88:31-43. [PMID: 23676708 DOI: 10.1266/ggs.88.31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic genomes comprise numerous retroelements that have a major impact on the structure and regulation of gene function. Retroelements are regulated by epigenetic controls, and they generate multiple miRNAs that are involved in the induction and progression of genomic instability. Elucidation of the biological roles of retroelements deserves continuous investigation to better understand their evolutionary features and implications for disease.
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Affiliation(s)
- Yi-Deun Jung
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
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14
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Alexandrova EA, Olovnikov IA, Malakhova GV, Zabolotneva AA, Suntsova MV, Dmitriev SE, Buzdin AA. Sense transcripts originated from an internal part of the human retrotransposon LINE-1 5' UTR. Gene 2012; 511:46-53. [PMID: 22982412 DOI: 10.1016/j.gene.2012.09.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/29/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
Abstract
L1 (LINE-1) is one of the most abundant families of human transposable elements. Full-length human L1 has an ~900 bp long 5' untranslated region (5' UTR) which harbors an internal promoter for the RNA polymerase II. It is generally accepted that the first 100 bp of the 5' UTR function as a "minimal promoter" which directs transcription of the entire LINE-1 unit from the extreme 5' terminus. We re-investigated promoter activities of the different DNA fragments that cover the whole L1 5' UTR in cultured human cells by using the luciferase reporter system. Analysis of both mRNA expression and luciferase activity levels indicated that the very important region for the effective transcription is located within the internal part of the L1 5' UTR between nucleotide positions +390 and +526. 5' RACE analysis revealed that in the context of the complete 5' UTR, this part drives mRNA synthesis both from the canonical 5'-terminal transcription start site (TSS) and from within the internal region. In the absence of the first 100 bp, the L1 5' UTR efficiently directed transcription from aberrant TSSs located within its 3' proximal part or the ORF1. Finally, we analyzed transcripts originated from endogenous (genomic) L1 elements and identified two novel TSSs located at positions +525 and +570. We propose a model in which the internal part (390-526) of the L1 5' UTR plays a key role for recruitment of transcription initiation complex, which then may be either positioned onto the 5' terminally located "minimal promoter", or used proximately to direct 5' truncated RNA copy. Intriguingly, this internal regulatory element substantially overlaps with the region of the L1 5' UTR that is known to drive transcription in the opposite direction suggesting the existence of a common core for the bidirectional transcription.
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Affiliation(s)
- Elena A Alexandrova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow 117997, Russia
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15
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Methylation markers for urine-based detection of bladder cancer: the next generation of urinary markers for diagnosis and surveillance of bladder cancer. Adv Urol 2012; 2012:503271. [PMID: 22761614 PMCID: PMC3385670 DOI: 10.1155/2012/503271] [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: 01/31/2012] [Accepted: 04/16/2012] [Indexed: 12/31/2022] Open
Abstract
Cancer of the urinary bladder is the fifth most common neoplasm in the industrialized countries. Diagnosis and surveillance are dependent on invasive evaluation with cystoscopy and to some degree cytology as an adjunct analysis. Nomuscle invasive bladder cancer is characterized by frequent recurrences after resection, and up to 30% will develop an aggressive phenotype. The journey towards a noninvasive test for diagnosing bladder cancer, in order to replace or extend time between cystoscopy, has been ongoing for more than a decade. However, only a handful of tests that aid in clinical decision making are commercially available. Recent reports of DNA methylation in urine specimens highlight a possible clinical use of this marker type, as high sensitivities and specificities have been shown. This paper will focus on the currently available markers NMP22, ImmunoCyt, and UroVysion as well as novel DNA methylation markers for diagnosis and surveillance of bladder cancer.
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16
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Wu HC, Delgado-Cruzata L, Flom JD, Perrin M, Liao Y, Ferris JS, Santella RM, Terry MB. Repetitive element DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry. Carcinogenesis 2012; 33:1946-52. [PMID: 22678115 DOI: 10.1093/carcin/bgs201] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Global decreases in DNA methylation, particularly in repetitive elements, have been associated with genomic instability and human cancer. Emerging, though limited, data suggest that in white blood cell (WBC) DNA levels of methylation, overall or in repetitive elements, may be associated with cancer risk. We measured methylation levels of three repetitive elements [Satellite 2 (Sat2)], long interspersed nuclear element-1 (LINE-1) and Alu) by MethyLight, and LINE-1 by pyrosequencing in a total of 282 breast cancer cases and 347 unaffected sisters from the New York site of the Breast Cancer Family Registry (BCFR) using DNA from both granulocytes and total WBC. We found that methylation levels in all markers were correlated between sisters (Spearman correlation coefficients ranged from 0.17 to 0.55). Sat2 methylation was statistically significantly associated with increased breast cancer risk [odds ratio (OR) = 2.09, 95% confidence interval (CI) = 1.09-4.03; for each unit decrease in the natural log of the methylation level, OR = 2.12, 95% CI = 0.88-5.11 for the lowest quartile compared with the highest quartile]. These associations were only observed in total WBC but not granulocyte DNA. There was no association between breast cancer and LINE-1 and Alu methylation. If replicated in larger prospective studies, these findings support that selected markers of epigenetic changes measured in WBC, such as Sat2, may be potential biomarkers of breast cancer risk.
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Affiliation(s)
- Hui-Chen Wu
- Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY 10032, USA
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17
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Kaer K, Branovets J, Hallikma A, Nigumann P, Speek M. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation. PLoS One 2011; 6:e26099. [PMID: 22022525 PMCID: PMC3192792 DOI: 10.1371/journal.pone.0026099] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/19/2011] [Indexed: 12/30/2022] Open
Abstract
Background Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown. Methodology/Principal Findings Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3′ ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs) and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals. Conclusions/Significance Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.
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Affiliation(s)
- Kristel Kaer
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Jelena Branovets
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Anni Hallikma
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Pilvi Nigumann
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Mart Speek
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- * E-mail:
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18
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Goering W, Ribarska T, Schulz WA. Selective changes of retroelement expression in human prostate cancer. Carcinogenesis 2011; 32:1484-92. [PMID: 21828060 DOI: 10.1093/carcin/bgr181] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Retroelements constitute a large part of the human genome. These sequences are mostly silenced in normal cells, but genome-wide DNA hypomethylation in cancers might lead to their re-expression. Whether this re-expression really occurs in human cancers is largely unkown. We therefore investigated expression and DNA methylation of several classes of retroelements in human prostate cancer tissues and cell lines by quantitative reverse transcription-polymerase chain reaction and pyrosequencing, respectively. The most striking finding was strong and generalized increased expression of the HERV-K_22q11.23 provirus in cancers, including de novo expression of a spliced accessory Np9 transcript in some tumors. In parallel, DNA methylation in the long terminal repeat (LTR) decreased. Conversely, HERVK17 expression was significantly diminished in cancer tissues, but this decrease was unrelated to LTR methylation. Expression of both proviruses was restricted to androgen-responsive prostate cancer cell lines and LTRs sequences containing steroid hormone-responsive elements bound the androgen receptor and conferred androgen responsiveness to reporter constructs. Expression of LINE-1 5'-untranslated region (UTR) and 3'-UTR sequences in prostate cancers rather decreased, despite significant hypomethylation of the internal LINE-1 promoter. Increased expression of the young AluYa5 and AluYb8 families was restricted to individual tumors. Our findings demonstrate a surprising specificity of changes in expression and DNA methylation of retroelements in prostate cancer. In particular, LINE-1 hypomethylation does not lead to generalized overexpression, but specific human endogenous retrovirus-K proviruses display conspicuous changes in their expression hinting at significant functions during prostate carcinogenesis.
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Affiliation(s)
- Wolfgang Goering
- Department of Urology, Heinrich Heine University, Düsseldorf, Germany
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19
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Ray DA, Batzer MA. Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res 2011; 21:813-20. [PMID: 21632748 PMCID: PMC3106314 DOI: 10.1101/gr.110528.110] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.
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Affiliation(s)
- David A. Ray
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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20
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Teneng I, Montoya-Durango DE, Quertermous JL, Lacy ME, Ramos KS. Reactivation of L1 retrotransposon by benzo(a)pyrene involves complex genetic and epigenetic regulation. Epigenetics 2011; 6:355-67. [PMID: 21150308 DOI: 10.4161/epi.6.3.14282] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Benzo(a)pyrene (BaP), is an environmental pollutant present in tobacco smoke and a byproduct of fossil fuel combustion which likely contributes to the tumorigenic processes in human cancers including lung and esophageal. Long Interspersed Nuclear Element-1 (LINE-1) or L1 is a mobile element within the mammalian genome that propagates via a "copy-and-paste" mechanism using reverse transcriptase and RNA intermediates. L1 is strongly expressed during early embryogenesis and then silenced as cells initiate differentiation programming. Although the complex transcriptional control mechanisms of L1 are not well understood, L1 reactivation has been described in several human cancers and following exposure of mouse or human cells to BaP. In this study we investigated the molecular mechanisms and epigenetic events that regulate L1 reactivation following BaP exposure. We show that challenge of HeLa cells with BaP induces early enrichment of the transcriptionally-active chromatin markers histone H3 trimethylated at lysine 4 (H3K4Me3) and histone H3 acetylated at lysine 9 (H3K9Ac), and reduces association of DNA methyltransferase-1 (DNMT1) with the L1 promoter. These changes are followed by proteasome-dependent decreases in cellular DNMT1 expression and sustained reduction of cytosine methylation within the L1 promoter CpG island. Pharmacological inhibition of the proteasome signaling pathway with the inhibitor MG132 blocks degradation of DNMT1 and alters BaP-mediated histone epigenetic modifications. We conclude that genetic reactivation of L1 by BaP involves an ordered cascade of epigenetic events that begin with nucleosomal histone modifications and is completed with alterations in DNMT1 recruitment to the L1 promoter and reduced DNA methylation of CpG islands.
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Affiliation(s)
- Ivo Teneng
- Department of Biochemistry and Molecular Biology, Center for Genetics and Molecular Medicine, University of Louisville, KY, USA
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21
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Repetitive element hypomethylation in blood leukocyte DNA and cancer incidence, prevalence, and mortality in elderly individuals: the Normative Aging Study. Cancer Causes Control 2010; 22:437-47. [PMID: 21188491 DOI: 10.1007/s10552-010-9715-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 12/07/2010] [Indexed: 12/29/2022]
Abstract
BACKGROUND Global genomic hypomethylation is a common epigenetic event in cancer that mostly results from hypomethylation of repetitive DNA elements. Case-control studies have associated blood leukocyte DNA hypomethylation with several cancers. Because samples in case-control studies are collected after disease development, whether DNA hypomethylation is causal or just associated with cancer development is still unclear. METHODS In 722 elderly subjects from the Normative Aging Study cohort, we examined whether DNA methylation in repetitive elements (Alu, LINE-1) was associated with cancer incidence (30 new cases, median follow-up: 89 months), prevalence (205 baseline cases), and mortality (28 deaths, median follow-up: 85 months). DNA methylation was measured by bisulfite pyrosequencing. RESULTS Individuals with low LINE-1 methylation (<median) had a 3.0-fold (95%CI 1.3-6.9) increased incidence of all cancers combined. LINE-1 and Alu methylation were not significantly associated with cancer prevalence at baseline (all cancers combined). However, individuals with low LINE-1 methylation (<median) had a 3.2-fold (95% CI 1.4-7.5) higher prevalence of lung cancer. Individuals with low LINE-1 or Alu methylation (<median) had increased cancer mortality (HR = 3.2, 95%CI 1.3-7.9 for LINE-1; HR = 2.5, 95%CI 1.1-5.8 for Alu). CONCLUSION These findings suggest that individuals with lower repetitive element methylation are at high risk of developing and dying from cancer.
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22
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Zackay A, Steinhoff C. MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing. BMC Res Notes 2010; 3:337. [PMID: 21159174 PMCID: PMC3012040 DOI: 10.1186/1756-0500-3-337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 12/15/2010] [Indexed: 11/23/2022] Open
Abstract
Background Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. Findings MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. Conclusions The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org.
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Affiliation(s)
- Arie Zackay
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany.
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23
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Hou L, Wang H, Sartori S, Gawron A, Lissowska J, Bollati V, Tarantini L, Zhang FF, Zatonski W, Chow WH, Baccarelli A. Blood leukocyte DNA hypomethylation and gastric cancer risk in a high-risk Polish population. Int J Cancer 2010; 127:1866-74. [PMID: 20099281 DOI: 10.1002/ijc.25190] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Global hypomethylation has been shown to increase genome instability potentially leading to increased cancer risk. We determined whether global methylation in blood leukocyte DNA was associated with gastric cancer in a population-based study on 302 gastric cancer cases and 421 age- and sex-matched controls in Warsaw, Poland, between 1994 and 1996. Using PCR-pyrosequencing, we analyzed methylation levels of Alu and LINE-1, 2 CG-rich repetitive elements, to measure global methylation levels. Gastric cancer risk was highest among those with lowest level of methylation in either Alu (OR = 1.3, 95% CI = 0.9-1.9) or LINE-1 (OR = 1.4, 95% CI = 0.9-2.0) relative to those with the highest levels, although the trends were not statistically significant. For Alu, the association was stronger among those aged 70 or older (OR = 2.6, 95% CI = 1.3-5.5, p for interaction = 0.02). We did not observe meaningful differences in the associations by other risk factors and polymorphisms examined. For LINE-1, the association tended to be stronger among individuals with a family history of cancer (OR = 3.1, 95% CI = 1.4-7.0, p for interaction = 0.01), current alcohol drinkers (OR = 1.9, 95% CI = 1.0-3.6, p for interaction = 0.05), current smokers (OR = 2.3, 95% CI = 1.1-4.6, p for interaction = 0.02), those who rarely or never consumed fruit (OR = 3.1, 95% CI = 1.2-8.1, p for interaction = 0.03), CC carriers for the MTRR Ex5+123C>T polymorphism (OR = 2.3, 95% CI = 1.2-4.4, p for interaction = 0.01) and TT carriers for the MTRR Ex15+572T>C polymorphism (OR = 1.7, 95% CI = 1.0-2.8, p for interaction = 0.06). The association was not different by sex, Helicobacter pylori infection, intake of folate, vitamin B6 and total protein and the remaining polymorphisms examined. Our results indicate that interactions between blood leukocyte DNA hypomethylation and host characteristics may determine gastric cancer risk.
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Affiliation(s)
- Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Abstract
Retrotransposons like L1 are silenced in somatic cells by a
variety of mechanisms acting at different levels. Protective
mechanisms include DNA methylation and packaging into inactive
chromatin to suppress transcription and prevent recombination,
potentially supported by cytidine deaminase editing of RNA.
Furthermore, DNA strand breaks arising during attempted
retrotranspositions ought to activate cellular checkpoints, and L1
activation outside immunoprivileged sites may elicit immune
responses. A number of observations indicate that L1 sequences
nevertheless become reactivated in human cancer. Prominently,
methylation of L1 sequences is diminished in many cancer types and
full-length L1 RNAs become detectable, although strong expression
is restricted to germ cell cancers. L1 elements have been found to
be enriched at sites of illegitimate recombination in many
cancers. In theory, lack of L1 repression in cancer might cause
transcriptional deregulation, insertional mutations, DNA breaks,
and an increased frequency of recombinations, contributing to
genome disorganization, expression changes, and chromosomal
instability. There is however little evidence that such effects
occur at a gross scale in human cancers. Rather, as a rule, L1
repression is only partly alleviated. Unfortunately, many
techniques commonly used to investigate genetic and epigenetic
alterations in cancer cells are not well suited to detect subtle
effects elicited by partial reactivation of retroelements like L1
which are present as abundant, but heterogeneous copies.
Therefore, effects of L1 sequences exerted on the local chromatin
structure, on the transcriptional regulation of individual genes,
and on chromosome fragility need to be more closely investigated
in normal and cancer cells.
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Affiliation(s)
- Wolfgang A. Schulz
- Department of Urology, Heinrich Heine University, Mooreustrasse 5, 40225 Düsseldorf, Germany
- *Wolfgang A. Schulz:
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25
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Koch P, Petri M, Paradowska A, Stenzinger A, Sturm K, Steger K, Wimmer M. PTPIP51 mRNA and protein expression in tissue microarrays and promoter methylation of benign prostate hyperplasia and prostate carcinoma. Prostate 2009; 69:1751-62. [PMID: 19691131 DOI: 10.1002/pros.21025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Protein tyrosine phosphatase interacting protein 51 (PTPIP51) shows a tissue-specific expression pattern and is associated with cellular differentiation and apoptosis in several mammalian tissues. Overexpression of the full-length protein enhances apoptosis. It is also expressed in various carcinomas. In this study the expression of PTPIP51 and its in vitro interaction partners was investigated in human benign prostate hyperplasia (BPH) and in prostate carcinoma (PCa). METHODS Tissue microarrays of human BPH and PCa were analyzed by immunohistochemistry. For polymerase chain reaction (PCR), cryo samples of BPH and PCa were used. Bisulfite DNA treatment, followed by sequencing of PCR products was performed in order to analyze CpGs methylation within the promoter region of the PTPIP51 gene. RESULTS PTPIP51 mRNA and protein expression was detected in prostatic epithelia of BPH and in tumor cells of PCa, respectively, and within smooth muscle cells of the stromal compartment. A stronger expression was present in nerve fibers, particularly in PCa, in immune cells and in smooth muscle and endothelial cells of vessels of BPH and PCa. On mRNA levels, a slightly elevated expression of PTPIP51 was observed in the PCa group as tested by real-time quantitative PCR analyses. Methylation experiments revealed that at least 70% of methylated CpGs in the CpG island of the PTPIP51 gene promoter region were identified in BPH samples. In contrast, a loss of methylation has been found in the PCa group. CONCLUSION The promoter methylation status of PTPIP51 seems to influence the expression of PTPIP51, which was seen as elevated in the PCa.
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Affiliation(s)
- Philipp Koch
- Institute of Anatomy and Cell Biology, Justus-Liebig-University Giessen, Giessen, Germany.
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26
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Abstract
DNA and histone methylation are linked and subjected to mitotic inheritance in mammals. Yet how methylation is propagated and maintained between successive cell divisions is not fully understood. A series of enzyme families that can add methylation marks to cytosine nucleobases, and lysine and arginine amino acid residues has been discovered. Apart from methyltransferases, there are also histone modification enzymes and accessory proteins, which can facilitate and/or target epigenetic marks. Several lysine and arginine demethylases have been discovered recently, and the presence of an active DNA demethylase is speculated in mammalian cells. A mammalian methyl DNA binding protein MBD2 and de novo DNA methyltransferase DNMT3A and DNMT3B are shown experimentally to possess DNA demethylase activity. Thus, complex mammalian epigenetic mechanisms appear to be dynamic yet reversible along with a well-choreographed set of events that take place during mammalian development.
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28
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Yegnasubramanian S, Haffner MC, Zhang Y, Gurel B, Cornish TC, Wu Z, Irizarry RA, Morgan J, Hicks J, DeWeese TL, Isaacs WB, Bova GS, De Marzo AM, Nelson WG. DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res 2008; 68:8954-67. [PMID: 18974140 DOI: 10.1158/0008-5472.can-07-6088] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Hypomethylation of CpG dinucleotides in genomic DNA was one of the first somatic epigenetic alterations discovered in human cancers. DNA hypomethylation is postulated to occur very early in almost all human cancers, perhaps facilitating genetic instability and cancer initiation and progression. We therefore examined the nature, extent, and timing of DNA hypomethylation changes in human prostate cancer. Contrary to the prevailing view that global DNA hypomethylation changes occur extremely early in all human cancers, we show that reductions in (5me)C content in the genome occur very late in prostate cancer progression, appearing at a significant extent only at the stage of metastatic disease. Furthermore, we found that, whereas some LINE1 promoter hypomethylation does occur in primary prostate cancers compared with normal tissues, this LINE1 hypomethylation is significantly more pronounced in metastatic prostate cancer. Next, we carried out a tiered gene expression microarray and bisulfite genomic sequencing-based approach to identify genes that are silenced by CpG island methylation in normal prostate cells but become overexpressed in prostate cancer cells as a result of CpG island hypomethylation. Through this analysis, we show that a class of cancer testis antigen genes undergoes CpG island hypomethylation and overexpression in primary prostate cancers, but more so in metastatic prostate cancers. Finally, we show that DNA hypomethylation patterns are quite heterogeneous across different metastatic sites within the same patients. These findings provide evidence that DNA hypomethylation changes occur later in prostate carcinogenesis than the CpG island hypermethylation changes and occur heterogeneously during prostate cancer progression and metastatic dissemination.
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Affiliation(s)
- Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.
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Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 2008; 177:1975-85. [PMID: 18073417 DOI: 10.1534/genetics.107.080234] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) represent approximately 45% of the human genome and 50-90% of some grass genomes. While most elements contain inactivating mutations, others are reversibly inactivated (silenced) by epigenetic mechanisms, including cytosine methylation. Previous studies have shown that retrotransposons can influence the expression of adjacent host genes. In this study, the methylation patterns of TEs and their flanking sequences in different tissues were undertaken using a novel technique called transposon methylation display (TMD). TMD was successfully applied on a highly copied (approximately 1000 copies), newly amplified LTR retrotransposon family in rice called Dasheng. We determined that the methylation status of a subset of LTRs varies in leaves vs. roots. In addition, we determined that tissue-specific LTR methylation correlated with tissue-specific expression of the flanking rice gene. Genes showing tissue-specific expression were in opposite orientation relative to the LTR. Antisense transcripts were detected in the tissue where the sense transcripts from that gene were not detected. Comparative analysis of Dasheng LTR methylation in the two subspecies, japonica vs. indica revealed LTR-mediated differences in subspecies gene expression. Subspecies-specific expression was due either to polymorphic Dasheng insertion sites between the two subspecies or to subspecies-specific methylation of LTRs at the same locus accounted for observed differences in the expression of adjacent genes.
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Olovnikov IA, Adyanova ZV, Galimov ER, Andreev DE, Terenin IM, Ivanov DS, Prassolov VS, Dmitriev SE. Key role of the internal 5′-UTR segment in the transcription activity of the human L1 retrotransposon. Mol Biol 2007. [DOI: 10.1134/s0026893307030119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Smith IM, Mydlarz WK, Mithani SK, Califano JA. DNA global hypomethylation in squamous cell head and neck cancer associated with smoking, alcohol consumption and stage. Int J Cancer 2007; 121:1724-8. [PMID: 17582607 DOI: 10.1002/ijc.22889] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Epigenetic changes have been implicated in the pathogenesis of solid tumors, including head and neck squamous cell carcinoma (HNSCC). Prior efforts have primarily examined regional promoter hypermethylation as a silencer of tumor suppressor gene expression. To analyze the global state of methylation in the HNSCC genome, we utilize pyrosequencing of repetitive elements (LINEs) to compare the state of global methylation in HNSCC to normal aerodigestive mucosa. 137 samples (119 HNSCC tumors and 18 normal mucosal tissues) were digested to extract DNA and subjected to bisulfite treatment. Treated DNA was amplified using PCR primers for the repetitive LINEs sequence and produced a heterogeneous sample of products, from many genomic loci. These products were pyrosequenced to quantitatively evaluate their global genomic methylation status. HNSCC specimens showed global hypomethylation, with a mean level of genomic methylation of 46.8% methylated with a standard deviation of 9.0. Conversely, the normal upper airway mucosa had a global methylation level of 54.0 and a standard deviation of 4.6 (Mann-Whitney p value < 0.001). The tumor specimens also showed an increasing degree of hypomethylation associated with advanced tumor stage (ANOVA p-value of 0.003). About 67% of HNSCC's are globally hypomethylated when evaluated against the minimum level of methylation in the normal mucosal specimens. Degree of global hypomethylation was associated with smoking history, alcohol use and stage in univariate analysis (p-value 0.02), however, only HNSCC diagnosis remained significant on multivariate analysis. Despite the presence of regional promoter hypermethylation, HNSCC demonstrates global genomic hypomethylation. The effects of stage, alcohol use and smoking on global hypomethylation were not independently significant.
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Affiliation(s)
- Ian M Smith
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287-0910, USA
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Wilson AS, Power BE, Molloy PL. DNA hypomethylation and human diseases. Biochim Biophys Acta Rev Cancer 2006; 1775:138-62. [PMID: 17045745 DOI: 10.1016/j.bbcan.2006.08.007] [Citation(s) in RCA: 327] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 08/24/2006] [Accepted: 08/27/2006] [Indexed: 12/14/2022]
Abstract
Changes in human DNA methylation patterns are an important feature of cancer development and progression and a potential role in other conditions such as atherosclerosis and autoimmune diseases (e.g., multiple sclerosis and lupus) is being recognised. The cancer genome is frequently characterised by hypermethylation of specific genes concurrently with an overall decrease in the level of 5 methyl cytosine. This hypomethylation of the genome largely affects the intergenic and intronic regions of the DNA, particularly repeat sequences and transposable elements, and is believed to result in chromosomal instability and increased mutation events. This review examines our understanding of the patterns of cancer-associated hypomethylation, and how recent advances in understanding of chromatin biology may help elucidate the mechanisms underlying repeat sequence demethylation. It also considers how global demethylation of repeat sequences including transposable elements and the site-specific hypomethylation of certain genes might contribute to the deleterious effects that ultimately result in the initiation and progression of cancer and other diseases. The use of hypomethylation of interspersed repeat sequences and genes as potential biomarkers in the early detection of tumors and their prognostic use in monitoring disease progression are also examined.
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Affiliation(s)
- Ann S Wilson
- Preventative Health National Research Flagship, North Ryde, NSW, Australia
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Schulz WA, Steinhoff C, Florl AR. Methylation of endogenous human retroelements in health and disease. Curr Top Microbiol Immunol 2006; 310:211-50. [PMID: 16909913 DOI: 10.1007/3-540-31181-5_11] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Retroelements constitute approximately 45% of the human genome. Long interspersed nuclear element (LINE) autonomous retrotransposons are predominantly represented by LINE-1, nonautonomous small interspersed nuclear elements (SINEs) are primarily represented by ALUs, and LTR retrotransposons by several families of human endogenous retroviruses (HERVs). The vast majority of LINE and HERV elements are densely methylated in normal somatic cells and contained in inactive chromatin. Methylation and chromatin structure together ensure a stable equilibrium between retroelements and their host. Hypomethylation and expression in developing germ cells opens a "window of opportunity" for retrotransposition and recombination that contribute to human evolution, but also inherited disease. In somatic cells, the presence of retroelements may be exploited to organize the genome into active and inactive regions, to separate domains and functional regions within one chromatin domain, to suppress transcriptional noise, and to regulate transcript stability. Retroelements, particularly ALUs, may also fulfill physiological roles during responses to stress and infections. Reactivation and hypomethylation of LINEs and HERVs may be important in the pathophysiology of cancer and various autoimmune diseases, contributing to chromosomal instability and chronically aberrant immune responses. The emerging insights into the pathophysiological importance of endogenous retroelements accentuate the gaps in our knowledge of how these elements are controlled in normal developing and mature cells.
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Affiliation(s)
- W A Schulz
- Urologische Klinik, Heinrich Heine Universität, Düsseldorf, Germany.
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Hoffmann MJ, Müller M, Engers R, Schulz WA. Epigenetic control of CTCFL/BORIS and OCT4 expression in urogenital malignancies. Biochem Pharmacol 2006; 72:1577-88. [PMID: 16854382 DOI: 10.1016/j.bcp.2006.06.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 06/13/2006] [Accepted: 06/14/2006] [Indexed: 12/31/2022]
Abstract
Aberrant hypomethylation in many cancers reactivates retrotransposons and selected single-copy genes such as cancer-testis antigens. Genes reactivated in this manner have recently been postulated to include CTCFL/BORIS, a presumptive testis-specific chromatin regulator, and OCT4/POU5F1, a transcriptional activator in pluripotent cells. We found both genes expressed at high levels in testis and at much lower levels in normal prostate tissue. In prostate and bladder carcinoma cell lines and cancer tissues expression remained largely unchanged, but individual prostate carcinomas showed modestly increased CTCFL expression compared to normal tissues. OCT4 expression was significantly decreased in cancer tissues. Promoter methylation in both genes paralleled expression levels. CTCFL, but not OCT4 was dramatically induced in cancer cell lines by 5-aza-2'-deoxycytidine, but neither gene by the histone deacetylase inhibitor suberoylanilide hydroxamic acid. Thus, CTCFL and OCT4 resemble cancer-testis antigens in being selectively hypomethylated and expressed in male germ cells but differ in lacking significant reexpression and hypomethylation in prostate carcinomas. DNA methylation appears the crucial mechanism in the control of CTCFL transcription, but less decisive in that of OCT4. These findings imply that inhibitors of DNA methylation used for cancer treatment may induce CTCFL expression. Immunohistochemistry demonstrated nuclear localization of CTCFL in developing spermatocytes, and cytoplasmatic localization in spermatogonia, Leydig cells, and epithelial prostate cells. Teratocarcinoma cell lines showed nuclear, and 5-aza-2'-deoxycytidine-treated prostate cancer lines nuclear or cytoplasmatic localization. These different localizations might indicate additional control of CTCFL function via intracellular compartmentation.
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Affiliation(s)
- Michèle J Hoffmann
- Department of Urology, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
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Asada K, Kotake Y, Asada R, Saunders D, Broyles RH, Towner RA, Fukui H, Floyd RA. LINE-1 hypomethylation in a choline-deficiency-induced liver cancer in rats: dependence on feeding period. J Biomed Biotechnol 2006; 2006:17142. [PMID: 16877811 PMCID: PMC1479888 DOI: 10.1155/jbb/2006/17142] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 11/28/2005] [Accepted: 12/04/2005] [Indexed: 12/30/2022] Open
Abstract
Chronic feeding of methyl-donor (methionine, choline, folic acid, and vitamin B12) deficient diet induces hepatocellular carcinoma formation in rats. Previous studies have shown that promoter CpG islands in various cancer-related genes are aberrantly methylated in this model. Moreover, the global genome in methyl-donor-deficient diet fed rats contains a lesser amount of 5-methylcytosine than control livers. It is speculated that more than 90% of all 5-methylcytosines lie within the CpG islands of the transposons, including the long/short interspersed nucleotide elements (LINE and SINE). It is considered that the 5-methylcytosines in LINE-1 limit the ability of retrotransposons to be activated and transcribed; therefore, the extent of hypomethylation of LINE-1 could be a surrogate marker for aberrant methylation in other tumor-related genes as well as genome instability. Additionally, LINE-1 methylation status has been shown to be a good indicator of genome-wide methylation. In this study, we determined cytosine methylation status in the LINE-1 repetitive sequences of rats fed a choline-deficient (CD) diet for various durations and compared these with rats fed a choline-sufficient (CS) diet. The methylation status of LINE-1 was assessed by the combined bisulfite restriction analysis (COBRA) method, where the amount of bisulfite-modified and RsaI-cleaved DNA was quantified using gel electrophoresis. Progressive hypomethylation was observed in LINE-1 of CD livers as a function of feeding time; that is, the amount of cytosine in total cytosine (methylated and unmethylated) increased from 11.1% (1 week) to 19.3% (56 weeks), whereas in the control CS livers, it increased from 9.2% to 12.9%. Hypomethylation in tumor tissues was slightly higher (6%) than the nontumorous surrounding tissue. The present result also indicates that age is a factor influencing the extent of cytosine methylation.
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Affiliation(s)
- Kiyoshi Asada
- Free Radical Biology and Aging Research Program,
Oklahoma Medical Research Foundation, Oklahoma City, Ok 73104, USA
- Third Department of Internal Medicine, Nara Medical
University, Kashihara, Nara 634-8521, Japan
| | - Yashige Kotake
- Free Radical Biology and Aging Research Program,
Oklahoma Medical Research Foundation, Oklahoma City, Ok 73104, USA
| | - Rumiko Asada
- Free Radical Biology and Aging Research Program,
Oklahoma Medical Research Foundation, Oklahoma City, Ok 73104, USA
| | - Deborah Saunders
- Free Radical Biology and Aging Research Program,
Oklahoma Medical Research Foundation, Oklahoma City, Ok 73104, USA
| | - Robert H. Broyles
- Free Radical Biology and Aging Research Program,
Oklahoma Medical Research Foundation, Oklahoma City, Ok 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Rheal A. Towner
- Free Radical Biology and Aging Research Program,
Oklahoma Medical Research Foundation, Oklahoma City, Ok 73104, USA
| | - Hiroshi Fukui
- Third Department of Internal Medicine, Nara Medical
University, Kashihara, Nara 634-8521, Japan
| | - Robert A. Floyd
- Free Radical Biology and Aging Research Program,
Oklahoma Medical Research Foundation, Oklahoma City, Ok 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Hoffmann MJ, Schulz WA. Causes and consequences of DNA hypomethylation in human cancer. Biochem Cell Biol 2005; 83:296-321. [PMID: 15959557 DOI: 10.1139/o05-036] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
While specific genes are hypermethylated in the genome of cancer cells, overall methylcytosine content is often decreased as a consequence of hypomethylation affecting many repetitive sequences. Hypomethylation is also observed at a number of single-copy genes. While global hypomethylation is highly prevalent across all cancer types, it often displays considerable specificity with regard to tumor type, tumor stage, and sequences affected. Following an overview of hypomethylation alterations in various cancers, this review focuses on 3 hypotheses. First, hypomethylation at a single-copy gene may occur as a 2-step process, in which selection for gene function follows upon random hypo methylation. In this fashion, hypomethylation facilitates the adaptation of cancer cells to the ever-changing tumor tissue microenvironment, particularly during metastasis. Second, the development of global hypomethylation is intimately linked to chromatin restructuring and nuclear disorganization in cancer cells, reflected in a large number of changes in histone-modifying enzymes and other chromatin regulators. Third, DNA hypomethylation may occur at least partly as a consequence of cell cycle deregulation disturbing the coordination between DNA replication and activity of DNA methyltransferases. Finally, because of their relation to tumor progression and metastasis, DNA hypomethylation markers may be particularly useful to classify cancer and predict their clinical course.
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