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Liu M, Xie XJ, Li X, Ren X, Sun J, Lin Z, Hemba-Waduge RUS, Ji JY. Transcriptional coupling of telomeric retrotransposons with the cell cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560321. [PMID: 37808851 PMCID: PMC10557779 DOI: 10.1101/2023.09.30.560321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Instead of employing telomerases to safeguard chromosome ends, dipteran species maintain their telomeres by transposition of telomeric-specific retrotransposons (TRs): in Drosophila , these are HeT-A , TART , and TAHRE . Previous studies have shown how these TRs create tandem repeats at chromosome ends, but the exact mechanism controlling TR transcription has remained unclear. Here we report the identification of multiple subunits of the transcription cofactor Mediator complex and transcriptional factors Scalloped (Sd, the TEAD homolog in flies) and E2F1-Dp as novel regulators of TR transcription and telomere length in Drosophila . Depletion of multiple Mediator subunits, Dp, or Sd increased TR expression and telomere length, while over-expressing E2F1-Dp or knocking down the E2F1 regulator Rbf1 (Retinoblastoma-family protein 1) stimulated TR transcription, with Mediator and Sd affecting TR expression through E2F1-Dp. The CUT&RUN analysis revealed direct binding of CDK8, Dp, and Sd to telomeric repeats. These findings highlight the essential role of the Mediator complex in maintaining telomere homeostasis by regulating TR transcription through E2F1-Dp and Sd, revealing the intricate coupling of TR transcription with the host cell-cycle machinery, thereby ensuring chromosome end protection and genomic stability during cell division.
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2
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Li X, Lu K, Chen X, Tu K, Xie D. capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements. Commun Biol 2023; 6:974. [PMID: 37741908 PMCID: PMC10517987 DOI: 10.1038/s42003-023-05349-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes. This method selectively identified TE-containing transcripts and outputted data with up to 90% TE reads, maintaining a comparable data yield to whole-transcriptome sequencing. We applied capTEs to human cancer cells and found that internal and inserted Alu elements may employ distinct regulatory mechanisms to upregulate gene expression. We expect that capTEs will be a critical tool for advancing our understanding of the biological functions of individual TEs at the locus level, revealing their roles as both mutagens and regulators in biological and pathogenic processes.
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Affiliation(s)
- Xuemei Li
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Keying Lu
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiao Chen
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kailing Tu
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Dan Xie
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Alkailani MI, Gibbings D. The Regulation and Immune Signature of Retrotransposons in Cancer. Cancers (Basel) 2023; 15:4340. [PMID: 37686616 PMCID: PMC10486412 DOI: 10.3390/cancers15174340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Advances in sequencing technologies and the bioinformatic analysis of big data facilitate the study of jumping genes' activity in the human genome in cancer from a broad perspective. Retrotransposons, which move from one genomic site to another by a copy-and-paste mechanism, are regulated by various molecular pathways that may be disrupted during tumorigenesis. Active retrotransposons can stimulate type I IFN responses. Although accumulated evidence suggests that retrotransposons can induce inflammation, the research investigating the exact mechanism of triggering these responses is ongoing. Understanding these mechanisms could improve the therapeutic management of cancer through the use of retrotransposon-induced inflammation as a tool to instigate immune responses to tumors.
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Affiliation(s)
- Maisa I. Alkailani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
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Ricci M, Peona V, Boattini A, Taccioli C. Comparative analysis of bats and rodents' genomes suggests a relation between non-LTR retrotransposons, cancer incidence, and ageing. Sci Rep 2023; 13:9039. [PMID: 37270634 DOI: 10.1038/s41598-023-36006-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/27/2023] [Indexed: 06/05/2023] Open
Abstract
The presence in nature of species showing drastic differences in lifespan and cancer incidence has recently increased the interest of the scientific community. In particular, the adaptations and the genomic features underlying the evolution of cancer-resistant and long-lived organisms have recently focused on transposable elements (TEs). In this study, we compared the content and dynamics of TE activity in the genomes of four rodent and six bat species exhibiting different lifespans and cancer susceptibility. Mouse, rat, and guinea pig genomes (short-lived and cancer-prone organisms) were compared with that of naked mole rat (Heterocephalus glaber) which is a cancer-resistant organism and the rodent with the longest lifespan. The long-lived bats of the genera Myotis, Rhinolophus, Pteropus and Rousettus were instead compared with Molossus molossus, which is one of the organisms with the shortest lifespan among the order Chiroptera. Despite previous hypotheses stating a substantial tolerance of TEs in bats, we found that long-lived bats and the naked mole rat share a marked decrease of non-LTR retrotransposons (LINEs and SINEs) accumulation in recent evolutionary times.
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Affiliation(s)
| | - Valentina Peona
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden.
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Health and Production, University of Padova, Padua, Italy
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5
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Ward JR, Khan A, Torres S, Crawford B, Nock S, Frisbie T, Moran J, Longworth M. Condensin I and condensin II proteins form a LINE-1 dependent super condensin complex and cooperate to repress LINE-1. Nucleic Acids Res 2022; 50:10680-10694. [PMID: 36169232 PMCID: PMC9561375 DOI: 10.1093/nar/gkac802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Condensin I and condensin II are multi-subunit complexes that are known for their individual roles in genome organization and preventing genomic instability. However, interactions between condensin I and condensin II subunits and cooperative roles for condensin I and condensin II, outside of their genome organizing functions, have not been reported. We previously discovered that condensin II cooperates with Gamma Interferon Activated Inhibitor of Translation (GAIT) proteins to associate with Long INterspersed Element-1 (LINE-1 or L1) RNA and repress L1 protein expression and the retrotransposition of engineered L1 retrotransposition in cultured human cells. Here, we report that the L1 3'UTR is required for condensin II and GAIT association with L1 RNA, and deletion of the L1 RNA 3'UTR results in increased L1 protein expression and retrotransposition. Interestingly, like condensin II, we report that condensin I also binds GAIT proteins, associates with the L1 RNA 3'UTR, and represses L1 retrotransposition. We provide evidence that the condensin I protein, NCAPD2, is required for condensin II and GAIT protein association with L1 RNA. Furthermore, condensin I and condensin II subunits interact to form a L1-dependent super condensin complex (SCC) which is located primarily within the cytoplasm of both transformed and primary epithelial cells. These data suggest that increases in L1 expression in epithelial cells promote cytoplasmic condensin protein associations that facilitate a feedback loop in which condensins may cooperate to mediate L1 repression.
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Affiliation(s)
- Jacqueline R Ward
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Afshin Khan
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sabrina Torres
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bert Crawford
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sarah Nock
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Trenton Frisbie
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, USA
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6
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Van der Mude A. A proposed Information-Based modality for the treatment of cancer. Biosystems 2021; 211:104587. [PMID: 34915101 DOI: 10.1016/j.biosystems.2021.104587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 11/20/2021] [Accepted: 12/01/2021] [Indexed: 11/02/2022]
Abstract
Treatment modalities for cancer involve physical manipulations such as surgery, immunology, radiation, chemotherapy or gene editing. This is a proposal for an information-based modality. This modality does not change the internal state of the cancer cell directly - instead, the cancer cell is manipulated by giving it information to instruct the cell to perform an action. This modality is based on a theory of Structure Encoding in DNA, where information about body part structure controls the epigenetic state of cells in the process of development from pluripotent cells to fully differentiated cells. It has been noted that cancer is often due to errors in morphogenetic differentiation accompanied by associated epigenetic processes. This implies a model of cancer called the Epigenetic Differentiation Model. A major feature of the Structure Encoding Theory is that the characteristics of the differentiated cell are affected by inter-cellular information passed in the tissue microenvironment, which specifies the exact location of a cell in a body part structure. This is done by exosomes that carry fragments of long non-coding RNA and transposons, which convey structure information. In the normal process of epigenetic differentiation, the information passed may lead to apoptosis due to the constraints of a particular body part structure. The proposed treatment involves determining what structure information is being passed in a particular tumor, then adding artificial exosomes that overwhelm the current information with commands for the cells to go into apoptosis.
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Alekseeva L, Mironova N. Role of Cell-Free DNA and Deoxyribonucleases in Tumor Progression. Int J Mol Sci 2021; 22:12246. [PMID: 34830126 PMCID: PMC8625144 DOI: 10.3390/ijms222212246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.
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Affiliation(s)
| | - Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia;
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8
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Human Recombinant DNase I (Pulmozyme ®) Inhibits Lung Metastases in Murine Metastatic B16 Melanoma Model That Correlates with Restoration of the DNase Activity and the Decrease SINE/LINE and c-Myc Fragments in Blood Cell-Free DNA. Int J Mol Sci 2021; 22:ijms222112074. [PMID: 34769514 PMCID: PMC8585023 DOI: 10.3390/ijms222112074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022] Open
Abstract
Tumor-associated cell-free DNAs (cfDNA) play an important role in the promotion of metastases. Previous studies proved the high antimetastatic potential of bovine pancreatic DNase I and identified short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs)and fragments of oncogenes in cfDNA as the main molecular targets of enzyme in the bloodstream. Here, recombinant human DNase I (commercial name Pulmozyme®), which is used for the treatment of cystic fibrosis in humans, was repurposed for the inhibition of lung metastases in the B16 melanoma model in mice. We found that Pulmozyme® strongly reduced migration and induced apoptosis of B16 cells in vitro and effectively inhibited metastases in lungs and liver in vivo. Pulmozyme® was shown to be two times more effective when administered intranasally (i.n.) than bovine DNase I, but intramuscular (i.m.) administration forced it to exhibit as high an antimetastatic activity as bovine DNase I. Both DNases administered to mice either i.m. or i.n. enhanced the DNase activity of blood serum to the level of healthy animals, significantly decreased cfDNA concentrations, efficiently degraded SINE and LINE repeats and c-Myc fragments in the bloodstream and induced apoptosis and disintegration of neutrophil extracellular traps in metastatic foci; as a result, this manifested as the inhibition of metastases spread. Thus, Pulmozyme®, which is already an approved drug, can be recommended for use in the treatment of lung metastases.
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Lee YR, Kim G, Lee HW, Tak WY, Park SY, Jang SY, Kweon YO, Park JG, Han YS, Chun JM, Han JR, Hur K. Long interspersed nuclear element-1 hypomethylation is associated with poor outcomes via the activation of ST18 in human hepatocellular carcinoma. Medicine (Baltimore) 2021; 100:e25552. [PMID: 33879706 PMCID: PMC8078304 DOI: 10.1097/md.0000000000025552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/25/2021] [Indexed: 01/04/2023] Open
Abstract
The level of long interspersed nuclear element-1 (LINE-1) methylation, representing the global deoxyribonucleic acid methylation level, could contribute to the prognosis of cancer via the activation of oncogenes. This study was performed to evaluate the prognostic implications of LINE-1 hypomethylation in patients with hepatocellular carcinoma (HCC) and the possible mechanisms related to oncogene activation.Seventy-seven HCC patients between October 2014 and September 2015 were enrolled in this prospective study. Quantitative pyrosequencing was performed to assess the LINE-1 methylation level of HCC and matched non-HCC tissue samples. The expression of suppression of tumorigenicity 18 was measured by immunohistochemistry and its correlation with LINE-1 methylation levels was examined.LINE-1 was significantly hypomethylated in the HCC tissue compared with the matched nontumor tissue (64.0 ± 11.6% vs 75.6 ± 4.0%, P < .001). LINE-1 hypomethylation was an independent risk factor for overall survival (hazard ratio = 27.291, P = .032) and disease progression (hazard ratio = 5.298, P = .005). The expression of suppression of tumorigenicity 18 was higher in the hypomethylated LINE-1 HCC tissue than the hypermethylated LINE-1 tumor tissue (P = .030).LINE-1 hypomethylation may serve as a potential prognostic marker for patients with HCC.
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Affiliation(s)
- Yu Rim Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Gyeonghwa Kim
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University
| | - Hye Won Lee
- Department of Pathology, Keimyung University School of Medicine
| | - Won Young Tak
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Soo Young Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Se Young Jang
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Young Oh Kweon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Jung Gil Park
- Department of Internal Medicine, College of Medicine, Yeungnam University
| | - Young Seok Han
- Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Jae Min Chun
- Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Ja Ryung Han
- Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University
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Keegan RM, Talbot LR, Chang YH, Metzger MJ, Dubnau J. Intercellular viral spread and intracellular transposition of Drosophila gypsy. PLoS Genet 2021; 17:e1009535. [PMID: 33886543 PMCID: PMC8096092 DOI: 10.1371/journal.pgen.1009535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 05/04/2021] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
It has become increasingly clear that retrotransposons (RTEs) are more widely expressed in somatic tissues than previously appreciated. RTE expression has been implicated in a myriad of biological processes ranging from normal development and aging, to age related diseases such as cancer and neurodegeneration. Long Terminal Repeat (LTR)-RTEs are evolutionary ancestors to, and share many features with, exogenous retroviruses. In fact, many organisms contain endogenous retroviruses (ERVs) derived from exogenous retroviruses that integrated into the germ line. These ERVs are inherited in Mendelian fashion like RTEs, and some retain the ability to transmit between cells like viruses, while others develop the ability to act as RTEs. The process of evolutionary transition between LTR-RTE and retroviruses is thought to involve multiple steps by which the element loses or gains the ability to transmit copies between cells versus the ability to replicate intracellularly. But, typically, these two modes of transmission are incompatible because they require assembly in different sub-cellular compartments. Like murine IAP/IAP-E elements, the gypsy family of retroelements in arthropods appear to sit along this evolutionary transition. Indeed, there is some evidence that gypsy may exhibit retroviral properties. Given that gypsy elements have been found to actively mobilize in neurons and glial cells during normal aging and in models of neurodegeneration, this raises the question of whether gypsy replication in somatic cells occurs via intracellular retrotransposition, intercellular viral spread, or some combination of the two. These modes of replication in somatic tissues would have quite different biological implications. Here, we demonstrate that Drosophila gypsy is capable of both cell-associated and cell-free viral transmission between cultured S2 cells of somatic origin. Further, we demonstrate that the ability of gypsy to move between cells is dependent upon a functional copy of its viral envelope protein. This argues that the gypsy element has transitioned from an RTE into a functional endogenous retrovirus with the acquisition of its envelope gene. On the other hand, we also find that intracellular retrotransposition of the same genomic copy of gypsy can occur in the absence of the Env protein. Thus, gypsy exhibits both intracellular retrotransposition and intercellular viral transmission as modes of replicating its genome.
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Affiliation(s)
- Richard M. Keegan
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Lillian R. Talbot
- Medical Scientist Training Program, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
| | - Michael J. Metzger
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Josh Dubnau
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
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Barone G, De Giudici G, Gimeno D, Lanzafame G, Podda F, Cannas C, Giuffrida A, Barchitta M, Agodi A, Mazzoleni P. Surface reactivity of Etna volcanic ash and evaluation of health risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143248. [PMID: 33183826 DOI: 10.1016/j.scitotenv.2020.143248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
This work is a part of a research project conducted in order to characterize the volcanic ash from Mount Etna, focusing in particular on the surface reactivity of ashes and possible consequence for human health. In this framework, a sampling campaign began on 16 March 2013, taking advantage of the intense volcanic activity on Etna. The interaction between volcanic ash and human organism was simulated treating two classes of representative Etnean particles with ultrapure water (grainsize of 850 um) and Gamble's solution mimic lug fluids (grainsize <38 μm) with the aim to evaluate the risk due to gastric and respiratory exposure to volcanic particles. The leachates were analysed by Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES), Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and Ionic Chromatography (CI) in order to highlight possible dangerous elements released in water solutions according to USGS protocol. Analyses of Gamble's solution highlighted a release of elements smaller than in watery solutions and always below the thresholds established by the Italian law. On the contrary, analyses of watery solutions evidenced, for some elements (B, Cd, Ni and As), levels higher than permitted by Italian law. Considering the effects of these elements on human health, further investigations are necessary and currently carried out in order to better constrain the release process and the specific effects on human organism.
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Affiliation(s)
- Germana Barone
- University of Catania, Department of Biological, Geological and Environmental Sciences, Corso Italia 57, 95129 Catania, Italy
| | - Giovanni De Giudici
- University of Cagliari, Department of Chemical and Geological Sciences, Universitary Campus, 09042 Monserrato, CA, Italy
| | - Domingo Gimeno
- Universitat de Barcelona, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, C/ Martí i Franquès s/n, 08028 Barcelona, Spain
| | - Gabriele Lanzafame
- University of Catania, Department of Biological, Geological and Environmental Sciences, Corso Italia 57, 95129 Catania, Italy
| | - Francesca Podda
- University of Cagliari, Department of Chemical and Geological Sciences, Universitary Campus, 09042 Monserrato, CA, Italy
| | - Carla Cannas
- University of Cagliari, Department of Chemical and Geological Sciences, Universitary Campus, 09042 Monserrato, CA, Italy
| | | | - Martina Barchitta
- University of Catania, Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", Via S. Sofia, 87, 95123 Catania, Italy
| | - Antonella Agodi
- University of Catania, Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", Via S. Sofia, 87, 95123 Catania, Italy
| | - Paolo Mazzoleni
- University of Catania, Department of Biological, Geological and Environmental Sciences, Corso Italia 57, 95129 Catania, Italy.
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12
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Liehr T. Repetitive Elements in Humans. Int J Mol Sci 2021; 22:ijms22042072. [PMID: 33669810 PMCID: PMC7922087 DOI: 10.3390/ijms22042072] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called 'genetic background', being able to at least potentially influence disease susceptibilities. Here, the known 'bad boys' among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
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Fukuda S, Varshney A, Fowler BJ, Wang SB, Narendran S, Ambati K, Yasuma T, Magagnoli J, Leung H, Hirahara S, Nagasaka Y, Yasuma R, Apicella I, Pereira F, Makin RD, Magner E, Liu X, Sun J, Wang M, Baker K, Marion KM, Huang X, Baghdasaryan E, Ambati M, Ambati VL, Pandey A, Pandya L, Cummings T, Banerjee D, Huang P, Yerramothu P, Tolstonog GV, Held U, Erwin JA, Paquola ACM, Herdy JR, Ogura Y, Terasaki H, Oshika T, Darwish S, Singh RK, Mozaffari S, Bhattarai D, Kim KB, Hardin JW, Bennett CL, Hinton DR, Hanson TE, Röver C, Parang K, Kerur N, Liu J, Werner BC, Sutton SS, Sadda SR, Schumann GG, Gelfand BD, Gage FH, Ambati J. Cytoplasmic synthesis of endogenous Alu complementary DNA via reverse transcription and implications in age-related macular degeneration. Proc Natl Acad Sci U S A 2021; 118:e2022751118. [PMID: 33526699 PMCID: PMC8017980 DOI: 10.1073/pnas.2022751118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alu retroelements propagate via retrotransposition by hijacking long interspersed nuclear element-1 (L1) reverse transcriptase (RT) and endonuclease activities. Reverse transcription of Alu RNA into complementary DNA (cDNA) is presumed to occur exclusively in the nucleus at the genomic integration site. Whether Alu cDNA is synthesized independently of genomic integration is unknown. Alu RNA promotes retinal pigmented epithelium (RPE) death in geographic atrophy, an untreatable type of age-related macular degeneration. We report that Alu RNA-induced RPE degeneration is mediated via cytoplasmic L1-reverse-transcribed Alu cDNA independently of retrotransposition. Alu RNA did not induce cDNA production or RPE degeneration in L1-inhibited animals or human cells. Alu reverse transcription can be initiated in the cytoplasm via self-priming of Alu RNA. In four health insurance databases, use of nucleoside RT inhibitors was associated with reduced risk of developing atrophic macular degeneration (pooled adjusted hazard ratio, 0.616; 95% confidence interval, 0.493-0.770), thus identifying inhibitors of this Alu replication cycle shunt as potential therapies for a major cause of blindness.
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Affiliation(s)
- Shinichi Fukuda
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Akhil Varshney
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Benjamin J Fowler
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536
| | - Shao-Bin Wang
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Siddharth Narendran
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Aravind Eye Hospital System, Madurai 625020, India
| | - Kameshwari Ambati
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Tetsuhiro Yasuma
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40536
- Department of Ophthalmology, Graduate School of Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Joseph Magagnoli
- Dorn Research Institute, Columbia Veterans Affairs Health Care System, Columbia, SC 29209
- Department of Clinical Pharmacy and Outcomes Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208
| | - Hannah Leung
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Shuichiro Hirahara
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan
| | - Yosuke Nagasaka
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Reo Yasuma
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, Graduate School of Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Ivana Apicella
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Felipe Pereira
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Ryan D Makin
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Eamonn Magner
- Department of Computer Science, University of Kentucky, Lexington, KY 40536
| | - Xinan Liu
- Department of Computer Science, University of Kentucky, Lexington, KY 40536
| | - Jian Sun
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Mo Wang
- Doheny Eye Institute, Los Angeles, CA 90033
| | | | | | - Xiwen Huang
- Department of Computer Science, University of Kentucky, Lexington, KY 40536
| | - Elmira Baghdasaryan
- Doheny Eye Institute, Los Angeles, CA 90033
- Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Meenakshi Ambati
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Center for Digital Image Evaluation, Charlottesville, VA 22901
| | - Vidya L Ambati
- Center for Digital Image Evaluation, Charlottesville, VA 22901
| | - Akshat Pandey
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Lekha Pandya
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Tammy Cummings
- Dorn Research Institute, Columbia Veterans Affairs Health Care System, Columbia, SC 29209
- Department of Clinical Pharmacy and Outcomes Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208
| | - Daipayan Banerjee
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Peirong Huang
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Praveen Yerramothu
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Genrich V Tolstonog
- Department of Otolaryngology-Head and Neck Surgery, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Ulrike Held
- Department of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Jennifer A Erwin
- The Lieber Institute for Brain Development, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Apua C M Paquola
- The Lieber Institute for Brain Development, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Joseph R Herdy
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Yuichiro Ogura
- Department of Ophthalmology, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Graduate School of Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Tetsuro Oshika
- Department of Ophthalmology, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Shaban Darwish
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, School of Pharmacy, Chapman University, Irvine, CA 92618
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Giza 12622, Egypt
| | - Ramendra K Singh
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, School of Pharmacy, Chapman University, Irvine, CA 92618
| | - Saghar Mozaffari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, School of Pharmacy, Chapman University, Irvine, CA 92618
| | - Deepak Bhattarai
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536
| | - Kyung Bo Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536
| | - James W Hardin
- Dorn Research Institute, Columbia Veterans Affairs Health Care System, Columbia, SC 29209
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC 29208
| | - Charles L Bennett
- Dorn Research Institute, Columbia Veterans Affairs Health Care System, Columbia, SC 29209
- Department of Clinical Pharmacy and Outcomes Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208
- Center for Medication Safety and Efficacy, College of Pharmacy, University of South Carolina, Columbia, SC 29208
| | - David R Hinton
- Department of Ophthalmology, University of Southern California Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Timothy E Hanson
- Medtronic, Inc., Minneapolis, MN 55432
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455
| | - Christian Röver
- Department of Medical Statistics, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, School of Pharmacy, Chapman University, Irvine, CA 92618
| | - Nagaraj Kerur
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Jinze Liu
- Department of Computer Science, University of Kentucky, Lexington, KY 40536
| | - Brian C Werner
- Department of Orthopaedic Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - S Scott Sutton
- Dorn Research Institute, Columbia Veterans Affairs Health Care System, Columbia, SC 29209
- Department of Clinical Pharmacy and Outcomes Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208
| | - Srinivas R Sadda
- Doheny Eye Institute, Los Angeles, CA 90033
- Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Gerald G Schumann
- Department of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Bradley D Gelfand
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Biomedical Engineering, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037;
| | - Jayakrishna Ambati
- Center for Advanced Vision Science, School of Medicine, University of Virginia, Charlottesville, VA 22908;
- Department of Ophthalmology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908
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Maugeri A. The Effects of Dietary Interventions on DNA Methylation: Implications for Obesity Management. Int J Mol Sci 2020; 21:ijms21228670. [PMID: 33212948 PMCID: PMC7698434 DOI: 10.3390/ijms21228670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Previous evidence from in vivo and observational research suggested how dietary factors might affect DNA methylation signatures involved in obesity risk. However, findings from experimental studies are still scarce and, if present, not so clear. The current review summarizes studies investigating the effect of dietary interventions on DNA methylation in the general population and especially in people at risk for or with obesity. Overall, these studies suggest how dietary interventions may induce DNA methylation changes, which in turn are likely related to the risk of obesity and to different response to weight loss programs. These findings might explain the high interindividual variation in weight loss after a dietary intervention, with some people losing a lot of weight while others much less so. However, the interactions between genetic, epigenetic, environmental and lifestyle factors make the whole framework even more complex and further studies are needed to support the hypothesis of personalized interventions against obesity.
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Affiliation(s)
- Andrea Maugeri
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, 95123 Catania, Italy
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15
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Misawa K, Yamada S, Mima M, Nakagawa T, Kurokawa T, Imai A, Mochizuki D, Shinmura D, Yamada T, Kita J, Ishikawa R, Yamaguchi Y, Misawa Y, Kanazawa T, Kawasaki H, Mineta H. Long interspersed nuclear element 1 hypomethylation has novel prognostic value and potential utility in liquid biopsy for oral cavity cancer. Biomark Res 2020; 8:53. [PMID: 33110605 PMCID: PMC7585304 DOI: 10.1186/s40364-020-00235-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Background New biomarkers are urgently needed to improve personalized treatment approaches for head and neck squamous cell carcinoma (HNSCC). Global DNA hypomethylation has wide-ranging functions in multistep carcinogenesis, and the hypomethylation of long interspersed nucleotide element-1 (LINE-1) is related to increased retrotransposon activity and induced genome instability. However, little information is available regarding LINE-1 hypomethylation and its prognostic implications in HNSCC. Methods In this study, we analyzed LINE-1 hypomethylation levels in a well-characterized dataset of 317 primary HNSCC tissues and 225 matched pairs of normal mucosa tissues, along with five oral cavity cancer (OCC) circulating tumor DNA (ctDNA) samples using quantitative real-time methylation and unmethylation PCR. The analysis was performed according to various clinical characteristics and prognostic implications. Results The results demonstrated that LINE-1 hypomethylation levels were significantly higher in the HNSCC tissues than in corresponding normal tissues from the same individuals (P < 0.001). Univariate analysis revealed that high levels of LINE-1 hypomethylation were correlated with poor disease-free survival (DFS; log-rank test, P = 0.038), whereas multivariate analysis demonstrated that they were significant independent prognostic factor for DFS (hazard ratio: 2.10, 95% confidence interval: 1.02–4.36; P = 0.045). Moreover, samples with high LINE-1 hypomethylation levels exhibited the greatest decrease in 5-hydroxymethylcytosine (5-hmC) levels and increase in tumor-suppressor gene methylation index (P = 0.006 and P < 0.001, respectively). Further, ctDNA studies also showed that LINE-1 hypomethylation had high predictive ability in OCC. Conclusions LINE-1 hypomethylation is associated with a higher risk of early OCC relapse, and is hence, a potential predictive biomarker for OCC. Furthermore, 5-hmC levels also exhibited predictive potential in OCC, based on their inverse correlation with LINE-1 hypomethylation levels. LINE-1 hypomethylation analysis, therefore, has applications in determining patient prognosis and real-time surveillance of disease recurrence, and could serve as an alternative method for OCC screening. Supplementary information Supplementary information accompanies this paper at 10.1186/s40364-020-00235-y.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Satoshi Yamada
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Masato Mima
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Takuya Nakagawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoya Kurokawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Imai
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Daiki Mochizuki
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Daichi Shinmura
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Taiki Yamada
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Junya Kita
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Ryuji Ishikawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Yuki Yamaguchi
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Yuki Misawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Takeharu Kanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi Japan
| | - Hideya Kawasaki
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Mineta
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
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Cusack M, King HW, Spingardi P, Kessler BM, Klose RJ, Kriaucionis S. Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors. Genome Res 2020; 30:1393-1406. [PMID: 32963030 PMCID: PMC7605266 DOI: 10.1101/gr.257576.119] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 08/21/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at retrotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements has elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation-deficient cells demonstrates that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression.
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Affiliation(s)
- Martin Cusack
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Paolo Spingardi
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7DQ, United Kingdom;
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Maugeri A, Barchitta M. How Dietary Factors Affect DNA Methylation: Lesson from Epidemiological Studies. MEDICINA (KAUNAS, LITHUANIA) 2020; 56:E374. [PMID: 32722411 PMCID: PMC7466216 DOI: 10.3390/medicina56080374] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023]
Abstract
Over the past decades, DNA methylation has been proposed as a molecular mechanism underlying the positive or negative effects of diet on human health. Despite the number of studies on this topic is rapidly increasing, the relationship between dietary factors, changes in DNA methylation and health outcomes remains unclear. In this review, we summarize the literature from observational studies (cross-sectional, retrospective, or prospective) which examined the association of dietary factors (nutrients, foods, and dietary patterns) with DNA methylation markers among diseased or healthy people during the lifetime. Next, we discuss the methodological pitfalls by examining strengths and limitations of published studies. Finally, we close with a discussion on future challenges of this field of research, raising the need for large-size prospective studies evaluating the association between diet and DNA methylation in health and diseases for appropriate public health strategies.
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Affiliation(s)
- Andrea Maugeri
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy;
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18
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Tawfik DS. Enzyme promiscuity and evolution in light of cellular metabolism. FEBS J 2020. [PMID: 32250557 DOI: 10.1111/febs.12650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This Special Issue is composed of 10 reviews that delve into the intricacies behind enzyme promiscuity and evolution, an area that is of increasing interest in the biological research community. In particular, the reviews in this Special Issue explore enzyme promiscuity and evolution in the context of cellular metabolism, as discussed in this introductory Editorial. It is our hope that you enjoy these fascinating and informative reviews and we wish to thank the authors for their compelling contributions to The FEBS Journal. doi: 10.1111/febs.12650.
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Affiliation(s)
- Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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19
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Clayton EA, Rishishwar L, Huang TC, Gulati S, Ban D, McDonald JF, Jordan IK. An atlas of transposable element-derived alternative splicing in cancer. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190342. [PMID: 32075558 PMCID: PMC7061986 DOI: 10.1098/rstb.2019.0342] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Transposable element (TE)-derived sequences comprise more than half of the human genome, and their presence has been documented to alter gene expression in a number of different ways, including the generation of alternatively spliced transcript isoforms. Alternative splicing has been associated with tumorigenesis for a number of different cancers. The objective of this study was to broadly characterize the role of human TEs in generating alternatively spliced transcript isoforms in cancer. To do so, we screened for the presence of TE-derived sequences co-located with alternative splice sites that are differentially used in normal versus cancer tissues. We analysed a comprehensive set of alternative splice variants characterized for 614 matched normal-tumour tissue pairs across 13 cancer types, resulting in the discovery of 4820 TE-generated alternative splice events distributed among 723 cancer-associated genes. Short interspersed nuclear elements (Alu) and long interspersed nuclear elements (L1) were found to contribute the majority of TE-generated alternative splice sites in cancer genes. A number of cancer-associated genes, including MYH11, WHSC1 and CANT1, were shown to have overexpressed TE-derived isoforms across a range of cancer types. TE-derived isoforms were also linked to cancer-specific fusion transcripts, suggesting a novel mechanism for the generation of transcriptome diversity via trans-splicing mediated by dispersed TE repeats. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Evan A. Clayton
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Tzu-Chuan Huang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Saurabh Gulati
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dongjo Ban
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - John F. McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
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Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
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21
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Pan Y, Zhang Y, Peng Z, Ba X, Zhao W, Li X, Guo Y, Ouyang G, Zhang S, Zhang B. Enrichment and determination of sixteen trace polycyclic aromatic hydrocarbons in barbecue smoke by using a continuous magnetic solid‐phase extraction and gas chromatography‐mass spectrometry. SEPARATION SCIENCE PLUS 2020. [DOI: 10.1002/sscp.201900068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yan Pan
- Chemistry CollegeZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Yanhao Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of ChemistryHong Kong Baptist University Hong Kong 999077 P. R. China
| | - Zifang Peng
- Chemistry CollegeZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Xin Ba
- Chemistry CollegeZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Wuduo Zhao
- Center of Advanced Analysis and Computational ScienceKey Laboratory of Molecular Sensing and Harmful Substances Detection TechnologyZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Xinglin Li
- Chemistry CollegeZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Yun Guo
- Center of Advanced Analysis and Computational ScienceKey Laboratory of Molecular Sensing and Harmful Substances Detection TechnologyZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Gangfeng Ouyang
- Center of Advanced Analysis and Computational ScienceKey Laboratory of Molecular Sensing and Harmful Substances Detection TechnologyZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Shusheng Zhang
- Center of Advanced Analysis and Computational ScienceKey Laboratory of Molecular Sensing and Harmful Substances Detection TechnologyZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
| | - Bin Zhang
- Physics CollegeZhengzhou University Kexue Avenue 100 Zhengzhou Henan 450001 P. R. China
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22
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Adney EM, Ochmann MT, Sil S, Truong DM, Mita P, Wang X, Kahler DJ, Fenyö D, Holt LJ, Boeke JD. Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function. Genetics 2019; 213:1401-1414. [PMID: 31666291 PMCID: PMC6893370 DOI: 10.1534/genetics.119.302601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022] Open
Abstract
Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only autonomous active transposable element in the human genome. The L1-encoded proteins ORF1p and ORF2p enable the element to jump from one locus to another via a "copy-and-paste" mechanism. ORF1p is an RNA-binding protein, and ORF2p has endonuclease and reverse transcriptase activities. The huge number of truncated L1 remnants in the human genome suggests that the host has likely evolved mechanisms to prevent full L1 replication, and thereby decrease the proliferation of active elements and reduce the mutagenic potential of L1. In turn, L1 appears to have a minimized length to increase the probability of successful full-length replication. This streamlining would be expected to lead to high information density. Here, we describe the construction and initial characterization of a library of 538 consecutive trialanine substitutions that scan along ORF1p and ORF2p to identify functionally important regions. In accordance with the streamlining hypothesis, retrotransposition was overall very sensitive to mutations in ORF1p and ORF2p; only 16% of trialanine mutants retained near-wild-type (WT) activity. All ORF1p mutants formed near-WT levels of mRNA transcripts and 75% formed near-WT levels of protein. Two ORF1p mutants presented a unique nucleolar-relocalization phenotype. Regions of ORF2p that are sensitive to mutagenesis but lack phylogenetic conservation were also identified. We provide comprehensive information on the regions most critical to retrotransposition. This resource will guide future studies of intermolecular interactions that form with RNA, proteins, and target DNA throughout the L1 life cycle.
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Affiliation(s)
- Emily M Adney
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Matthias T Ochmann
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Srinjoy Sil
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - David M Truong
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Paolo Mita
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Xuya Wang
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - David J Kahler
- High Throughput Biology Laboratory, NYU Langone Health, New York 10016
| | - David Fenyö
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Liam J Holt
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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Interferon-Inducible MicroRNA miR-128 Modulates HIV-1 Replication by Targeting TNPO3 mRNA. J Virol 2019; 93:JVI.00364-19. [PMID: 31341054 DOI: 10.1128/jvi.00364-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
The HIV/AIDS pandemic remains an important threat to human health. We have recently demonstrated that a novel microRNA (miR), miR-128, represses retrotransposon long interspaced element 1 (L1) by a dual mechanism, namely, by directly targeting the coding region of the L1 RNA and by repressing a required nuclear import factor (TNPO1). We have further determined that miR-128 represses the expression of all three TNPO proteins (transportins TNPO1, TNPO2, and TNPO3). Here, we establish that miR-128 also influences HIV-1 replication by repressing TNPO3, a factor that regulates HIV-1 nuclear import and viral; replication of TNPO3 is well established to regulate HIV-1 nuclear import and viral replication. Here, we report that type I interferon (IFN)-inducible miR-128 directly targets two sites in the TNPO3 mRNA, significantly downregulating TNPO3 mRNA and protein expression levels. Challenging miR-modulated Jurkat cells or primary CD4+ T-cells with wild-type (WT), replication-competent HIV-1 demonstrated that miR-128 reduces viral replication and delays spreading of infection. Manipulation of miR-128 levels in HIV-1 target cell lines and in primary CD4+ T-cells by overexpression or knockdown showed that reduction of TNPO3 levels by miR-128 significantly affects HIV-1 replication but not murine leukemia virus (MLV) infection and that miR-128 modulation of HIV-1 replication is reduced with TNPO3-independent HIV-1 virus, suggesting that miR-128-indued TNPO3 repression contributes to the inhibition of HIV-1 replication. Finally, we determine that anti-miR-128 partly neutralizes the IFN-mediated block of HIV-1. Thus, we have established a novel role of miR-128 in antiviral defense in human cells, namely inhibiting HIV-1 replication by altering the cellular milieu through targeting factors that include TNPO3.IMPORTANCE HIV-1 is the causative agent of AIDS. During HIV-1 infection, type I interferons (IFNs) are induced, and their effectors limit HIV-1 replication at multiple steps in its life cycle. However, the cellular targets of INFs are still largely unknown. In this study, we identified the interferon-inducible microRNA (miR) miR-128, a novel antiviral mediator that suppresses the expression of the host gene TNPO3, which is known to modulate HIV-1 replication. Notably, we observe that anti-miR-128 partly neutralizes the IFN-mediated block of HIV-1. Elucidation of the mechanisms through which miR-128 impairs HIV-1 replication may provide novel candidates for the development of therapeutic interventions.
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24
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Navarro FCP, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput Biol 2019; 15:e1007293. [PMID: 31425522 PMCID: PMC6715295 DOI: 10.1371/journal.pcbi.1007293] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/29/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022] Open
Abstract
The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome. Repetitive sequences, such as LINEs, comprise more than half of the human genome. Due to their repetitive nature, LINEs are hard to grasp. In particular, we find that pervasive transcription is a major confounding factor in transcriptome data. We observe that, on average, more than 90% of LINE signal derives from pervasive transcription. To investigate this issue, we developed and validated a new method called TeXP. TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells. By removing the pervasive transcription component, we find that (1) LINE-1 is broadly expressed in healthy somatic tissues; (2) Adult brain show small levels of LINE transcription and; (3) LINE-1 transcription level is correlated with tissue cell turnover. Our method thus offers insights into how repetitive sequences and influenced by pervasive transcription. Moreover, we uncover the activity of LINE-1 in somatic tissues at an unmatched scale.
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Affiliation(s)
- Fabio CP Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jacob Hoops
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Lauren Bellfy
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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25
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Barchitta M, Maugeri A, Li Destri G, Basile G, Agodi A. Epigenetic Biomarkers in Colorectal Cancer Patients Receiving Adjuvant or Neoadjuvant Therapy: A Systematic Review of Epidemiological Studies. Int J Mol Sci 2019; 20:ijms20153842. [PMID: 31390840 PMCID: PMC6696286 DOI: 10.3390/ijms20153842] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) represents the third-most common cancer worldwide and one of the main challenges for public health. Despite great strides in the application of neoadjuvant and adjuvant therapies for rectal and colon cancer patients, each of these treatments is still associated with certain adverse effects and different response rates. Thus, there is an urgent need for identifying novel potential biomarkers that might guide personalized treatments for specific subgroups of patients. However, until now, there are no biomarkers to predict the manifestation of adverse effects and the response to treatment in CRC patients. Herein, we provide a systematic review of epidemiological studies investigating epigenetic biomarkers in CRC patients receiving neoadjuvant or adjuvant therapy, and their potential role for the prediction of outcomes and response to treatment. With this aim in mind, we identified several epigenetic markers in CRC patients who received surgery with adjuvant or neoadjuvant therapy. However, none of them currently has the robustness to be translated into the clinical setting. Thus, more efforts and further large-size prospective studies and/or trials should be encouraged to develop epigenetic biomarker panels for personalized prevention and medicine in CRC cancer.
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Affiliation(s)
- Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, via S. Sofia, 87, 95123 Catania, Italy
| | - Andrea Maugeri
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, via S. Sofia, 87, 95123 Catania, Italy
| | - Giovanni Li Destri
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, via S. Sofia, 87, 95123 Catania, Italy
| | - Guido Basile
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, via S. Sofia, 78, 95123 Catania, Italy
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, via S. Sofia, 87, 95123 Catania, Italy.
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26
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Banuelos-Sanchez G, Sanchez L, Benitez-Guijarro M, Sanchez-Carnerero V, Salvador-Palomeque C, Tristan-Ramos P, Benkaddour-Boumzaouad M, Morell S, Garcia-Puche JL, Heras SR, Franco-Montalban F, Tamayo JA, Garcia-Perez JL. Synthesis and Characterization of Specific Reverse Transcriptase Inhibitors for Mammalian LINE-1 Retrotransposons. Cell Chem Biol 2019; 26:1095-1109.e14. [DOI: 10.1016/j.chembiol.2019.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/29/2019] [Accepted: 04/19/2019] [Indexed: 12/24/2022]
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27
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Chang YH, Keegan RM, Prazak L, Dubnau J. Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies. PLoS Biol 2019; 17:e3000278. [PMID: 31095565 PMCID: PMC6541305 DOI: 10.1371/journal.pbio.3000278] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/29/2019] [Accepted: 05/03/2019] [Indexed: 12/11/2022] Open
Abstract
Evidence is rapidly mounting that transposable element (TE) expression and replication may impact biology more widely than previously thought. This includes potential effects on normal physiology of somatic tissues and dysfunctional impacts in diseases associated with aging, such as cancer and neurodegeneration. Investigation of the biological impact of mobile elements in somatic cells will be greatly facilitated by the use of donor elements that are engineered to report de novo events in vivo. In multicellular organisms, reporter constructs demonstrating engineered long interspersed nuclear element (LINE-1; L1) mobilization have been in use for quite some time, and strategies similar to L1 retrotransposition reporter assays have been developed to report replication of Ty1 elements in yeast and mouse intracisternal A particle (IAP) long terminal repeat (LTR) retrotransposons in cultivated cells. We describe a novel approach termed cellular labeling of endogenous retrovirus replication (CLEVR), which reports replication of the gypsy element within specific cells in vivo in Drosophila. The gypsy-CLEVR reporter reveals gypsy replication both in cell culture and in individual neurons and glial cells of the aging adult fly. We also demonstrate that the gypsy-CLEVR replication rate is increased when the short interfering RNA (siRNA) silencing system is genetically disrupted. This CLEVR strategy makes use of universally conserved features of retroviruses and should be widely applicable to other LTR retrotransposons, endogenous retroviruses (ERVs), and exogenous retroviruses.
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Affiliation(s)
- Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
| | - Richard M. Keegan
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
| | - Lisa Prazak
- Biology, Farmingdale State College, Farmingdale, New York, United States of America
| | - Josh Dubnau
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
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28
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Carmignac V, Barberet J, Iranzo J, Quéré R, Guilleman M, Bourc’his D, Fauque P. Effects of assisted reproductive technologies on transposon regulation in the mouse pre-implanted embryo. Hum Reprod 2019; 34:612-622. [DOI: 10.1093/humrep/dez020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 01/25/2019] [Accepted: 02/12/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
| | - Julie Barberet
- Université Bourgogne Franche-Comté – INSERM UMR1231, Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, Dijon, France
| | - Julian Iranzo
- Institut Curie, PSL University, CNRS, INSERM, Paris, France
| | - Ronan Quéré
- Université Bourgogne Franche-Comté – INSERM UMR1231, Dijon, France
| | - Magali Guilleman
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, Dijon, France
| | | | - Patricia Fauque
- Université Bourgogne Franche-Comté – INSERM UMR1231, Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, Dijon, France
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29
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Rozek LS, Virani S, Bellile EL, Taylor JMG, Sartor MA, Zarins KR, Virani A, Cote C, Worden FP, Mark MEP, McLean SA, Duffy SA, Yoo GH, Saba NF, Shin DM, Kucuk O, Wolf GT. Soy Isoflavone Supplementation Increases Long Interspersed Nucleotide Element-1 (LINE-1) Methylation in Head and Neck Squamous Cell Carcinoma. Nutr Cancer 2019; 71:772-780. [PMID: 30862188 PMCID: PMC6513708 DOI: 10.1080/01635581.2019.1577981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/13/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022]
Abstract
AIM Soy isoflavones have been suggested as epigenetic modulating agents with effects that could be important in carcinogenesis. Hypomethylation of LINE-1 has been associated with head and neck squamous cell carcinoma (HNSCC) development from oral premalignant lesions and with poor prognosis. To determine if neoadjuvant soy isoflavone supplementation could modulate LINE-1 methylation in HNSCC, we undertook a clinical trial. METHODS Thirty-nine patients received 2-3 weeks of soy isoflavone supplements (300 mg/day) orally prior to surgery. Methylation of LINE-1, and 6 other genes was measured by pyrosequencing in biopsy, resection, and whole blood (WB) specimens. Changes in methylation were tested using paired t tests and ANOVA. Median follow up was 45 months. RESULTS LINE-1 methylation increased significantly after soy isoflavone (P < 0.005). Amount of change correlated positively with days of isoflavone taken (P = 0.04). Similar changes were not seen in corresponding WB samples. No significant changes in tumor or blood methylation levels were seen in the other candidate genes. CONCLUSION This is the first demonstration of in vivo increases in tissue-specific global methylation associated with soy isoflavone intake in patients with HNSCC. Prior associations of LINE-1 hypomethylation with genetic instability, carcinogenesis, and prognosis suggest that soy isoflavones maybe potential chemopreventive agents in HNSCC.
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Affiliation(s)
- Laura S Rozek
- a University of Michigan , Ann Arbor , Michigan, USA
| | - Shama Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - A Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | - C Cote
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - George H Yoo
- c Karmanos Cancer Institute , Wayne State University , Detroit , Michigan 48201, USA
| | - Nabil F Saba
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Dong M Shin
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Omer Kucuk
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
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30
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Jiao J, Sagnelli M, Shi B, Fang Y, Shen Z, Tang T, Dong B, Li D, Wang X. Genetic and epigenetic characteristics in ovarian tissues from polycystic ovary syndrome patients with irregular menstruation resemble those of ovarian cancer. BMC Endocr Disord 2019; 19:30. [PMID: 30866919 PMCID: PMC6416936 DOI: 10.1186/s12902-019-0356-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/03/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Irregular menstruation is clinically associated with an increased risk for ovarian cancer and disease-related mortality. This relationship remains poorly understood, and a mechanism explaining it has yet to be described. METHODS Ovarian tissues from women with polycystic ovary syndrome (PCOS) and regular menstruation (n = 10) or irregular menstruation (n = 10) were subjected to DNA methylation sequencing, real-time PCR array, whole-exome sequencing, and bioinformatics analysis. RESULTS We demonstrated that ovarian tissue from PCOS patients with irregular menstruation displayed global DNA hypomethylation, as well as hypomethylation at several functionally and oncologically significant regions. Furthermore, we showed that several cancer-related genes were aberrantly expressed in ovarian tissue from patients with irregular menstruation, and that their mRNA and microRNA profiles shared appreciable levels of coincidence with those from ovarian cancer tissue. We identified multiple point mutations in both the BRCA1 and MLH1 genes in patients with irregular menstruation, and predicted the potential pathogenicity of these mutations using bioinformatics analyses. CONCLUSIONS Due to the nature of ovarian cancer, it is important to broaden our understanding of the pathogenesis and risk factors of the disease. Herein, we provide the first description of a genetic and epigenetic basis for the clinical relationship between irregular menstruation and an increased risk for ovarian cancer.
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Affiliation(s)
- Jiao Jiao
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Matthew Sagnelli
- University of Connecticut School of Medicine, Farmington, CT 06030 USA
| | - Bei Shi
- Department of Physiology, College of Life Science, China Medical University, Shenyang, 110122 China
- Functional Laboratory Center, College of Basic Medical Science, China Medical University, Shenyang, 110122 China
| | - Yuanyuan Fang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Ziqi Shen
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Tianyu Tang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Bingying Dong
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Da Li
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
| | - Xiuxia Wang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004 China
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31
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Characterization of SIRT1/DNMTs Functions and LINE-1 Methylation in Patients with Age-Related Macular Degeneration. J Clin Med 2019; 8:jcm8020159. [PMID: 30717113 PMCID: PMC6406755 DOI: 10.3390/jcm8020159] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 01/27/2019] [Accepted: 01/29/2019] [Indexed: 11/17/2022] Open
Abstract
Previous studies proposed the application of DNA methylation signatures as clinical biomarkers of age-related macular degeneration (AMD). However, the characterization of Long Interspersed Nuclear Element-1 (LINE-1) methylation levels—a surrogate marker of global DNA methylation—in AMD patients has not been investigated so far. In the present study, we first characterized DNA methyltransferases (DNMTs) and Sirtuin 1 (SIRT1) functions in blood samples of 40 AMD patients and 10 age- and sex-matched controls. Then, we evaluated whether changes in DNMTs functions were associated with different LINE-1 methylation levels in leukocyte DNA. We demonstrated that total DNMTs activity was 48% higher in AMD patients than in controls (p = 0.005). AMD patients also exhibited up-regulation of DNMT1 and DNMT3B expression (FC = 2.6; p = 0.003 and FC = 2.4; p = 0.018, respectively). In line with increased DNMTs functions, the LINE-1 methylation level was higher in AMD patients than in controls (mean = 69.10%; SE = 0.68 vs. mean = 65.73%; SE = 0.59; p = 0.020). All p-values were adjusted by Bonferroni correction. In AMD patients, LINE-1 methylation level was positively associated with total DNMTs activity (r = 0.694; p < 0.001), DNMT1 (r = 0.579; p < 0.001), and DNMT3B (r = 0.521; p = 0.001) expression. Our results encourage further large-size prospective research to understand the relationship between LINE-1 methylation and AMD aetiology, and its usefulness in the clinical setting.
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Jaguva Vasudevan AA, Kreimer U, Schulz WA, Krikoni A, Schumann GG, Häussinger D, Münk C, Goering W. APOBEC3B Activity Is Prevalent in Urothelial Carcinoma Cells and Only Slightly Affected by LINE-1 Expression. Front Microbiol 2018; 9:2088. [PMID: 30233553 PMCID: PMC6132077 DOI: 10.3389/fmicb.2018.02088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022] Open
Abstract
The most common mutational signature in urothelial carcinoma (UC), the most common type of urinary bladder cancer is assumed to be caused by the misdirected activity of APOBEC3 (A3) cytidine deaminases, especially A3A or A3B, which are known to normally restrict the propagation of exogenous viruses and endogenous retroelements such as LINE-1 (L1). The involvement of A3 proteins in urothelial carcinogenesis is unexpected because, to date, UC is thought to be caused by chemical carcinogens rather than viral activity. Therefore, we explored the relationship between A3 expression and L1 activity, which is generally upregulated in UC. We found that UC cell lines highly express A3B and in some cases A3G, but not A3A, and exhibit corresponding cytidine deamination activity in vitro. While we observed evidence suggesting that L1 expression has a weak positive effect on A3B and A3G expression and A3B promoter activity, neither efficient siRNA-mediated knockdown nor overexpression of functional L1 elements affected catalytic activity of A3 proteins consistently. However, L1 knockdown diminished proliferation of a UC cell line exhibiting robust endogenous L1 expression, but had little impact on a cell line with low L1 expression levels. Our results indicate that UC cells express A3B at levels exceeding A3A levels by far, making A3B the prime candidate for causing genomic mutations. Our data provide evidence that L1 activation constitutes only a minor and negligible factor involved in induction or upregulation of endogenous A3 expression in UC.
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Affiliation(s)
- Ananda Ayyappan Jaguva Vasudevan
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ulrike Kreimer
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Aikaterini Krikoni
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, 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
| | - Wolfgang Goering
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Pathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Maugeri A, Barchitta M, Mazzone MG, Giuliano F, Basile G, Agodi A. Resveratrol Modulates SIRT1 and DNMT Functions and Restores LINE-1 Methylation Levels in ARPE-19 Cells under Oxidative Stress and Inflammation. Int J Mol Sci 2018; 19:E2118. [PMID: 30037017 PMCID: PMC6073744 DOI: 10.3390/ijms19072118] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022] Open
Abstract
The role of epigenetic alterations in the pathogenesis of retinal degenerative diseases, including age-related macular degeneration (AMD), has been pending so far. Our study investigated the effect of oxidative stress and inflammation on DNA methyltransferases (DNMTs) and Sirtuin 1 (SIRT1) functions, as well as on long interspersed nuclear element-1 (LINE-1) methylation, in human retinal pigment epithelial (ARPE-19) cells. Therefore, we evaluated whether treatment with resveratrol may modulate DNMT and SIRT1 functions and restore changes in LINE-1 methylation. Cells were treated with 25 mU/mL glucose oxidase (GOx) or 10 µg/mL lipopolysaccharide (LPS) to mimic oxidative or inflammatory conditions, respectively. Oxidative stress decreased DNMT1, DNMT3a, DNMT3b, and SIRT1 expression (p-values < 0.05), as well as total DNMTs (-28.5%; p < 0.0001) and SIRT1 (-29.0%; p < 0.0001) activities. Similarly, inflammatory condition decreased DNMT1 and SIRT1 expression (p-values < 0.05), as well as total DNMTs (-14.9%; p = 0.007) and SIRT1 (-20.1%; p < 0.002) activities. Interestingly, GOx- and LPS-treated cells exhibited lower LINE-1 methylation compared to controls (p-values < 0.001). We also demonstrated that treatment with 10 μM resveratrol for 24 h counteracted the detrimental effect on DNMT and SIRT1 functions, and LINE-1 methylation, in cells under oxidative and inflammatory conditions. However, further studies should explore the perspectives of resveratrol as a suitable strategy for the prevention and/or treatment of retinal degenerative diseases.
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Affiliation(s)
- Andrea Maugeri
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, via S. Sofia, 87, 95123 Catania, Italy.
| | - Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, via S. Sofia, 87, 95123 Catania, Italy.
| | - Maria Grazia Mazzone
- SIFI SpA, Research and Development Department, Via Ercole Patti 36, 95025 Catania, Italy.
| | - Francesco Giuliano
- SIFI SpA, Research and Development Department, Via Ercole Patti 36, 95025 Catania, Italy.
| | - Guido Basile
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Via Plebiscito, 628, 95124 Catania, Italy.
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, via S. Sofia, 87, 95123 Catania, Italy.
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Faulkner GJ, Billon V. L1 retrotransposition in the soma: a field jumping ahead. Mob DNA 2018; 9:22. [PMID: 30002735 PMCID: PMC6035798 DOI: 10.1186/s13100-018-0128-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022] Open
Abstract
Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.
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Affiliation(s)
- Geoffrey J. Faulkner
- Mater Research Institute – University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
| | - Victor Billon
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 61 Avenue du Président Wilson, 94230 Cachan, France
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Curcumin Modulates DNA Methyltransferase Functions in a Cellular Model of Diabetic Retinopathy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:5407482. [PMID: 30057682 PMCID: PMC6051042 DOI: 10.1155/2018/5407482] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
Hyperglycaemia-induced oxidative stress appears to be involved in the aetiology of diabetic retinopathy (DR), a major public health issue, via altering DNA methylation process. We investigated the effect of hyperglycaemia on retinal DNA methyltransferase (DNMT) expression in diabetic mice, using Gene Expression Omnibus datasets. We also evaluated the effect of curcumin both on high glucose-induced reactive oxygen species (ROS) production and altered DNMT functions, in a cellular model of DR. We observed that three months of hyperglycaemia, in insulin-deficient Ins2Akita mice, decrease DNMT1 and DNMT3a expression levels. In retinal pigment epithelium (RPE) cells, we also demonstrated that high glucose-induced ROS production precedes upregulation of DNMT expression and activity, suggesting that changes in DNMT function could be mediated by oxidative stress via a potential dual effect. The early effect results in decreased DNMT activity, accompanied by the highest ROS production, while long-term oxidative stress increases DNMT activity and DNMT1 expression. Interestingly, treatment with 25 μM curcumin for 6 hours restores ROS production, as well as DNMT functions, altered by the exposure of RPE to acute and chronic high glucose concentration. Our study suggests that curcumin may represent an effective antioxidant compound against DR, via restoring oxidative stress and DNMT functions, though further studies are recommended.
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Schauer SN, Carreira PE, Shukla R, Gerhardt DJ, Gerdes P, Sanchez-Luque FJ, Nicoli P, Kindlova M, Ghisletti S, Santos AD, Rapoud D, Samuel D, Faivre J, Ewing AD, Richardson SR, Faulkner GJ. L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Res 2018; 28:639-653. [PMID: 29643204 PMCID: PMC5932605 DOI: 10.1101/gr.226993.117] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/26/2018] [Indexed: 12/15/2022]
Abstract
The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is a continuing source of germline and somatic mutagenesis in mammals. Deregulated L1 activity is a hallmark of cancer, and L1 mutagenesis has been described in numerous human malignancies. We previously employed retrotransposon capture sequencing (RC-seq) to analyze hepatocellular carcinoma (HCC) samples from patients infected with hepatitis B or hepatitis C virus and identified L1 variants responsible for activating oncogenic pathways. Here, we have applied RC-seq and whole-genome sequencing (WGS) to an Abcb4 (Mdr2)-/- mouse model of hepatic carcinogenesis and demonstrated for the first time that L1 mobilization occurs in murine tumors. In 12 HCC nodules obtained from 10 animals, we validated four somatic L1 insertions by PCR and capillary sequencing, including TF subfamily elements, and one GF subfamily example. One of the TF insertions carried a 3' transduction, allowing us to identify its donor L1 and to demonstrate that this full-length TF element retained retrotransposition capacity in cultured cancer cells. Using RC-seq, we also identified eight tumor-specific L1 insertions from 25 HCC patients with a history of alcohol abuse. Finally, we used RC-seq and WGS to identify three tumor-specific L1 insertions among 10 intra-hepatic cholangiocarcinoma (ICC) patients, including one insertion traced to a donor L1 on Chromosome 22 known to be highly active in other cancers. This study reveals L1 mobilization as a common feature of hepatocarcinogenesis in mammals, demonstrating that the phenomenon is not restricted to human viral HCC etiologies and is encountered in murine liver tumors.
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Affiliation(s)
- Stephanie N Schauer
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ruchi Shukla
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- Invenra, Incorporated, Madison, Wisconsin 53719, USA
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Paola Nicoli
- Department of Experimental Oncology, European Institute of Oncology, 20146 Milan, Italy
| | - Michaela Kindlova
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | | | - Alexandre Dos Santos
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Delphine Rapoud
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Didier Samuel
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Pôle de Biologie Médicale, Paul-Brousse University Hospital, Villejuif 94800, France
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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Khazina E, Weichenrieder O. Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. eLife 2018; 7:34960. [PMID: 29565245 PMCID: PMC5940361 DOI: 10.7554/elife.34960] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
LINE-1 (L1) is an autonomous retrotransposon, which acted throughout mammalian evolution and keeps contributing to human genotypic diversity, genetic disease and cancer. L1 encodes two essential proteins: L1ORF1p, a unique RNA-binding protein, and L1ORF2p, an endonuclease and reverse transcriptase. L1ORF1p contains an essential, but rapidly evolving N-terminal portion, homo-trimerizes via a coiled coil and packages L1RNA into large assemblies. Here, we determined crystal structures of the entire coiled coil domain of human L1ORF1p. We show that retrotransposition requires a non-ideal and metastable coiled coil structure, and a strongly basic L1ORF1p amino terminus. Human L1ORF1p therefore emerges as a highly calibrated molecular machine, sensitive to mutation but functional in different hosts. Our analysis rationalizes the locally rapid L1ORF1p sequence evolution and reveals striking mechanistic parallels to coiled coil-containing membrane fusion proteins. It also suggests how trimeric L1ORF1p could form larger meshworks and indicates critical novel steps in L1 retrotransposition. Almost half of the human genome consists of DNA strings that have been copied and pasted from one part of the genome to another many thousands of times. These strings of DNA are called mobile genetic elements. Mobile elements can disrupt important genes, causing disease and cancer, but they can also drive evolution. Presently, only one type of mobile element, called LINE-1, is active in the human genome and able to multiply without help from other mobile elements. LINE-1 DNA is ‘transcribed’ to form molecules of LINE-1 RNA, which can then be ‘translated’ into two distinct proteins. These bind to LINE-1 RNA, which then gets back-transcribed into DNA and inserted as a new LINE-1 element in a new region of the genome. One of the two proteins, called L1ORF1p, forms complexes where three copies of the protein come together. These ‘trimers’ cover and protect LINE-1 RNA and are required for LINE-1 mobility. Different versions of L1ORF1p are found in different animals. Part of the protein is the same across all mammals, and this ‘conserved’ part controls the ability of L1ORF1p to bind to RNA. The non-conserved part of L1ORF1p differs even between humans and their closest animal relatives and little was known about its structure or role. However, this rapidly evolving part of L1ORF1p is essential for LINE-1 mobility. Using X-ray crystallography, Khazina and Weichenrieder obtained a molecular snapshot of the part of L1ORF1p that interacts with other copies of the protein to form trimers. Combined with earlier snapshots of L1ORF1p’s conserved part, this generated a complete structural model of the L1ORF1p trimer. Additional biophysical characterizations suggest that L1ORF1p trimers form a semi-stable structure that can partially open up, indicating how trimers could form larger assemblies of L1ORF1p on LINE-1 RNA. Indeed, the need to maintain a semi-stable structure could explain why L1ORF1p is evolving so rapidly. A second important finding is that the beginning of L1ORF1p needs to be positively charged – a requirement that warrants further exploration. The structural and mechanistic insight into L1ORF1p points to critical new steps in LINE-1 mobilization. It will help to design inhibitor molecules with the goal to halt the mobilization process at various points and to dissect such steps in great detail. Understanding how to control LINE-1 mobility could help to improve stem cell therapies and reproduction assistance techniques, due to the fact that LINE-1 mobility is a potential source of mutation in stem cells, egg and sperm cells, and newly formed embryos.
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Affiliation(s)
- Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Abstract
DNA methylation is a dynamic epigenetic mark that characterizes different cellular developmental stages, including tissue-specific profiles. This CpG dinucleotide modification cooperates in the regulation of the output of the cellular genetic content, in both healthy and pathological conditions. According to endogenous and exogenous stimuli, DNA methylation is involved in gene transcription, alternative splicing, imprinting, X-chromosome inactivation, and control of transposable elements. When these dinucleotides are organized in dense regions are called CpG islands (CGIs), being commonly known as transcriptional regulatory regions frequently associated with the promoter region of several genes. In cancer, promoter DNA hypermethylation events sustained the mechanistic hypothesis of epigenetic transcriptional silencing of an increasing number of tumor suppressor genes. CGI hypomethylation-mediated reactivation of oncogenes was also documented in several cancer types. In this chapter, we aim to summarize the functional consequences of the differential DNA methylation at CpG dinucleotides in cancer, focused in CGIs. Interestingly, cancer methylome is being recently explored, looking for biomarkers for diagnosis, prognosis, and predictors of drug response.
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Affiliation(s)
- Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.
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Gainetdinov IV, Kondratieva SA, Skvortsova YV, Zinovyeva MV, Stukacheva EA, Klimov A, Tryakin AA, Azhikina TL. Distinguishing epigenetic features of preneoplastic testis tissues adjacent to seminomas and nonseminomas. Oncotarget 2017; 7:22439-47. [PMID: 26843623 PMCID: PMC5008371 DOI: 10.18632/oncotarget.7074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/12/2016] [Indexed: 01/02/2023] Open
Abstract
PIWI pathway proteins are expressed during spermatogenesis where they play a key role in germ cell development. Epigenetic loss of PIWI proteins expression was previously demonstrated in testicular germ cell tumors (TGCTs), implying their involvement in TGCT development. In this work, apart from studying only normal testis and TGCT samples, we also analyzed an intermediate stage, i.e. preneoplastic testis tissues adjacent to TGCTs. Importantly, in this study, we minimized the contribution of patient-to-patient heterogeneity by using matched preneoplastic/TGCT samples. Surprisingly, expression of germ cell marker DDX4 suggests that spermatogenesis is retained in premalignant testis tissues adjacent to nonseminoma, but not those adjacent to seminoma. Moreover, this pattern is followed by expression of PIWI pathway genes, which impacts one of their functions: DNA methylation level over LINE-1 promoters is higher in preneoplastic testis tissues adjacent to nonseminomas than those adjacent to seminomas. This finding might imply distinct routes for development of the two types of TGCTs and could be used as a novel diagnostic marker, possibly, noninvasively. Finally, we studied the role of CpG island methylation in expression of PIWI genes in patient samples and using in vitro experiments in cell line models: a more complex interrelation between DNA methylation and expression of the corresponding genes was revealed.
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Affiliation(s)
- Ildar V Gainetdinov
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sofia A Kondratieva
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yulia V Skvortsova
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Zinovyeva
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Stukacheva
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Klimov
- Department of Oncology, Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Alexey A Tryakin
- Department of Clinical Pharmacology and Chemotherapy, Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Tatyana L Azhikina
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Hall LL, Byron M, Carone DM, Whitfield TW, Pouliot GP, Fischer A, Jones P, Lawrence JB. Demethylated HSATII DNA and HSATII RNA Foci Sequester PRC1 and MeCP2 into Cancer-Specific Nuclear Bodies. Cell Rep 2017; 18:2943-2956. [PMID: 28329686 DOI: 10.1016/j.celrep.2017.02.072] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/03/2017] [Accepted: 02/23/2017] [Indexed: 02/05/2023] Open
Abstract
This study reveals that high-copy satellite II (HSATII) sequences in the human genome can bind and impact distribution of chromatin regulatory proteins and that this goes awry in cancer. In many cancers, master regulatory proteins form two types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII. DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci with reduced PRC1 become derepressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci. Large nuclear foci of HSATII RNA form and sequester copious MeCP2 into Cancer-Associated Satellite Transcript (CAST) bodies. Hence, HSATII DNA and RNA have an exceptional capacity to act as molecular sponges and sequester chromatin regulatory proteins into abnormal nuclear bodies in cancer. The compartmentalization of regulatory proteins within nuclear structure, triggered by demethylation of "junk" repeats, raises the possibility that this contributes to further compromise of the epigenome and neoplastic progression.
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Affiliation(s)
- Lisa L Hall
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Dawn M Carone
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Troy W Whitfield
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gayle P Pouliot
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Andrew Fischer
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Peter Jones
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells. PLoS Genet 2017; 13:e1007051. [PMID: 29028794 PMCID: PMC5656329 DOI: 10.1371/journal.pgen.1007051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/25/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) retrotransposons can mobilize (retrotranspose) within the human genome, and mutagenic de novo L1 insertions can lead to human diseases, including cancers. As a result, cells are actively engaged in preventing L1 retrotransposition. This work reveals that the human Condensin II complex restricts L1 retrotransposition in both non-transformed and transformed cell lines through inhibition of L1 transcription and translation. Condensin II subunits, CAP-D3 and CAP-H2, interact with members of the Gamma-Interferon Activated Inhibitor of Translation (GAIT) complex including the glutamyl-prolyl-tRNA synthetase (EPRS), the ribosomal protein L13a, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and NS1 associated protein 1 (NSAP1). GAIT has been shown to inhibit translation of mRNAs encoding inflammatory proteins in myeloid cells by preventing the binding of the translation initiation complex, in response to Interferon gamma (IFN-γ). Excitingly, our data show that Condensin II promotes complexation of GAIT subunits. Furthermore, RNA-Immunoprecipitation experiments in epithelial cells demonstrate that Condensin II and GAIT subunits associate with L1 RNA in a co-dependent manner, independent of IFN-γ. These findings suggest that cooperation between the Condensin II and GAIT complexes may facilitate a novel mechanism of L1 repression, thus contributing to the maintenance of genome stability in somatic cells.
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Hempfling AL, Lim SL, Adelson DL, Evans J, O'Connor AE, Qu ZP, Kliesch S, Weidner W, O'Bryan MK, Bergmann M. Expression patterns of HENMT1 and PIWIL1 in human testis: implications for transposon expression. Reproduction 2017; 154:363-374. [PMID: 28676534 DOI: 10.1530/rep-16-0586] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/08/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022]
Abstract
This study aimed to define the expression patterns of HENMT1 and PIWI proteins in human testis and investigate their association with transposon expression, infertility sub-type or development of testicular germ cell tumours (TGCTs). Testis biopsies showing normal spermatogenesis were used to identify normal localisation patterns of HENMT1 and PIWIL1 by immunolocalisation and RT-PCR after laser microdissection. 222 testis biopsies representing normal spermatogenesis, hypospermatogenesis, spermatogenic arrests, Sertoli cell-only (SCO) tumours and TGCTs were analysed by RT-qPCR for expression of HENMT1/PIWIL1/PIWIL2/PIWIL3/PIWIL4 and LINE-1 Additionally, HENMT1-overexpressing TCam2 seminoma cell lines were analysed for the same parameters by RT-qPCR. We found that HENMT1 and PIWIL1 are coexpressed in pachytene spermatocytes and spermatids. Expression of HENMT1, PIWIL1 and PIWIL2 was mainly dependent on germ cell content but low levels of expression were also detected in some SCO samples. Levels of HENMT1, PIWIL1 and PIWIL2 expression were low in TGCT. Samples with HENMT1, PIWIL2 and PIWIL4 expression showed significantly (P < 0.05) lower transposon expression compared to samples without expression in the same histological group. HENMT1-overexpressing TCam2 cells showed lower LINE-1 expression than empty vector-transfected control lines. Our findings support that the transposon-regulating function of the piRNA pathway found in the mouse is conserved in adult human testis. HENMT1 and PIWI proteins are expressed in a germ-cell-specific manner and required for transposon control.
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Affiliation(s)
- A L Hempfling
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia .,Institute for Veterinary AnatomyHistology and Embryology, Justus Liebig University, Giessen, Germany
| | - S L Lim
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia
| | - D L Adelson
- School of Biological SciencesThe University of Adelaide, Adelaide, Australia
| | - J Evans
- Centre for Reproductive HealthHudson Institute of Medical Research, Clayton, Australia
| | - A E O'Connor
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia
| | - Z P Qu
- School of Biological SciencesThe University of Adelaide, Adelaide, Australia
| | - S Kliesch
- Centre of Reproductive Medicine and AndrologyMuenster, Germany
| | - W Weidner
- Clinic for UrologyPediatric Urology and Andrology, Justus-Liebig-University, Giessen, Germany
| | - M K O'Bryan
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia.,The School of Biological SciencesMonash University, Clayton, Australia
| | - M Bergmann
- Institute for Veterinary AnatomyHistology and Embryology, Justus Liebig University, Giessen, Germany
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Miousse IR, Murphy LA, Lin H, Schisler MR, Sun J, Chalbot MCG, Sura R, Johnson K, LeBaron MJ, Kavouras IG, Schnackenberg LK, Beger RD, Rasoulpour RJ, Koturbash I. Dose-response analysis of epigenetic, metabolic, and apical endpoints after short-term exposure to experimental hepatotoxicants. Food Chem Toxicol 2017; 109:690-702. [PMID: 28495587 DOI: 10.1016/j.fct.2017.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/16/2022]
Abstract
Identification of sensitive and novel biomarkers or endpoints associated with toxicity and carcinogenesis is of a high priority. There is increasing interest in the incorporation of epigenetic and metabolic biomarkers to complement apical data; however, a number of questions, including the tissue specificity, dose-response patterns, early detection of those endpoints, and the added value need to be addressed. In this study, we investigated the dose-response relationship between apical, epigenetic, and metabolomics endpoints following short-term exposure to experimental hepatotoxicants, clofibrate (CF) and phenobarbital (PB). Male F344 rats were exposed to PB (0, 5, 25, and 100 mg/kg/day) or CF (0, 10, 50, and 250 mg/kg/day) for seven days. Exposure to PB or CF resulted in dose-dependent increases in relative liver weights, hepatocellular hypertrophy and proliferation, and increases in Cyp2b1 and Cyp4a1 transcripts. These changes were associated with altered histone modifications within the regulatory units of cytochrome genes, LINE-1 DNA hypomethylation, and altered microRNA profiles. Metabolomics data indicated alterations in the metabolism of bile acids. This study provides the first comprehensive analysis of the apical, epigenetic and metabolic alterations, and suggests that the latter two occur within or near the dose response curve of apical endpoint alterations following exposure to experimental hepatotoxicants.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Lynea A Murphy
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Haixia Lin
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Melissa R Schisler
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Marie-Cecile G Chalbot
- Department of Environmental Health Sciences, Ryals School of Public Health, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35246, USA.
| | - Radhakrishna Sura
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Kamin Johnson
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Matthew J LeBaron
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Ilias G Kavouras
- Department of Environmental Health Sciences, Ryals School of Public Health, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35246, USA.
| | - Laura K Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Reza J Rasoulpour
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Igor Koturbash
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
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Alekseeva LA, Mironova NL, Brenner EV, Kurilshikov AM, Patutina OA, Zenkova MA. Alteration of the exDNA profile in blood serum of LLC-bearing mice under the decrease of tumour invasion potential by bovine pancreatic DNase I treatment. PLoS One 2017; 12:e0171988. [PMID: 28222152 PMCID: PMC5319761 DOI: 10.1371/journal.pone.0171988] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
Taking into account recently obtained data indicating the participation of circulating extracellular DNA (exDNA) in tumorigenesis, enzymes with deoxyribonucleic activity have again been considered as potential antitumour and antimetastatic drugs. Previously, using murine Lewis lung carcinoma and hepatocellular carcinoma A1 tumour models, we have shown the antimetastatic activity of bovine DNase I, which correlates with an increase of DNase activity and a decrease of exDNA concentration in the blood serum of tumour-bearing mice. In this work, using next-generation sequencing on the ABS SOLiD™ 5.500 platform, we performed a search for molecular targets of DNase I by comparing the exDNA profiles of healthy animals, untreated animals with Lewis lung carcinoma (LLC) and those with LLC treated with DNase I. We found that upon DNase I treatment of LLC-bearing mice, together with inhibition of metastasis, a number of strong alterations in the patterns of exDNA were observed. The major differences in exDNA profiles between groups were: i) the level of GC-poor sequences increased during tumour development was reduced to that of healthy mice; ii) levels of sequences corresponding to tumour-associated genes Hmga2, Myc and Jun were reduced in the DNase I-treated group in comparison with non-treated mice; iii) 224 types of tandem repeat over-presented in untreated LLC-bearing mice were significantly reduced after DNase I treatment. The most important result obtained in the work is that DNase I decreased the level of B-subfamily repeats having homology to human ALU repeats, known as markers of carcinogenesis, to the level of healthy animals. Thus, the obtained data lead us to suppose that circulating exDNA plays a role in tumour dissemination, and alteration of multiple molecular targets in the bloodstream by DNase I reduces the invasive potential of tumours.
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Affiliation(s)
- Ludmila A. Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Nadezhda L. Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Evgenyi V. Brenner
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | | | - Olga A. Patutina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
- * E-mail:
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45
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Papasotiriou I, Pantopikou K, Apostolou P. L1 retrotransposon expression in circulating tumor cells. PLoS One 2017; 12:e0171466. [PMID: 28166262 PMCID: PMC5293242 DOI: 10.1371/journal.pone.0171466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/21/2017] [Indexed: 11/18/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1 or L1) belongs to the non-long terminal repeat (non-LTR) retrotransposon family, which has been implicated in carcinogenesis and disease progression. Circulating tumor cells (CTCs) are also known to be involved in cancer progression. The present study aimed to compare the L1 expression between circulating tumor cells and non-cancerous samples. Blood samples were collected from 10 healthy individuals and 22 patients with different types of cancer. The whole blood cells were isolated using enrichment protocols and the DNA and RNA were extracted. RT-qPCR was performed for L1-ORF1 (open reading frame 1) and L1-ORF2, using 18S rRNA as the reference gene. The data were analyzed with the Livak method and statistical analyses were carried out with the Mann-Whitney and Kruskal-Wallis tests. In parallel with the above molecular biology experiments, FISH experiments were performed on the interphase nuclei of the cells for the detection of ORF2 RNA. DNA analysis revealed the presence of both ORF1 and ORF2 in all samples. RNA expression experiments demonstrated that ORF1 was not expressed in all samples, while ORF2 was expressed at varying levels in the non-cancer samples and the samples representing the different cancer types. A significant difference in ORF2 expression was observed between the CTCs and non-cancer samples (p = 0,00043), and significant differences were also observed between normal and lung (p = 0,034), pancreatic (p = 0,022), prostate (p = 0,014), and unknown primary of origin (p = 0,0039) cancer samples. Cytogenetic analysis revealed higher levels of ORF2 in the nuclei of CTCs than in normal samples. This study highlights the significant difference in L1-ORF2 expression between CTCs and normal samples. The increased expression levels observed for CTCs may be correlated with the characteristic features of these cells.
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46
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Dudley JP, Golovkina TV, Ross SR. Lessons Learned from Mouse Mammary Tumor Virus in Animal Models. ILAR J 2017; 57:12-23. [PMID: 27034391 DOI: 10.1093/ilar/ilv044] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mouse mammary tumor virus (MMTV), which was discovered as a milk-transmitted, infectious, cancer-inducing agent in the 1930s, has been used as an animal model for the study of retroviral infection and transmission, antiviral immune responses, and breast cancer and lymphoma biology. The main target cells for MMTV infection in vivo are cells of the immune system and mammary epithelial cells. Although the host mounts an immune response to the virus, MMTV has evolved multiple means of evading this response. MMTV causes mammary tumors when the provirus integrates into the mammary epithelial and lymphoid cell genome during viral replication and thereby activates cellular oncogene expression. Thus, tumor induction is a by-product of the infection cycle. A number of important oncogenes have been discovered by carrying out MMTV integration site analysis, some of which may play a role in human breast cancer.
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Affiliation(s)
- Jaquelin P Dudley
- Jaquelin P. Dudley, PhD, is a professor in the Department of Molecular Biosciences, Center for Infectious Disease and Institute for Cellular and Molecular Biology at the University of Texas at Austin. Tatyana V. Golovkina, PhD, is a professor in the Department of Microbiology at the University of Chicago in Chicago, Illinois. Susan R. Ross, PhD, is a professor in the Department of Microbiology in the Perelman School of Medicine of the University of Pennsylvania in Philadelphia, Pennsylvania
| | - Tatyana V Golovkina
- Jaquelin P. Dudley, PhD, is a professor in the Department of Molecular Biosciences, Center for Infectious Disease and Institute for Cellular and Molecular Biology at the University of Texas at Austin. Tatyana V. Golovkina, PhD, is a professor in the Department of Microbiology at the University of Chicago in Chicago, Illinois. Susan R. Ross, PhD, is a professor in the Department of Microbiology in the Perelman School of Medicine of the University of Pennsylvania in Philadelphia, Pennsylvania
| | - Susan R Ross
- Jaquelin P. Dudley, PhD, is a professor in the Department of Molecular Biosciences, Center for Infectious Disease and Institute for Cellular and Molecular Biology at the University of Texas at Austin. Tatyana V. Golovkina, PhD, is a professor in the Department of Microbiology at the University of Chicago in Chicago, Illinois. Susan R. Ross, PhD, is a professor in the Department of Microbiology in the Perelman School of Medicine of the University of Pennsylvania in Philadelphia, Pennsylvania
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47
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Macia A, Widmann TJ, Heras SR, Ayllon V, Sanchez L, Benkaddour-Boumzaouad M, Muñoz-Lopez M, Rubio A, Amador-Cubero S, Blanco-Jimenez E, Garcia-Castro J, Menendez P, Ng P, Muotri AR, Goodier JL, Garcia-Perez JL. Engineered LINE-1 retrotransposition in nondividing human neurons. Genome Res 2016; 27:335-348. [PMID: 27965292 PMCID: PMC5340962 DOI: 10.1101/gr.206805.116] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 12/01/2016] [Indexed: 12/21/2022]
Abstract
Half the human genome is made of transposable elements (TEs), whose ongoing activity continues to impact our genome. LINE-1 (or L1) is an autonomous non-LTR retrotransposon in the human genome, comprising 17% of its genomic mass and containing an average of 80-100 active L1s per average genome that provide a source of inter-individual variation. New LINE-1 insertions are thought to accumulate mostly during human embryogenesis. Surprisingly, the activity of L1s can further impact the somatic human brain genome. However, it is currently unknown whether L1 can retrotranspose in other somatic healthy tissues or if L1 mobilization is restricted to neuronal precursor cells (NPCs) in the human brain. Here, we took advantage of an engineered L1 retrotransposition assay to analyze L1 mobilization rates in human mesenchymal (MSCs) and hematopoietic (HSCs) somatic stem cells. Notably, we have observed that L1 expression and engineered retrotransposition is much lower in both MSCs and HSCs when compared to NPCs. Remarkably, we have further demonstrated for the first time that engineered L1s can retrotranspose efficiently in mature nondividing neuronal cells. Thus, these findings suggest that the degree of somatic mosaicism and the impact of L1 retrotransposition in the human brain is likely much higher than previously thought.
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Affiliation(s)
- Angela Macia
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Thomas J Widmann
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Sara R Heras
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Veronica Ayllon
- Department of Oncology, GENYO, Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Laura Sanchez
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Meriem Benkaddour-Boumzaouad
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Martin Muñoz-Lopez
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Alejandro Rubio
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Suyapa Amador-Cubero
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | - Eva Blanco-Jimenez
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain
| | | | - Pablo Menendez
- Department of Oncology, GENYO, Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain.,Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Instituciò Catalana Recerca Estudis Avançats (ICREA), 08036 Barcelona, Spain
| | - Philip Ng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Alysson R Muotri
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California 92093, USA
| | - John L Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jose L Garcia-Perez
- Department of Genomic Medicine and Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016 Granada, Spain.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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48
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Cook PR, Tabor GT. Deciphering fact from artifact when using reporter assays to investigate the roles of host factors on L1 retrotransposition. Mob DNA 2016; 7:23. [PMID: 27895722 PMCID: PMC5120415 DOI: 10.1186/s13100-016-0079-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 11/04/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The Long INterspersed Element-1 (L1, LINE-1) is the only autonomous mobile DNA element in humans and has generated as much as half of the genome. Due to increasing clinical interest in the roles of L1 in cancer, embryogenesis and neuronal development, it has become a priority to understand L1-host interactions and identify host factors required for its activity. Apropos to this, we recently reported that L1 retrotransposition in HeLa cells requires phosphorylation of the L1 protein ORF1p at motifs targeted by host cell proline-directed protein kinases (PDPKs), which include the family of mitogen-activated protein kinases (MAPKs). Using two engineered L1 reporter assays, we continued our investigation into the roles of MAPKs in L1 activity. RESULTS We found that the MAPK p38δ phosphorylated ORF1p on three of its four PDPK motifs required for L1 activity. In addition, we found that a constitutively active p38δ mutant appeared to promote L1 retrotransposition in HeLa cells. However, despite the consistency of these findings with our earlier work, we identified some technical concerns regarding the experimental methodology. Specifically, we found that exogenous expression of p38δ appeared to affect at least one heterologous promoter in an engineered L1 reporter, as well as generate opposing effects on two different reporters. We also show that two commercially available non-targeting control (NTC) siRNAs elicit drastically different effects on the apparent retrotransposition reported by both L1 assays, which raises concerns about the use of NTCs as normalizing controls. CONCLUSIONS Engineered L1 reporter assays have been invaluable for determining the functions and critical residues of L1 open reading frames, as well as elucidating many aspects of L1 replication. However, our results suggest that caution is required when interpreting data obtained from L1 reporters used in conjunction with exogenous gene expression or siRNA.
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Affiliation(s)
- Pamela R. Cook
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD 20892 USA
| | - G. Travis Tabor
- National Institute of Child Health and Human Development, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892 USA
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Clayton EA, Wang L, Rishishwar L, Wang J, McDonald JF, Jordan IK. Patterns of Transposable Element Expression and Insertion in Cancer. Front Mol Biosci 2016; 3:76. [PMID: 27900322 PMCID: PMC5110550 DOI: 10.3389/fmolb.2016.00076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data. We applied these new sequence analysis techniques to matched normal and primary tumor patient samples from the Cancer Genome Atlas (TCGA) in order to analyze the patterns of TE expression and insertion for three cancer types: breast invasive carcinoma, head and neck squamous cell carcinoma, and lung adenocarcinoma. Our analysis focused on the three most abundant families of active human TEs: Alu, SVA, and L1. We found evidence for high levels of somatic TE activity for these three families in normal and cancer samples across diverse tissue types. Abundant transcripts for all three TE families were detected in both normal and cancer tissues along with an average of ~80 unique TE insertions per individual patient/tissue. We observed an increase in L1 transcript expression and L1 insertional activity in primary tumor samples for all three cancer types. Tumor-specific TE insertions are enriched for private mutations, consistent with a potentially causal role in tumorigenesis. We used genome feature analysis to investigate two specific cases of putative cancer-causing TE mutations in further detail. An Alu insertion in an upstream enhancer of the CBL tumor suppressor gene is associated with down-regulation of the gene in a single breast cancer patient, and an L1 insertion in the first exon of the BAALC gene also disrupts its expression in head and neck squamous cell carcinoma. Our results are consistent with widespread somatic activity of human TEs leading to numerous insertion mutations that can contribute to tumorigenesis in a variety of tissues.
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Affiliation(s)
- Evan A Clayton
- Integrated Cancer Research Center, School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; Ovarian Cancer InstituteAtlanta, GA, USA
| | - Lu Wang
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia
| | - Lavanya Rishishwar
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia; Applied Bioinformatics LaboratoryAtlanta, GA, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University East Lansing, MI, USA
| | - John F McDonald
- Integrated Cancer Research Center, School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; Ovarian Cancer InstituteAtlanta, GA, USA
| | - I King Jordan
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia; Applied Bioinformatics LaboratoryAtlanta, GA, USA
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50
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De Luca C, Guadagni F, Sinibaldi-Vallebona P, Sentinelli S, Gallucci M, Hoffmann A, Schumann GG, Spadafora C, Sciamanna I. Enhanced expression of LINE-1-encoded ORF2 protein in early stages of colon and prostate transformation. Oncotarget 2016; 7:4048-61. [PMID: 26716650 PMCID: PMC4826189 DOI: 10.18632/oncotarget.6767] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/30/2015] [Indexed: 12/11/2022] Open
Abstract
LINE-1 (L1) retrotransposons are a source of endogenous reverse transcriptase (RT) activity, which is expressed as part of the L1-encoded ORF2 protein (L1-ORF2p). L1 elements are highly expressed in many cancer types, while being silenced in most differentiated somatic tissues. We previously found that RT inhibition reduces cell proliferation and promotes differentiation in neoplastic cells, indicating that high endogenous RT activity promotes cancer growth. Here we investigate the expression of L1-ORF2p in several human types of cancer. We have developed a highly specific monoclonal antibody (mAb chA1-L1) to study ORF2p expression and localization in human cancer cells and tissues. We uncover new evidence for high levels of L1-ORF2p in transformed cell lines and staged epithelial cancer tissues (colon, prostate, lung and breast) while no or only basal ORF2p expression was detected in non-transformed cells. An in-depth analysis of colon and prostate tissues shows ORF2p expression in preneoplastic stages, namely transitional mucosa and prostate intraepithelial neoplasia (PIN), respectively. Our results show that L1-ORF2p is overexpressed in tumor and in preneoplastic colon and prostate tissues; this latter finding suggests that ORF2p could be considered as a potential early diagnostic biomarker.
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Affiliation(s)
| | - Fiorella Guadagni
- Laboratory BioDAT SR Research, IRCCS San Raffaele Pisana, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine and Surgery, University "Tor Vergata", Rome, Italy.,Institute of Translational Pharmacology, CNR, Rome, Italy
| | - Steno Sentinelli
- I.F.O. Regina Elena, UOC Pathological Anatomy/Urology, Rome, Italy
| | - Michele Gallucci
- I.F.O. Regina Elena, UOC Pathological Anatomy/Urology, Rome, Italy
| | - Andreas Hoffmann
- Department of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Gerald G Schumann
- Department of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
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