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Lamontagne RJ, Soldan SS, Su C, Wiedmer A, Won KJ, Lu F, Goldman AR, Wickramasinghe J, Tang HY, Speicher DW, Showe L, Kossenkov AV, Lieberman PM. A multi-omics approach to Epstein-Barr virus immortalization of B-cells reveals EBNA1 chromatin pioneering activities targeting nucleotide metabolism. PLoS Pathog 2021; 17:e1009208. [PMID: 33497421 PMCID: PMC7864721 DOI: 10.1371/journal.ppat.1009208] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/05/2021] [Accepted: 12/02/2020] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) immortalizes resting B-lymphocytes through a highly orchestrated reprogramming of host chromatin structure, transcription and metabolism. Here, we use a multi-omics-based approach to investigate these underlying mechanisms. ATAC-seq analysis of cellular chromatin showed that EBV alters over a third of accessible chromatin during the infection time course, with many of these sites overlapping transcription factors such as PU.1, Interferon Regulatory Factors (IRFs), and CTCF. Integration of RNA-seq analysis identified a complex transcriptional response and associations with EBV nuclear antigens (EBNAs). Focusing on EBNA1 revealed enhancer-binding activity at gene targets involved in nucleotide metabolism, supported by metabolomic analysis which indicated that adenosine and purine metabolism are significantly altered by EBV immortalization. We further validated that adenosine deaminase (ADA) is a direct and critical target of the EBV-directed immortalization process. These findings reveal that purine metabolism and ADA may be useful therapeutic targets for EBV-driven lymphoid cancers.
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Affiliation(s)
| | - Samantha S. Soldan
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Chenhe Su
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Andreas Wiedmer
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Fang Lu
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Aaron R. Goldman
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | | | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - David W. Speicher
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Louise Showe
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | | | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
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Attenuation of Equine Lentivirus Alters Mitochondrial Protein Expression Profile from Inflammation to Apoptosis. J Virol 2019; 93:JVI.00653-19. [PMID: 31391270 DOI: 10.1128/jvi.00653-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/23/2019] [Indexed: 12/18/2022] Open
Abstract
Equine infectious anemia virus (EIAV) is an equine lentivirus similar to HIV-1, targets host immune cells, and causes a life-long infection in horses. The Chinese live EIAV vaccine is attenuated from long-term passaging of a highly virulent strain in vitro The parent pathogenic strain (EIAVDLV34) induces a host inflammatory storm to cause severe pathological injury of animals. However, the vaccine strain (EIAVDLV121) induces a high level of apoptosis to eliminate infected cells. To investigate how these processes are regulated, we performed a comparative proteomics analysis and functional study in equine monocyte-derived macrophages (eMDMs) and found that the divergent mitochondrial protein expression profiles caused by EIAV strains with different virulence led to disparate mitochondrial function, morphology, and metabolism. This in turn promoted the distinct transformation of macrophage inflammatory polarization and intrinsic apoptosis. In EIAVDLV34-infected cells, a high level of glycolysis and increased mitochondrial fragmentation were induced, resulting in the M1-polarized proinflammatory-type transformation of macrophages and the subsequent production of a strong inflammatory response. Following infection with EIAVDLV121, the infected cells were transformed into M2-polarized anti-inflammatory macrophages by inhibition of glycolysis. In this case, a decrease in the mitochondrial membrane potential and impairment of the electron transport chain led to increased levels of apoptosis and reactive oxygen species. These results correlated with viral pathogenicity loss and may help provide an understanding of the key mechanism of lentiviral attenuation.IMPORTANCE Following viral infection, the working pattern and function of the cell can be transformed through the impact on mitochondria. It still unknown how the mitochondrial response changes in cells infected with viruses in the process of virulence attenuation. EIAVDLV121 is the only effective lentiviral vaccine for large-scale use in the world. EIAVDLV34 is the parent pathogenic strain. Unlike EIAVDLV34-induced inflammation storms, EIAVDLV121 can induce high levels of apoptosis. For the first time, we found that, after the mitochondrial protein expression profile is altered, EIAVDLV34-infected cells are transformed into M1-polarized-type macrophages and cause inflammatory injury and that the intrinsic apoptosis pathway is activated in EIAVDLV121-infected cells. These studies shed light on how the mitochondrial protein expression profile changes between cells infected by pathogenic lentivirus strains and cells infected by attenuated lentivirus strains to drive different cellular responses, especially from inflammation to apoptosis.
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Schaeffner M, Mrozek-Gorska P, Buschle A, Woellmer A, Tagawa T, Cernilogar FM, Schotta G, Krietenstein N, Lieleg C, Korber P, Hammerschmidt W. BZLF1 interacts with chromatin remodelers promoting escape from latent infections with EBV. Life Sci Alliance 2019; 2:e201800108. [PMID: 30926617 PMCID: PMC6441497 DOI: 10.26508/lsa.201800108] [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: 06/15/2018] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022] Open
Abstract
A hallmark of EBV infections is its latent phase, when all viral lytic genes are repressed. Repression results from a high nucleosome occupancy and epigenetic silencing by cellular factors such as the Polycomb repressive complex 2 (PRC2) and DNA methyltransferases that, respectively, introduce repressive histone marks and DNA methylation. The viral transcription factor BZLF1 acts as a molecular switch to induce transition from the latent to the lytic or productive phase of EBV's life cycle. It is unknown how BZLF1 can bind to the epigenetically silenced viral DNA and whether it directly reactivates the viral genome through chromatin remodeling. We addressed these fundamental questions and found that BZLF1 binds to nucleosomal DNA motifs both in vivo and in vitro. BZLF1 co-precipitates with cellular chromatin remodeler ATPases, and the knock-down of one of them, INO80, impaired lytic reactivation and virus synthesis. In Assay for Transposase-Accessible Chromatin-seq experiments, non-accessible chromatin opens up locally when BZLF1 binds to its cognate sequence motifs in viral DNA. We conclude that BZLF1 reactivates the EBV genome by directly binding to silenced chromatin and recruiting cellular chromatin-remodeling enzymes, which implement a permissive state for lytic viral transcription. BZLF1 shares this mode of action with a limited number of cellular pioneer factors, which are instrumental in transcriptional activation, differentiation, and reprogramming in all eukaryotic cells.
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Affiliation(s)
- Marisa Schaeffner
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Paulina Mrozek-Gorska
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Alexander Buschle
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Anne Woellmer
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Takanobu Tagawa
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Filippo M Cernilogar
- Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität Munich, Planegg, Germany
| | - Gunnar Schotta
- Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität Munich, Planegg, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
| | - Nils Krietenstein
- Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität Munich, Planegg, Germany
| | - Corinna Lieleg
- Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität Munich, Planegg, Germany
| | - Philipp Korber
- Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität Munich, Planegg, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
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Rajčáni J, Bánáti F, Szenthe K, Szathmary S. The potential of currently unavailable herpes virus vaccines. Expert Rev Vaccines 2018; 17:239-248. [PMID: 29313728 DOI: 10.1080/14760584.2018.1425620] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Despite overwhelming experimental work, there are no licensed vaccines against the most frequent Alphaherpesviruses, namely herpes simplex virus 1 and 2 (HSV1 and 2) nor against the Epstein-Barr virus (EBV), a member of the subfamily Gammaherpesvirus. AREAS COVERED Since the DNAs of both HSVs reside in the regional sensory ganglia in a latent state (i.e. as circularized episomal molecules), a corresponding vaccine might be useful for immunotherapy rather than for prevention of primary infection. Here we describe the design of a purified subunit vaccine as well as the preparation and efficacy of a recombinant fusion protein consisting of the gD ectodomain from our domestic attenuated HSV1 strain HSZP. The EBV vaccines considered so far, were destined for prevention of infectious mononucleosis (IM) or to prevent formation of EBV related tumors. To design the EBV peptide vaccine, at least 15 carefully selected immunogenic epitopes coming from 12 virus coded proteins were bound to synthetic micro-particle carriers along with a non-specific pathogen recognizing receptor (PRR) stimulating both the T as well as B lymphocytes. EXPERT COMMENTARY The efficacy of a novel EBV peptide in the rabbit model was based on criteria such as antibody formation (EA-D detected by ELISA, early and capsid proteins tested by immunoblot), presence of LMP1 antigen and of viral DNA in peripheral white blood cells. Out of 19 peptide combinations used for vaccination, at least 6 showed a satisfactory protective effect.
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Affiliation(s)
- Július Rajčáni
- a RT-Europe Nonprofit Research Center , Mosonmagyaróvár , Hungary
| | - Ferenc Bánáti
- a RT-Europe Nonprofit Research Center , Mosonmagyaróvár , Hungary
| | - Kálmán Szenthe
- a RT-Europe Nonprofit Research Center , Mosonmagyaróvár , Hungary
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Dreyfus DH. Gene sharing between Epstein–Barr virus and human immune response genes. Immunol Res 2016; 65:37-45. [DOI: 10.1007/s12026-016-8814-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Epigenetic Alterations in Epstein-Barr Virus-Associated Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 879:39-69. [DOI: 10.1007/978-3-319-24738-0_3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Niller HH, Tarnai Z, Decsi G, Zsedényi A, Bánáti F, Minarovits J. Role of epigenetics in EBV regulation and pathogenesis. Future Microbiol 2015; 9:747-56. [PMID: 25046522 DOI: 10.2217/fmb.14.41] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epigenetic modifications of the viral and host cell genomes regularly occur in EBV-associated lymphomas and carcinomas. The cell type-dependent usage of latent EBV promoters is determined by the cellular epigenetic machinery. Viral oncoproteins interact with the very same epigenetic regulators and alter the cellular epigenotype and gene-expression pattern: there are common gene sets hypermethylated in both EBV-positive and EBV-negative neoplasms of different histological types. A group of hypermethylated promoters may represent, however, a unique EBV-associated epigenetic signature in EBV-positive gastric carcinomas. By contrast, EBV-immortalized B-lymphoblastoid cell lines are characterized by genome-wide demethylation and loss and rearrangement of heterochromatic histone marks. Early steps of EBV infection may also contribute to reprogramming of the cellular epigenome.
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Affiliation(s)
- Hans Helmut Niller
- Department of Microbiology & Hygiene, University of Regensburg, Franz-Josef-Strauss Allee 11, D-93053 Regensburg, Germany
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Niller HH, Szenthe K, Minarovits J. Epstein-Barr virus-host cell interactions: an epigenetic dialog? Front Genet 2014; 5:367. [PMID: 25400657 PMCID: PMC4212275 DOI: 10.3389/fgene.2014.00367] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/02/2014] [Indexed: 12/23/2022] Open
Abstract
Here, we wish to highlight the genetic exchange and epigenetic interactions between Epstein–Barr virus (EBV) and its host. EBV is associated with diverse lymphoid and epithelial malignancies. Their molecular pathogenesis is accompanied by epigenetic alterations which are distinct for each of them. While lymphoblastoid cell lines derived from B cells transformed by EBV in vitro are characterized by a massive demethylation and euchromatinization of the viral and cellular genomes, the primarily malignant lymphoid tumor Burkitt’s lymphoma and the epithelial tumors nasopharyngeal carcinoma and EBV-associated gastric carcinoma are characterized by hypermethylation of a multitude of cellular tumor suppressor gene loci and of the viral genomes. In some cases, the viral latency and oncoproteins including the latent membrane proteins LMP1 and LMP2A and several nuclear antigens affect the level of cellular DNA methyltransferases or interact with the histone modifying machinery. Specific molecular mechanisms of the epigenetic dialog between virus and host cell remain to be elucidated.
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Affiliation(s)
- Hans H Niller
- Institute of Medical Microbiology and Hygiene, University of Regensburg , Regensburg, Germany
| | - Kalman Szenthe
- RT-Europe Nonprofit Research Ltd, Mosonmagyaróvár , Hungary
| | - Janos Minarovits
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged , Szeged, Hungary
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Niller HH, Banati F, Nagy K, Buzas K, Minarovits J. Update on microbe-induced epigenetic changes: bacterial effectors and viral oncoproteins as epigenetic dysregulators. Future Virol 2013. [DOI: 10.2217/fvl.13.97] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Pathoepigenetics is a new discipline describing how disturbances in epigenetic regulation alter the epigenotype and gene-expression pattern of human, animal or plant cells. Such ‘epigenetic reprogramming’ may play an important role in the initiation and progression of a wide variety of diseases. Infectious diseases also belong to this category: recent data demonstrated that microbial pathogens, including bacteria and viruses, are capable of dysregulating the epigenetic machinery of their host cell. The resulting heritable changes in host cell gene expression may favor the colonization, growth or spread of infectious pathogens. It may also facilitate the establishment of latency and malignant cell transformation. In this article, we review how bacterial epigenetic effectors and inflammatory processes elicited by bacteria alter the host cell epigenotype, and describe how oncoproteins encoded by human tumor viruses act as epigenetic dysregulators to alter the phenotype and behavior of host cells.
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Affiliation(s)
- Hans Helmut Niller
- Institute for Medical Microbiology & Hygiene, University of Regensburg, Franz-Josef-Strauss Allee 11, Regensburg D93053, Germany
| | - Ferenc Banati
- RT-Europe Nonprofit Research Center, H-9200 Mosonmagyarovar, Pozsonyi út 88, Hungary
| | - Katalin Nagy
- University of Szeged, Faculty of Dentistry, Department of Oral Surgery, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
| | - Krisztina Buzas
- University of Szeged, Faculty of Dentistry, Department of Oral Biology & Experimental Dental Research, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
| | - Janos Minarovits
- University of Szeged, Faculty of Dentistry, Department of Oral Biology & Experimental Dental Research, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
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Potential cellular functions of Epstein-Barr Nuclear Antigen 1 (EBNA1) of Epstein-Barr Virus. Viruses 2013; 5:226-40. [PMID: 23325328 PMCID: PMC3564119 DOI: 10.3390/v5010226] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 12/23/2012] [Accepted: 01/11/2013] [Indexed: 11/17/2022] Open
Abstract
Epstein-Barr Nuclear Antigen 1 (EBNA1) is a multifunctional protein encoded by EBV. EBNA1’s role in maintaining EBV in latently proliferating cells, by mediating EBV genome synthesis and nonrandom partitioning to daughter cells, as well as regulating viral gene transcription, is well characterized. Less understood are the roles of EBNA1 in affecting the host cell to provide selective advantages to those cells that harbor EBV. In this review we will focus on the interactions between EBNA1 and the host cell that may provide EBV-infected cells selective advantages beyond the maintenance of EBV.
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