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Cirac A, Poirey R, Dieckmeyer M, Witter K, Delecluse HJ, Behrends U, Mautner J. Immunoinformatic Analysis Reveals Antigenic Heterogeneity of Epstein-Barr Virus Is Immune-Driven. Front Immunol 2021; 12:796379. [PMID: 34975903 PMCID: PMC8716887 DOI: 10.3389/fimmu.2021.796379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/30/2021] [Indexed: 12/05/2022] Open
Abstract
Whole genome sequencing of Epstein-Barr virus (EBV) isolates from around the world has uncovered pervasive strain heterogeneity, but the forces driving strain diversification and the impact on immune recognition remained largely unknown. Using a data mining approach, we analyzed more than 300 T-cell epitopes in 168 published EBV strains. Polymorphisms were detected in approximately 65% of all CD8+ and 80% of all CD4+ T-cell epitopes and these numbers further increased when epitope flanking regions were included. Polymorphisms in CD8+ T-cell epitopes often involved MHC anchor residues and resulted in changes of the amino acid subgroup, suggesting that only a limited number of conserved T-cell epitopes may represent generic target antigens against different viral strains. Although considered the prototypic EBV strain, the rather low degree of overlap with most other viral strains implied that B95.8 may not represent the ideal reference strain for T-cell epitopes. Instead, a combinatorial library of consensus epitopes may provide better targets for diagnostic and therapeutic purposes when the infecting strain is unknown. Polymorphisms were significantly enriched in epitope versus non-epitope protein sequences, implicating immune selection in driving strain diversification. Remarkably, CD4+ T-cell epitopes in EBNA2, EBNA-LP, and the EBNA3 family appeared to be under negative selection pressure, hinting towards a beneficial role of immune responses against these latency type III antigens in virus biology. These findings validate this immunoinformatics approach for providing novel insight into immune targets and the intricate relationship of host defense and virus evolution that may also pertain to other pathogens.
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Affiliation(s)
- Ana Cirac
- Children’s Hospital, School of Medicine, Technische Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Remy Poirey
- German Cancer Research Center (DKFZ) Unit F100 and Institut National de la Santé et de la Recherche Médicale Unit U1074, Heidelberg, Germany
| | - Michael Dieckmeyer
- Department of Diagnostic and Interventional Neuroradiology, Technische Universität München, Munich, Germany
| | - Klaus Witter
- Laboratory of Immunogenetics, Ludwig-Maximilians-Universität, München, Germany
| | - Henri-Jacques Delecluse
- German Cancer Research Center (DKFZ) Unit F100 and Institut National de la Santé et de la Recherche Médicale Unit U1074, Heidelberg, Germany
| | - Uta Behrends
- Children’s Hospital, School of Medicine, Technische Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), partner site Munich, Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Josef Mautner
- Children’s Hospital, School of Medicine, Technische Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), partner site Munich, Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- *Correspondence: Josef Mautner,
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Dheekollu J, Wiedmer A, Ayyanathan K, Deakyne JS, Messick TE, Lieberman PM. Cell-cycle-dependent EBNA1-DNA crosslinking promotes replication termination at oriP and viral episome maintenance. Cell 2021; 184:643-654.e13. [PMID: 33482082 DOI: 10.1016/j.cell.2020.12.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/17/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023]
Abstract
Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that persists as a multicopy episome in proliferating host cells. Episome maintenance is strictly dependent on EBNA1, a sequence-specific DNA-binding protein with no known enzymatic activities. Here, we show that EBNA1 forms a cell cycle-dependent DNA crosslink with the EBV origin of plasmid replication oriP. EBNA1 tyrosine 518 (Y518) is essential for crosslinking to oriP and functionally required for episome maintenance and generation of EBV-transformed lymphoblastoid cell lines (LCLs). Mechanistically, Y518 is required for replication fork termination at oriP in vivo and for formation of SDS-resistant complexes in vitro. EBNA1-DNA crosslinking corresponds to single-strand endonuclease activity specific to DNA structures enriched at replication-termination sites, such as 4-way junctions. These findings reveal that EBNA1 forms tyrosine-dependent DNA-protein crosslinks and single-strand cleavage at oriP required for replication termination and viral episome maintenance.
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Dheekollu J, Malecka K, Wiedmer A, Delecluse HJ, Chiang AKS, Altieri DC, Messick TE, Lieberman PM. Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency. Oncotarget 2018; 8:7248-7264. [PMID: 28077791 PMCID: PMC5352318 DOI: 10.18632/oncotarget.14540] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 12/26/2016] [Indexed: 12/27/2022] Open
Abstract
Epstein-Barr Virus (EBV) latent infection is a causative co-factor for endemic Nasopharyngeal Carcinoma (NPC). NPC-associated variants have been identified in EBV-encoded nuclear antigen EBNA1. Here, we solve the X-ray crystal structure of an NPC-derived EBNA1 DNA binding domain (DBD) and show that variant amino acids are found on the surface away from the DNA binding interface. We show that NPC-derived EBNA1 is compromised for DNA replication and episome maintenance functions. Recombinant virus containing the NPC EBNA1 DBD are impaired in their ability to immortalize primary B-lymphocytes and suppress lytic transcription during early stages of B-cell infection. We identify Survivin as a host protein deficiently bound by the NPC variant of EBNA1 and show that Survivin depletion compromises EBV episome maintenance in multiple cell types. We propose that endemic variants of EBNA1 play a significant role in EBV-driven carcinogenesis by altering key regulatory interactions that destabilize latent infection.
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Affiliation(s)
| | | | | | | | - Alan K S Chiang
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
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Abstract
Lymphoblastoid cell lines (LCLs) can be generated easily by in vitro EBV infection of B lymphocytes collected from any individual. In vitro, these EBV-infected B cell cultures yield proliferating, transformed lines referred to as lymphoblastoid cell lines (LCLs).
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Affiliation(s)
- Noemi Nagy
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, SE-171 77, Stockholm, Sweden.
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van Gent M, Gram AM, Boer IGJ, Geerdink RJ, Lindenbergh MFS, Lebbink RJ, Wiertz EJ, Ressing ME. Silencing the shutoff protein of Epstein–Barr virus in productively infected B cells points to (innate) targets for immune evasion. J Gen Virol 2015; 96:858-865. [DOI: 10.1099/jgv.0.000021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Michiel van Gent
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anna M. Gram
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ingrid G. J. Boer
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruben J. Geerdink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J. Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maaike E. Ressing
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Emerging topics in human tumor virology. Int J Cancer 2011; 129:1289-99. [DOI: 10.1002/ijc.26087] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 03/11/2011] [Indexed: 12/17/2022]
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Porta C, Riboldi E, Sica A. Mechanisms linking pathogens-associated inflammation and cancer. Cancer Lett 2010; 305:250-62. [PMID: 21093147 DOI: 10.1016/j.canlet.2010.10.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 09/29/2010] [Accepted: 10/14/2010] [Indexed: 02/07/2023]
Abstract
It has been estimated that chronic infections with viruses, bacteria and parasites are the causative agents of 8-17% of global cancers burden. Carcinogenesis associated with infections is a complex process, often mediated by chronic inflammatory conditions and accumulating evidence indicate that a smouldering inflammation is a component of the tumor microenvironment and represents the 7th hallmark of cancer. Selected infectious agents promote a cascade of events culminating in chronic inflammatory responses, thus predisposing target tissues to increased cancer susceptibility. A causal link also exists between an inflammatory microenvironment, consisting of inflammatory cells and mediators, and tumor progression. Tumor-Associated Macrophages (TAM) represent the major inflammatory population present in tumors, orchestrating various aspects of cancer, including: diversion and skewing of adaptive responses; cell growth; angiogenesis; matrix deposition and remodelling; construction of a metastatic niche and actual metastasis; response to hormones and chemotherapeutic agents. Recent studies on human and murine tumors indicate that TAM show a remarkable degree of plasticity and functional heterogeneity, during tumour development. In established tumors, TAM acquire an M2 polarized phenotype are engaged in immunosuppression and the promotion of tumor angiogenesis and metastasis. Being a first line of the innate defence mechanisms, macrophages are also equipped with pathogen-recognition receptors, to sense the presence of danger signals, including onco-pathogens. Here we discuss the evidence suggesting a causal relationship between selected infectious agents and the pro-tumoral reprogramming of inflammatory cells, as well as its significance in tumor development. Finally, we discuss the implications of this phenomenon for both cancer prevention and therapy.
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Affiliation(s)
- Chiara Porta
- DISCAFF, University of Piemonte Orientale A. Avogadro, via Bovio 6, Novara, Italy
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Abstract
It has been estimated that viruses are etiological agents in approximately 12% of human cancers. Most of these cancers can be attributed to infections by human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), Epstein-Barr virus (EBV), and Kaposi's sarcoma-associated herpesvirus (KSHV). Prophylactic vaccines against other pathogenic viruses have an excellent record as public health interventions in terms of safety, effectiveness, and ability to reach economically disadvantaged populations. These considerations should prompt efforts to develop and implement vaccines against oncoviruses. Safe and effective HBV and HPV vaccines, based on virus-like particles, are commercially available, and the major focus is now on vaccine delivery, especially to low-resource settings. HCV and EBV vaccines are under active development, but few clinical trials have been conducted, and none of the candidate vaccines has proven to be sufficiently effective to warrant commercialization. Efforts to develop KSHV vaccines have been more limited.
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Affiliation(s)
- John T Schiller
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA.
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Ressing ME, Wiertz EJ. Manipulation of the immune response by Epstein–Barr virus and Kaposi's sarcoma-associated herpesvirus: Consequences for tumor development. Semin Cancer Biol 2008; 18:379-80. [DOI: 10.1016/j.semcancer.2008.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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