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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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Ba Z, Meng FL, Gostissa M, Huang PY, Ke Q, Wang Z, Dao MN, Fujiwara Y, Rajewsky K, Zhang B, Alt FW. A Rapid Embryonic Stem Cell-Based Mouse Model for B-cell Lymphomas Driven by Epstein-Barr Virus Protein LMP1. Cancer Immunol Res 2015; 3:641-9. [PMID: 25934172 DOI: 10.1158/2326-6066.cir-15-0058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 03/17/2015] [Indexed: 01/21/2023]
Abstract
The Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) contributes to oncogenic human B-cell transformation. Mouse B cells conditionally expressing LMP1 are not predisposed to B-cell malignancies, as LMP1-expressing B cells are eliminated by T cells. However, mice with conditional B-cell LMP1 expression and genetic elimination of α/β and γ/δ T cells ("CLT" mice) die early in association with B-cell lymphoproliferation and lymphomagenesis. Generation of CLT mice involves in-breeding multiple independently segregating alleles. Thus, although introduction of additional activating or knockout mutations into the CLT model is desirable for further B-cell expansion and immunosurveillance studies, doing such experiments by germline breeding is time-consuming, expensive, and sometimes unfeasible. To generate a more tractable model, we generated clonal CLT embryonic stem (ES) cells from CLT embryos and injected them into RAG2-deficient blastocysts to generate chimeric mice, which, like germline CLT mice, harbor splenic CLT B cells and lack T cells. CLT chimeric mice generated by this RAG2-deficient blastocyst complementation ("RDBC") approach die rapidly in association with B-cell lymphoproliferation and lymphoma. Because CLT lymphomas routinely express the activation-induced cytidine deaminase (AID) antibody diversifier, we tested potential AID roles by eliminating the AID gene in CLT ES cells and testing them via RDBC. We found that CLT and AID-deficient CLT ES chimeras had indistinguishable phenotypes, showing that AID is not essential for LMP1-induced lymphomagenesis. Beyond expanding accessibility and utility of CLT mice as a cancer immunotherapy model, our studies provide a new approach for facilitating generation of genetically complex mouse cancer models.
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Affiliation(s)
- Zhaoqing Ba
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Fei-Long Meng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Monica Gostissa
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Pei-Yi Huang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Qiang Ke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Diagnostics, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zhe Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mai N Dao
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Yuko Fujiwara
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Klaus Rajewsky
- Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
| | - Baochun Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Department of Genetics, Harvard Medical School, Boston, Massachusetts.
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