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Xu M, Feng R, Liu Z, Zhou X, Chen Y, Cao Y, Valeri L, Li Z, Liu Z, Cao SM, Liu Q, Xie SH, Chang ET, Jia WH, Shen J, Yao Y, Cai YL, Zheng Y, Zhang Z, Huang G, Ernberg I, Tang M, Ye W, Adami HO, Zeng YX, Lin X. Host genetic variants, Epstein-Barr virus subtypes, and the risk of nasopharyngeal carcinoma: Assessment of interaction and mediation. CELL GENOMICS 2024; 4:100474. [PMID: 38359790 PMCID: PMC10879020 DOI: 10.1016/j.xgen.2023.100474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/29/2023] [Accepted: 12/06/2023] [Indexed: 02/17/2024]
Abstract
Epstein-Barr virus (EBV) and human leukocyte antigen (HLA) polymorphisms are well-known risk factors for nasopharyngeal carcinoma (NPC). However, the combined effects between HLA and EBV on the risk of NPC are unknown. We applied a causal inference framework to disentangle interaction and mediation effects between two host HLA SNPs, rs2860580 and rs2894207, and EBV variant 163364 with a population-based case-control study in NPC-endemic southern China. We discovered the strong interaction effects between the high-risk EBV subtype and both HLA SNPs on NPC risk (rs2860580, relative excess risk due to interaction [RERI] = 4.08, 95% confidence interval [CI] = 2.03-6.14; rs2894207, RERI = 3.37, 95% CI = 1.59-5.15), accounting for the majority of genetic risk effects. These results indicate that HLA genes and the high-risk EBV have joint effects on NPC risk. Prevention strategies targeting the high-risk EBV subtype would largely reduce NPC risk associated with EBV and host genetic susceptibility.
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Affiliation(s)
- Miao Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Ruimei Feng
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030012, Shanxi, China
| | - Zhonghua Liu
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Xiang Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Yanhong Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yulu Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Linda Valeri
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA; School of Mathematics and Statistics, Northeast Normal University, Changchun, China
| | - Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Su-Mei Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qing Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shang-Hang Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ellen T Chang
- Center for Health Sciences, Menlo Park, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jincheng Shen
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Youyuan Yao
- Department of Geriatric Oncology, Jiangsu Province Hospital, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Yong-Lin Cai
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, China
| | - Yuming Zheng
- Guangxi Health Commission Key Laboratory of Molecular Epidemiology of Nasopharyngeal Carcinoma, Wuzhou Red Cross Hospital, Wuzhou, China
| | - Zhe Zhang
- Department of Otolaryngology/Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guangwu Huang
- Department of Otolaryngology/Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Minzhong Tang
- Department of Otolaryngology/Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Epidemiology and Health Statistics & Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.
| | - Hans-Olov Adami
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Clinical Effectiveness Group, Institute of Health and Society, University of Oslo, Oslo, Norway.
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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2
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Palmer WH, Telford M, Navarro A, Santpere G, Norman PJ. Human herpesvirus diversity is altered in HLA class I binding peptides. Proc Natl Acad Sci U S A 2022; 119:e2123248119. [PMID: 35486690 PMCID: PMC9170163 DOI: 10.1073/pnas.2123248119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Herpesviruses are ubiquitous, genetically diverse DNA viruses, with long-term presence in humans associated with infrequent but significant pathology. Human leukocyte antigen (HLA) class I presents intracellularly derived peptide fragments from infected tissue cells to CD8+ T and natural killer cells, thereby directing antiviral immunity. Allotypes of highly polymorphic HLA class I are distinguished by their peptide binding repertoires. Because this HLA class I variation is a major determinant of herpesvirus disease, we examined if sequence diversity of virus proteins reflects evasion of HLA presentation. Using population genomic data from Epstein–Barr virus (EBV), human cytomegalovirus (HCMV), and Varicella–Zoster virus, we tested whether diversity differed between the regions of herpesvirus proteins that can be recognized, or not, by HLA class I. Herpesviruses exhibit lytic and latent infection stages, with the latter better enabling immune evasion. Whereas HLA binding peptides of lytic proteins are conserved, we found that EBV and HCMV proteins expressed during latency have increased peptide sequence diversity. Similarly, latent, but not lytic, herpesvirus proteins have greater population structure in HLA binding than nonbinding peptides. Finally, we found patterns consistent with EBV adaption to the local HLA environment, with less efficient recognition of EBV isolates by high-frequency HLA class I allotypes. Here, the frequency of CD8+ T cell epitopes inversely correlated with the frequency of HLA class I recognition. Previous analyses have shown that pathogen-mediated natural selection maintains exceptional polymorphism in HLA residues that determine peptide recognition. Here, we show that HLA class I peptide recognition impacts diversity of globally widespread pathogens.
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Affiliation(s)
- William H. Palmer
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, CO 80045
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO 80045
| | - Marco Telford
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (Universitat Pompeu Fabra - Consejo Superior de Investigaciones Científicas), Department of Medicine and Life Sciences (MELIS), Barcelona Biomedical Research Park, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats and Universitat Pompeu Fabra, 08010 Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Barcelona Beta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain
| | - Gabriel Santpere
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, CO 80045
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO 80045
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3
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Zhang WL, Zhang JB, Wang TM, Wu YX, He YQ, Xue WQ, Liao Y, Deng CM, Li DH, Wu ZY, Yang DW, Zheng XH, Li XZ, Zhou T, Zhang PF, Zhang SD, Hu YZ, Jia WH. Genomic landscape of Epstein–Barr virus in familial nasopharyngeal carcinoma. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To better understand the genomic characteristics of Epstein–Barr virus (EBV) in familial nasopharyngeal carcinoma (NPC), we sequenced the EBV genomes by whole-genome capture in 38 unrelated patients with NPC family history in first-degree relatives and 47 healthy controls, including 13 with family history and 34 without. Compared with type 1 reference genome, mutation hotspots were observed in the latent gene regions of EBV in familial NPC cases. Population structure analysis showed that one cluster has a higher frequency in familial cases than in controls (OR=5.33, 95 % CI 2.50–11.33, P=1.42×10−5), and similar population structure composition was observed among familial and sporadic NPC cases in high-endemic areas. By genome-wide association analysis, four variants were found to be significantly associated with familial NPC. Consistent results were observed in the meta-analysis integrating two published case-control EBV sequencing studies in NPC high-endemic areas. High-risk haplotypes of EBV composed of 34 variants were associated with familial NPC risk (OR=13.85, 95 % CI 4.13–46.44, P=2.06×10−5), and higher frequency was observed in healthy blood-relative controls with NPC family history (9/13, 69.23 %) than those without family history (16/34, 47.06%). This study suggested the potential contribution of EBV high-risk subtypes to familial aggregation of NPC.
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Affiliation(s)
- Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Zi-Yi Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-sen University, Guangzhou, PR China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Wei-Hua Jia
- School of Public Health, Sun Yat-sen University, Guangzhou, PR China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, PR China
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4
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Rostgaard K, Stensballe LG, Søegaard SH, Kamper-Jørgensen M, Hjalgrim H. Childcare attendance and risk of infectious mononucleosis: A population-based Danish cohort study. PLoS One 2021; 16:e0261665. [PMID: 34937060 PMCID: PMC8694440 DOI: 10.1371/journal.pone.0261665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 12/07/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The risk of infectious mononucleosis (IM) is affected both by crowding and by sibship structure, i.e., number and signed age differential between an index child and a sibling. Siblings provide protection against IM by pre-empting delayed primary Epstein-Barr virus infection with its associated high risk of IM. The association between childcare attendance and risk of IM, on the other hand, has never been studied in a large, well-characterized cohort. METHODS Danish children born in July 1992 through 2016 with a completely known simple childcare attendance history before age 1.5 years (n = 908,866) were followed up for a hospital contact with an IM diagnosis at ages 1.5-26 years. Hazard ratios (HRs) of IM for an additional year of exposure were obtained from stratified Cox regression analyses, stratified by sex and year of birth, with age as the underlying time scale, adjusted for sibship structure, and sociodemographic variables including parental ethnicity and maternal age. RESULTS An additional year of exclusively attending a daycare home (max 5 children) yielded HR = 0.90 (95% confidence interval 0.81-1.00), and similarly, each year of exclusively attending a childcare institution (e.g., crèche) yielded HR = 0.94 (0.84-1.06). CONCLUSIONS Forwarding enrollment in childcare by a year lowers the risk of IM later in life much less than having an additional sibling of comparable age and has no practical public health implications. We find our results suggestive of a random threshold for successful Epstein-Barr virus infection that is more easily reached by a sibling than the collective of playmates in daycare homes or childcare institutions.
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Affiliation(s)
- Klaus Rostgaard
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Lone Graff Stensballe
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Signe Holst Søegaard
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark.,Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
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5
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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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6
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Wang H, Fu BB, Gale RP, Liang Y. NK-/T-cell lymphomas. Leukemia 2021; 35:2460-2468. [PMID: 34117356 PMCID: PMC8410593 DOI: 10.1038/s41375-021-01313-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 01/31/2023]
Abstract
Natural killer/T-cell lymphoma (NKTL) is a sub-type of Epstein-Barr virus (EBV)-related non-Hodgkin lymphomas common in Asia and Latin America but rare elsewhere. Its pathogenesis is complex and incompletely understood. Lymphoma cells are transformed from NK- or T-cells, sometimes both. EBV-infection and subsequent genetic alterations in infected cells are central to NKTL development. Hemophagocytic syndrome is a common complication. Accurate staging is important to predict outcomes but there is controversy which system is best. More than two-thirds of NKTL lympohmas are localized at diagnosis, are frequently treated with radiation therapy only and have 5-year survival of about 70 percent. Persons with advanced NKTLs receive radiation therapy synchronously or metachronously with diverse multi-drug chemotherapy typically including L-asparginase with 5-year survival of about 40 percent. Some persons with widespread NKTL receive chemotherapy only. There are few data on safety and efficacy of high-dose therapy and a haematopoietic cell autotransplant. Immune therapies, histone deacetylase (HDAC)-inhibitors and other drugs are in early clinical trials. There are few randomized controlled clinical trials in NKTLs and no therapy strategy is clearly best; more effective therapy(ies) are needed. Some consensus recommendations are not convincingly evidence-based. Mechanisms of multi-drug resistance are considered. We discuss these issues including recent advances in our understanding of and therapy of NKTLs.
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Affiliation(s)
- Hua Wang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Bi-Bo Fu
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Robert Peter Gale
- Haematology Research Centre, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Yang Liang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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7
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Saleem A, Natkunam Y. Extranodal NK/T-Cell Lymphomas: The Role of Natural Killer Cells and EBV in Lymphomagenesis. Int J Mol Sci 2020; 21:E1501. [PMID: 32098335 PMCID: PMC7073055 DOI: 10.3390/ijms21041501] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
Keywords: NK cells, extranodal NK/T-cell lymphoma, EBV.
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Affiliation(s)
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
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8
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Chen JN, Zhou L, Qiu XM, Yang RH, Liang J, Pan YH, Li HF, Peng GR, Shao CK. Determination and genome-wide analysis of Epstein-Barr virus (EBV) sequences in EBV-associated gastric carcinoma from Guangdong, an endemic area of nasopharyngeal carcinoma. J Med Microbiol 2018; 67:1614-1627. [PMID: 30239329 DOI: 10.1099/jmm.0.000839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
About 10 % of gastric carcinoma worldwide is associated with EBV, which is defined as EBV-associated gastric carcinoma (EBVaGC). To date, EBV sequence data from EBVaGC in Guangdong, China, an endemic area of nasopharyngeal carcinoma (NPC), are not available. In the present study, two EBV genomes from EBVaGC specimens from Guangdong (designated as GDGC1 and GDGC2) were determined by next-generation sequencing, de novo assembly and joining of contigs by Sanger sequencing. In addition, we sequenced EBV from two Korean EBVaGC cell lines, YCCEL1 and SNU-719. Genomic diversity, including single nucleotide polymorphisms (SNPs) and insertions and deletions (indels), phylogenetic analysis and rates of protein evolution, was performed using bioinformatics software. The four gastric carcinoma-derived EBV (GC-EBV) were all type I. Compared with the reference EBV genome, a total of 1815 SNPs (146 indels), 1519 SNPs (106 indels), 1812 SNPs (126 indels) and 1484 SNPs (106 indels) were found in GDGC1, GDGC2, YCCEL1 and SNU-719, respectively. These variations were distributed across the entire genome, especially in latent genes. In contrast, the sequences of promoters and non-coding RNAs were strictly conserved. Phylogenetic analyses suggested the presence of at least two parental lineages of EBV among the GC-EBV genomes. Rates of protein evolution analyses showed that lytic genes were under purifying selection; in contrast, latency genes were under positive selection. In conclusion, this study determined the EBV genomes in EBVaGC from Guangdong and performed a detailed genome-wide analysis of GC-EBV, which would be helpful for further understanding of the relationship between EBV genomic variation and EBVaGC carcinogenesis.
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Affiliation(s)
- Jian-Ning Chen
- 1Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No.600 Tianhe Road, Guangzhou 510630, PR China
| | - Lu Zhou
- 1Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No.600 Tianhe Road, Guangzhou 510630, PR China
| | - Xin-Min Qiu
- 2Genetic Testing Lab, Guangdong Provincial Hospital of Chinese Medicine, No. 111 Dade Road, Guangzhou 510120, PR China.,3DRIGEN Co. Ltd., No.121-122 Chuangye Yuan, Shenzhen 518100, PR China
| | - Ri-Hong Yang
- 1Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No.600 Tianhe Road, Guangzhou 510630, PR China
| | - Jing Liang
- 1Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No.600 Tianhe Road, Guangzhou 510630, PR China
| | - Yu-Hang Pan
- 1Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No.600 Tianhe Road, Guangzhou 510630, PR China
| | - Hai-Feng Li
- 1Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No.600 Tianhe Road, Guangzhou 510630, PR China
| | - Guo-Rong Peng
- 3DRIGEN Co. Ltd., No.121-122 Chuangye Yuan, Shenzhen 518100, PR China
| | - Chun-Kui Shao
- 1Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No.600 Tianhe Road, Guangzhou 510630, PR China
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9
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Abstract
Epstein-Barr virus (EBV) is a common human herpes virus known to infect the majority of the world population. Infection with EBV is often asymptomatic but can manifest in a range of pathologies from infectious mononucleosis to severe cancers of epithelial and lymphocytic origin. Indeed, in the past decade, EBV has been linked to nearly 10% of all gastric cancers. Furthermore, recent advances in high-throughput next-generation sequencing and the development of humanized mice, which effectively model EBV pathogenesis, have led to a wealth of knowledge pertaining to strain variation and host-pathogen interaction. This review highlights some recent advances in our understanding of EBV biology, focusing on new findings on the early events of infection, the role EBV plays in gastric cancer, new strain variation, and humanized mouse models of EBV infection.
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Affiliation(s)
- Brent A Stanfield
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University Medical Center, Durham, NC, USA
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University Medical Center, Durham, NC, USA
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10
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Zhou L, Chen JN, Qiu XM, Pan YH, Zhang ZG, Shao CK. Comparative analysis of 22 Epstein-Barr virus genomes from diseased and healthy individuals. J Gen Virol 2017; 98:96-107. [PMID: 28036243 DOI: 10.1099/jgv.0.000699] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) infects most of the world's population and is causally associated with several human cancers, but little is known about how EBV genetic variations might influence EBV-associated diseases and their geographical patterns. In the present study, 22 EBV whole-genome sequences from diseased and healthy individuals were analysed to explore EBV sequence variations at the whole-genome level. We found that the 22 EBV genomes were generally highly similar to each other at the genome level. However, varying degrees of genetic diversity were detected across the entire genome, especially in the latent genes. In contrast, the sequences of promoters and non-coding RNAs were strictly conserved. These findings suggested that both latent genes and non-coding RNAs play important roles in the EBV life cycle. When we investigated changes in known T-cell epitopes in some latent and lytic proteins, we observed that some T-cell epitopes were changed, while others were conserved. These findings indicate that the effect of EBV variations in protein sequences that seem to have been selected by the host immune system should be considered when conducting EBV-targeted immunotherapy. Taken together, our results provide a global view of EBV genome sequence variation, which not only is important for designing vaccines and immunotherapy for EBV but also adds to the understanding of EBV biology and the relationships between viral sequence variation and EBV-associated diseases.
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Affiliation(s)
- Lu Zhou
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No. 600 Tianhe Road, Guangzhou 510630, PR China
| | - Jian-Ning Chen
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No. 600 Tianhe Road, Guangzhou 510630, PR China
| | - Xin-Min Qiu
- DRIGEN Co. Ltd, No. 121-122 Chuangye Yuan, Shenzhen 518100, PR China
| | - Yu-Hang Pan
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No. 600 Tianhe Road, Guangzhou 510630, PR China
| | - Zhi-Gang Zhang
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No. 600 Tianhe Road, Guangzhou 510630, PR China
| | - Chun-Kui Shao
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, No. 600 Tianhe Road, Guangzhou 510630, PR China
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Epstein-Barr virus microRNAs reduce immune surveillance by virus-specific CD8+ T cells. Proc Natl Acad Sci U S A 2016; 113:E6467-E6475. [PMID: 27698133 DOI: 10.1073/pnas.1605884113] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Infection with Epstein-Barr virus (EBV) affects most humans worldwide and persists life-long in the presence of robust virus-specific T-cell responses. In both immunocompromised and some immunocompetent people, EBV causes several cancers and lymphoproliferative diseases. EBV transforms B cells in vitro and encodes at least 44 microRNAs (miRNAs), most of which are expressed in EBV-transformed B cells, but their functions are largely unknown. Recently, we showed that EBV miRNAs inhibit CD4+ T-cell responses to infected B cells by targeting IL-12, MHC class II, and lysosomal proteases. Here we investigated whether EBV miRNAs also counteract surveillance by CD8+ T cells. We have found that EBV miRNAs strongly inhibit recognition and killing of infected B cells by EBV-specific CD8+ T cells through multiple mechanisms. EBV miRNAs directly target the peptide transporter subunit TAP2 and reduce levels of the TAP1 subunit, MHC class I molecules, and EBNA1, a protein expressed in most forms of EBV latency and a target of EBV-specific CD8+ T cells. Moreover, miRNA-mediated down-regulation of the cytokine IL-12 decreases the recognition of infected cells by EBV-specific CD8+ T cells. Thus, EBV miRNAs use multiple, distinct pathways, allowing the virus to evade surveillance not only by CD4+ but also by antiviral CD8+ T cells.
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12
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Identification and Characterization of Epstein-Barr Virus Genomes in Lung Carcinoma Biopsy Samples by Next-Generation Sequencing Technology. Sci Rep 2016; 6:26156. [PMID: 27189712 PMCID: PMC4870493 DOI: 10.1038/srep26156] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/27/2016] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) has been detected in the tumor cells of several cancers, including some cases of lung carcinoma (LC). However, the genomic characteristics and diversity of EBV strains associated with LC are poorly understood. In this study, we sequenced the EBV genomes isolated from four primary LC tumor biopsy samples, designated LC1 to LC4. Comparative analysis demonstrated that LC strains were more closely related to GD1 strain. Compared to GD1 reference genome, a total of 520 variations in all, including 498 substitutions, 12 insertions, and 10 deletions were found. Latent genes were found to harbor the most numbers of nonsynonymous mutations. Phylogenetic analysis showed that all LC strains were closely related to Asian EBV strains, whereas different from African/American strains. LC2 genome was distinct from the other three LC genomes, suggesting at least two parental lineages of EBV among the LC genomes may exist. All LC strains could be classified as China 1 and V-val subtype according to the amino acid sequence of LMP1 and EBNA1, respectively. In conclusion, our results showed the genomic diversity among EBV genomes isolated from LC, which might facilitate to uncover the previously unknown variations of pathogenic significance.
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13
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Abstract
BACKGROUND Posttransplant lymphoproliferative disorder (PTLD) is an infrequent but serious complication of solid organ transplantation. Early detection and initiation of therapy may improve outcomes. The purpose of this study was to identify human leukocyte antigen (HLA) type as risk and prognostic factors for PTLD. METHODS A review was undertaken to identify PTLD cases treated at our institution over the past 25 years. Logistic regression and Cox Proportional Hazards were used to model risk factors for PTLD and clinical outcomes in patients with PTLD. RESULTS One hundred six cases of PTLD were identified with 1392 solid-organ transplant recipient controls. Epstein-Barr virus (EBV) seronegative status pretransplant (odds ratio [OR] = 7.61, 95% confidence interval [95% CI] = 3.83-15.1) and receipt of a nonkidney transplant were associated with an increased risk of PTLD. Being African American and receipt of a living-related kidney transplant were associated with a decreased risk of PTLD. The HLA-B40 group was a risk factor for PTLD in EBV-seronegative individuals (OR = 8.38, 95% CI = 2.18-32.3), whereas HLA-B8 was a risk factor for PTLD in EBV-seropositive individuals (OR = 3.29, 95% CI = 1.52-7.09). Specific HLA types were not associated with graft failure or mortality after PTLD diagnosis. In PTLD patients, central nervous system (CNS) involvement, bone marrow involvement, T-cell PTLD, and age were associated with increased mortality. CONCLUSION Human leukocyte antigen-B40 group and HLA-B8 were identified as novel susceptibility factors for PTLD in EBV-seropositive and EBV-seronegative individuals, respectively. Multicentered, large prospective studies of PTLD with correlative immunologic work are needed to test the significance of these observed associations.
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14
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Palser AL, Grayson NE, White RE, Corton C, Correia S, Ba Abdullah MM, Watson SJ, Cotten M, Arrand JR, Murray PG, Allday MJ, Rickinson AB, Young LS, Farrell PJ, Kellam P. Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection. J Virol 2015; 89:5222-37. [PMID: 25787276 PMCID: PMC4442510 DOI: 10.1128/jvi.03614-14] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/08/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Epstein-Barr virus (EBV) infects most of the world's population and is causally associated with several human cancers, but little is known about how EBV genetic variation might influence infection or EBV-associated disease. There are currently no published wild-type EBV genome sequences from a healthy individual and very few genomes from EBV-associated diseases. We have sequenced 71 geographically distinct EBV strains from cell lines, multiple types of primary tumor, and blood samples and the first EBV genome from the saliva of a healthy carrier. We show that the established genome map of EBV accurately represents all strains sequenced, but novel deletions are present in a few isolates. We have increased the number of type 2 EBV genomes sequenced from one to 12 and establish that the type 1/type 2 classification is a major feature of EBV genome variation, defined almost exclusively by variation of EBNA2 and EBNA3 genes, but geographic variation is also present. Single nucleotide polymorphism (SNP) density varies substantially across all known open reading frames and is highest in latency-associated genes. Some T-cell epitope sequences in EBNA3 genes show extensive variation across strains, and we identify codons under positive selection, both important considerations for the development of vaccines and T-cell therapy. We also provide new evidence for recombination between strains, which provides a further mechanism for the generation of diversity. Our results provide the first global view of EBV sequence variation and demonstrate an effective method for sequencing large numbers of genomes to further understand the genetics of EBV infection. IMPORTANCE Most people in the world are infected by Epstein-Barr virus (EBV), and it causes several human diseases, which occur at very different rates in different parts of the world and are linked to host immune system variation. Natural variation in EBV DNA sequence may be important for normal infection and for causing disease. Here we used rapid, cost-effective sequencing to determine 71 new EBV sequences from different sample types and locations worldwide. We showed geographic variation in EBV genomes and identified the most variable parts of the genome. We identified protein sequences that seem to have been selected by the host immune system and detected variability in known immune epitopes. This gives the first overview of EBV genome variation, important for designing vaccines and immune therapy for EBV, and provides techniques to investigate relationships between viral sequence variation and EBV-associated diseases.
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MESH Headings
- Amino Acid Sequence
- Antigens, Viral/genetics
- Carrier State/virology
- Cell Line, Tumor
- DNA, Viral/genetics
- Epitopes, T-Lymphocyte/genetics
- Epstein-Barr Virus Infections/virology
- Epstein-Barr Virus Nuclear Antigens/genetics
- Genetic Variation
- Genome, Viral
- Herpesvirus 4, Human/classification
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/isolation & purification
- Humans
- Phylogeny
- Polymorphism, Single Nucleotide
- Recombination, Genetic
- Viral Matrix Proteins/genetics
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Affiliation(s)
- Anne L Palser
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Robert E White
- Section of Virology, Imperial College Faculty of Medicine, London, United Kingdom
| | - Craig Corton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Samantha Correia
- Section of Virology, Imperial College Faculty of Medicine, London, United Kingdom
| | | | - Simon J Watson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - John R Arrand
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paul G Murray
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Martin J Allday
- Section of Virology, Imperial College Faculty of Medicine, London, United Kingdom
| | - Alan B Rickinson
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Lawrence S Young
- University of Warwick, University House, Coventry, United Kingdom
| | - Paul J Farrell
- Section of Virology, Imperial College Faculty of Medicine, London, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom Division of Infection and Immunity, UCL, London, United Kingdom
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15
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Epstein-Barr Virus: From the Detection of Sequence Polymorphisms to the Recognition of Viral Types. Curr Top Microbiol Immunol 2015; 390:119-48. [PMID: 26424646 DOI: 10.1007/978-3-319-22822-8_7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The Epstein-Barr virus is etiologically linked with the development of benign and malignant diseases, characterized by their diversity and a heterogeneous geographic distribution across the world. The virus possesses a 170-kb-large genome that encodes for multiple proteins and non-coding RNAs. Early on there have been numerous attempts to link particular diseases with particular EBV strains, or at least with viral genetic polymorphisms. This has given rise to a wealth of information whose value has been difficult to evaluate for at least four reasons. First, most studies have looked only at one particular gene and missed the global picture. Second, they usually have not studied sufficient numbers of diseased and control cases to reach robust statistical significance. Third, the functional significance of most polymorphisms has remained unclear, although there are exceptions such as the 30-bp deletion in LMP1. Fourth, different biological properties of the virus do not necessarily equate with a different pathogenicity. This was best illustrated by the type 1 and type 2 viruses that markedly differ in terms of their transformation abilities, yet do not seem to cause different diseases. Reciprocally, environmental and genetic factors in the host are likely to influence the outcome of infections with the same virus type. However, with recent developments in recombinant virus technology and in the availability of high throughput sequencing, the tide is now turning. The availability of 23 complete or nearly complete genomes has led to the recognition of viral subtypes, some of which possess nearly identical genotypes. Furthermore, there is growing evidence that some genetic polymorphisms among EBV strains markedly influence the biological and clinical behavior of the virus. Some virus strains are endowed with biological properties that explain crucial clinical features of patients with EBV-associated diseases. Although we now have a better overview of the genetic diversity within EBV genomes, it has also become clear that defining phenotypic traits evinced by cells infected by different viruses usually result from the combination of multiple polymorphisms that will be difficult to identify in their entirety. However, the steadily increasing number of sequenced EBV genomes and cloned EBV BACS from diseased and healthy patients will facilitate the identification of the key polymorphisms that condition the biological and clinical behavior of the viruses. This will allow the development of preventative and therapeutic approaches against highly pathogenic viral strains.
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16
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Abstract
What is wild-type Epstein-Barr virus and are there genetic differences in EBV strains that contribute to some of the EBV-associated diseases? Recent progress in DNA sequencing has resulted in many new Epstein-Barr virus (EBV) genome sequences becoming available. EBV isolates worldwide can be grouped into type 1 and type 2, a classification based on the EBNA2 gene sequence. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than type 2 EBV and molecular mechanisms that may account for this difference in cell transformation are now becoming understood. Study of geographic variation of EBV strains independent of the type 1/type 2 classification and systematic investigation of the relationship between viral strains, infection and disease are now becoming possible. So we should consider more directly whether viral sequence variation might play a role in the incidence of some EBV-associated diseases.
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Affiliation(s)
- Paul J Farrell
- Section of Virology, Department of Medicine, Imperial College, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
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17
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Taylor GS, Jia H, Harrington K, Lee LW, Turner J, Ladell K, Price DA, Tanday M, Matthews J, Roberts C, Edwards C, McGuigan L, Hartley A, Wilson S, Hui EP, Chan ATC, Rickinson AB, Steven NM. A recombinant modified vaccinia ankara vaccine encoding Epstein-Barr Virus (EBV) target antigens: a phase I trial in UK patients with EBV-positive cancer. Clin Cancer Res 2014; 20:5009-22. [PMID: 25124688 PMCID: PMC4340506 DOI: 10.1158/1078-0432.ccr-14-1122-t] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE Epstein-Barr virus (EBV) is associated with several cancers in which the tumor cells express EBV antigens EBNA1 and LMP2. A therapeutic vaccine comprising a recombinant vaccinia virus, MVA-EL, was designed to boost immunity to these tumor antigens. A phase I trial was conducted to demonstrate the safety and immunogenicity of MVA-EL across a range of doses. EXPERIMENTAL DESIGN Sixteen patients in the United Kingdom (UK) with EBV-positive nasopharyngeal carcinoma (NPC) received three intradermal vaccinations of MVA-EL at 3-weekly intervals at dose levels between 5 × 10(7) and 5 × 10(8) plaque-forming units (pfu). Blood samples were taken at screening, after each vaccine cycle, and during the post-vaccination period. T-cell responses were measured using IFNγ ELISpot assays with overlapping EBNA1/LMP2 peptide mixes or HLA-matched epitope peptides. Polychromatic flow cytometry was used to characterize functionally responsive T-cell populations. RESULTS Vaccination was generally well tolerated. Immunity increased after vaccination to at least one antigen in 8 of 14 patients (7/14, EBNA1; 6/14, LMP2), including recognition of epitopes that vary between EBV strains associated with different ethnic groups. Immunophenotypic analysis revealed that vaccination induced differentiation and functional diversification of responsive T-cell populations specific for EBNA1 and LMP2 within the CD4 and CD8 compartments, respectively. CONCLUSIONS MVA-EL is safe and immunogenic across diverse ethnicities and thus suitable for use in trials against different EBV-positive cancers globally as well as in South-East Asia where NPC is most common. The highest dose (5 × 10(8) pfu) is recommended for investigation in current phase IB and II trials.
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Affiliation(s)
- Graham S Taylor
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Hui Jia
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kevin Harrington
- Division of Cancer Biology, The Institute of Cancer Research/The Royal Marsden Hospital, London, United Kingdom
| | - Lip Wai Lee
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - James Turner
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Manjit Tanday
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jen Matthews
- Division of Cancer Biology, The Institute of Cancer Research/The Royal Marsden Hospital, London, United Kingdom
| | - Claudia Roberts
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ceri Edwards
- Cancer Research UK Drug Development Office, London, United Kingdom
| | - Lesley McGuigan
- Cancer Research UK Drug Development Office, London, United Kingdom
| | - Andrew Hartley
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Steve Wilson
- Health Protection Agency, West Midlands Public Health Laboratory, Heart of England Foundation Trust, Bordesley Green East, Birmingham, United Kingdom
| | - Edwin P Hui
- Partner State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Hong Kong Cancer Institute and Li Ka Shing Institute for Health Sciences, Department of Clinical Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Anthony T C Chan
- Partner State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Hong Kong Cancer Institute and Li Ka Shing Institute for Health Sciences, Department of Clinical Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Alan B Rickinson
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Neil M Steven
- Cancer Research UK Centre, School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom.
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18
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Genomic diversity of Epstein-Barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples. J Virol 2014; 88:10662-72. [PMID: 24991008 DOI: 10.1128/jvi.01665-14] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Undifferentiated nasopharyngeal carcinoma (NPC) has a 100% association with Epstein-Barr virus (EBV). However, only three EBV genomes isolated from NPC patients have been sequenced to date, and the role of EBV genomic variations in the pathogenesis of NPC is unclear. We sought to obtain the sequences of EBV genomes in multiple NPC biopsy specimens in the same geographic location in order to reveal their sequence diversity. Three published EBV (B95-8, C666-1, and HKNPC1) genomes were first resequenced using the sequencing workflow of target enrichment of EBV DNA by hybridization, followed by next-generation sequencing, de novo assembly, and joining of contigs by Sanger sequencing. The sequences of eight NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated HKNPC2 to HKNPC9, were then determined. They harbored 1,736 variations in total, including 1,601 substitutions, 64 insertions, and 71 deletions, compared to the reference EBV. Furthermore, genes encoding latent, early lytic, and tegument proteins and glycoproteins were found to contain nonsynonymous mutations of potential biological significance. Phylogenetic analysis showed that the HKNPC6 and -7 genomes, which were isolated from tumor biopsy specimens of advanced metastatic NPC cases, were distinct from the other six NPC-EBV genomes, suggesting the presence of at least two parental lineages of EBV among the NPC-EBV genomes. In conclusion, much greater sequence diversity among EBV isolates derived from NPC biopsy specimens is demonstrated on a whole-genome level through a complete sequencing workflow. Large-scale sequencing and comparison of EBV genomes isolated from NPC and normal subjects should be performed to assess whether EBV genomic variations contribute to NPC pathogenesis. IMPORTANCE This study established a sequencing workflow from EBV DNA capture and sequencing to de novo assembly and contig joining. We reported eight newly sequenced EBV genomes isolated from primary NPC biopsy specimens and revealed the sequence diversity on a whole-genome level among these EBV isolates. At least two lineages of EBV strains are observed, and recombination among these lineages is inferred. Our study has demonstrated the value of, and provided a platform for, genome sequencing of EBV.
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19
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Godinho-Silva C, Marques S, Fontinha D, Veiga-Fernandes H, Stevenson PG, Simas JP. Defining immune engagement thresholds for in vivo control of virus-driven lymphoproliferation. PLoS Pathog 2014; 10:e1004220. [PMID: 24967892 PMCID: PMC4072806 DOI: 10.1371/journal.ppat.1004220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/13/2014] [Indexed: 12/26/2022] Open
Abstract
Persistent infections are subject to constant surveillance by CD8+ cytotoxic T cells (CTL). Their control should therefore depend on MHC class I-restricted epitope presentation. Many epitopes are described for γ-herpesviruses and form a basis for prospective immunotherapies and vaccines. However the quantitative requirements of in vivo immune control for epitope presentation and recognition remain poorly defined. We used Murid Herpesvirus-4 (MuHV-4) to determine for a latently expressed viral epitope how MHC class-I binding and CTL functional avidity impact on host colonization. Tracking MuHV-4 recombinants that differed only in epitope presentation, we found little latitude for sub-optimal MHC class I binding before immune control failed. By contrast, control remained effective across a wide range of T cell functional avidities. Thus, we could define critical engagement thresholds for the in vivo immune control of virus-driven B cell proliferation. Chronic viral infections cause huge morbidity and mortality worldwide. γ-herpesviruses provide an example relevant to all human demographics, causing, inter alia, Hodgkin's disease, Burkitt's lymphoma, Kaposi's Sarcoma, and nasopharyngeal carcinoma. The proliferation of latently infected B cells and their control by CD8+ T cells are central to pathogenesis. Although many viral T cell targets have been identified in vitro, the functional impact of their engagement in vivo remains ill-defined. With the well-established Murid Herpesvirus-4 infection model, we used a range of recombinant viruses to define functional thresholds for the engagement of a latently expressed viral epitope. These data advance significantly our understanding of how the immune system must function to control γ-herpesvirus infection, with implications for vaccination and anti-cancer immunotherapy.
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Affiliation(s)
- Cristina Godinho-Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Sofia Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Henrique Veiga-Fernandes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Philip G. Stevenson
- Sir Albert Sakzewski Virus Research Center and Queensland and Children's Medical Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - J. Pedro Simas
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
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20
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Feng BJ. Descriptive, Environmental and Genetic Epidemiology of Nasopharyngeal Carcinoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013. [DOI: 10.1007/978-1-4614-5947-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Epstein-barr virus sequence variation-biology and disease. Pathogens 2012; 1:156-74. [PMID: 25436768 PMCID: PMC4235690 DOI: 10.3390/pathogens1020156] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 10/16/2012] [Accepted: 10/30/2012] [Indexed: 12/12/2022] Open
Abstract
Some key questions in Epstein-Barr virus (EBV) biology center on whether naturally occurring sequence differences in the virus affect infection or EBV associated diseases. Understanding the pattern of EBV sequence variation is also important for possible development of EBV vaccines. At present EBV isolates worldwide can be grouped into Type 1 and Type 2, a classification based on the EBNA2 gene sequence. Type 1 EBV is the most prevalent worldwide but Type 2 is common in parts of Africa. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than Type 2 EBV. Molecular mechanisms that may account for this difference in cell transformation are now becoming clearer. Advances in sequencing technology will greatly increase the amount of whole EBV genome data for EBV isolated from different parts of the world. Study of regional variation of EBV strains independent of the Type 1/Type 2 classification and systematic investigation of the relationship between viral strains, infection and disease will become possible. The recent discovery that specific mutation of the EBV EBNA3B gene may be linked to development of diffuse large B cell lymphoma illustrates the importance that mutations in the virus genome may have in infection and human disease.
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22
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Kwok H, Tong AHY, Lin CH, Lok S, Farrell PJ, Kwong DLW, Chiang AKS. Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy. PLoS One 2012; 7:e36939. [PMID: 22590638 PMCID: PMC3349645 DOI: 10.1371/journal.pone.0036939] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 04/16/2012] [Indexed: 12/15/2022] Open
Abstract
Whether certain Epstein-Barr virus (EBV) strains are associated with pathogenesis of nasopharyngeal carcinoma (NPC) is still an unresolved question. In the present study, EBV genome contained in a primary NPC tumor biopsy was amplified by Polymerase Chain Reaction (PCR), and sequenced using next-generation (Illumina) and conventional dideoxy-DNA sequencing. The EBV genome, designated HKNPC1 (Genbank accession number JQ009376) is a type 1 EBV of approximately 171.5 kb. The virus appears to be a uniform strain in line with accepted monoclonal nature of EBV in NPC but is heterogeneous at 172 nucleotide positions. Phylogenetic analysis with the four published EBV strains, B95-8, AG876, GD1, and GD2, indicated HKNPC1 was more closely related to the Chinese NPC patient-derived strains, GD1 and GD2. HKNPC1 contains 1,589 single nucleotide variations (SNVs) and 132 insertions or deletions (indels) in comparison to the reference EBV sequence (accession number NC007605). When compared to AG876, a strain derived from Ghanaian Burkitt's lymphoma, we found 322 SNVs, of which 76 were non-synonymous SNVs and were shared amongst the Chinese GD1, GD2 and HKNPC1 isolates. We observed 88 non-synonymous SNVs shared only by HKNPC1 and GD2, the only other NPC tumor-derived strain reported thus far. Non-synonymous SNVs were mainly found in the latent, tegument and glycoprotein genes. The same point mutations were found in glycoprotein (BLLF1 and BALF4) genes of GD1, GD2 and HKNPC1 strains and might affect cell type specific binding. Variations in LMP1 and EBNA3B epitopes and mutations in Cp (11404 C>T) and Qp (50134 G>C) found in GD1, GD2 and HKNPC1 could potentially affect CD8+ T cell recognition and latent gene expression pattern in NPC, respectively. In conclusion, we showed that whole genome sequencing of EBV in NPC may facilitate discovery of previously unknown variations of pathogenic significance.
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Affiliation(s)
- Hin Kwok
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Amy H. Y. Tong
- Genome Research Centre, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chi Ho Lin
- Genome Research Centre, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Si Lok
- Genome Research Centre, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul J. Farrell
- Section of Virology, Imperial College Faculty of Medicine, London, United Kingdom
| | - Dora L. W. Kwong
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alan K. S. Chiang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail:
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23
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Ho WL, Lu MY, Hu FC, Lee CC, Huang LM, Jou ST, Lin DT, Lin KH. Clinical features and major histocompatibility complex genes as potential susceptibility factors in pediatric immune thrombocytopenia. J Formos Med Assoc 2012; 111:370-9. [PMID: 22817814 DOI: 10.1016/j.jfma.2011.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 06/13/2011] [Accepted: 06/22/2011] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND/PURPOSE Immune thrombocytopenia (ITP) is a heterogeneous autoimmune disorder with diverse response rates to treatments that include corticosteroids, intravenous immunoglobulins (IVIG), and splenectomy. The predisposing causes of this autoimmune disorder, one of which is immunogenetic susceptibility, have not been fully determined. We investigated whether clinical features and human leukocyte antigen (HLA) genotypes influence the occurrence, treatment response, and disease duration of childhood ITP in Taiwan. METHODS We performed HLA genotyping of 70 Taiwanese children with ITP and of 70 healthy controls and compared the data. Demographic data were also collected and evaluated. RESULTS The frequencies of heterozygous HLA-A11 and the HLA-Cw1 allele were both significantly decreased in the ITP group (p = 0.0160 and p = 0.0089, respectively), whereas the frequency of heterozygous HLA-DQ5 was significantly increased in the ITP group (p = 0.0057). Patients with HLA-DRB1*11 or -DRB1*15 were more likely to respond poorly to corticosteroids than IVIG (p = 0.0446 and p = 0.0008, respectively). In addition, we observed a positive association between HLA-A11 homozygosity and the development of persistent or chronic ITP [odds ratio (OR) = 6.3165, p = 0.0479]. The presence of HLA-DRB1*08 was, however, negatively correlated with the development of persistent or chronic ITP (OR = 0.1729, p = 0.0657). Children with antecedent of preceding illness (API) and with a younger age of onset were more likely to experience a better treatment response and shorter course of ITP. CONCLUSION We suggest that API, age of onset, and particular HLA class I and class II alleles, may be involved in and influence the occurrence and disease duration of childhood ITP, as well as responses to different therapeutic approaches.
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Affiliation(s)
- Wan-Ling Ho
- Department of Pediatrics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
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24
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Specific mutation of a gammaherpesvirus-expressed antigen in response to CD8 T cell selection in vivo. J Virol 2011; 86:2887-93. [PMID: 22171269 DOI: 10.1128/jvi.06101-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herpesviruses are thought to be highly genetically stable, and their use as vaccine vectors has been proposed. However, studies of the human gammaherpesvirus, Epstein-Barr virus, have found viral isolates containing mutations in HLA class I-restricted epitopes. Using murine gammaherpesvirus 68 expressing ovalbumin (OVA), we examined the stability of a gammaherpesvirus antigenic locus under strong CD8 T cell selection in vivo. OVA-specific CD8 T cells selected viral isolates containing mutations in the OVA locus but minimal alterations in other genomic regions. Thus, a CD8 T cell response to a gammaherpesvirus-expressed antigen that is not essential for replication or pathogenesis can result in selective mutation of that antigen in vivo. This finding may have relevance for the use of herpesvirus vectors for chronic antigen expression in vivo.
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25
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Venturi V, Davenport MP, Swan NG, Doherty PC, Kedzierska K. Consequences of suboptimal priming are apparent for low-avidity T-cell responses. Immunol Cell Biol 2011; 90:216-23. [PMID: 21556018 DOI: 10.1038/icb.2011.36] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The emergence of the novel reassortant A(H1N1)-2009 influenza virus highlighted the threat to the global population posed by an influenza pandemic. Pre-existing CD8(+) T-cell immunity targeting conserved epitopes provides immune protection against newly emerging strains of influenza virus, when minimal antibody immunity exists. However, the occurrence of mutations within T-cell antigenic peptides that enable the virus to evade T-cell recognition constitutes a substantial issue for virus control and vaccine design. Recent evidence suggests that it might be feasible to elicit CD8(+) T-cell memory pools to common virus mutants by pre-emptive vaccination. However, there is a need for a greater understanding of CD8(+) T-cell immunity towards commonly emerging mutants. The present analysis focuses on novel and immunodominant, although of low pMHC-I avidity, CD8(+) T-cell responses directed at the mutant influenza D(b)NP(366) epitope, D(b)NPM6A, following different routes of infection. We used a C57BL/6J model of influenza to dissect the effectiveness of the natural intranasal (i.n.) versus intraperitoneal (i.p.) priming for generating functional CD8(+) T cells towards the D(b)NPM6A epitope. In contrast to comparable CD8(+) T-cell responses directed at the wild-type epitopes, D(b)NP(366) and D(b)PA(224), we found that the priming route greatly affected the numbers, cytokine profiles and TCR repertoire of the responding CD8(+) T cells directed at the D(b)NPM6A viral mutant. As the magnitude, polyfunctionality, and T-cell repertoire diversity are potential determinants of the protective efficacy of CD8(+) T-cell responses, our data have implications for the development of vaccines to combat virus mutants.
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Affiliation(s)
- Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
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26
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Sawada A, Croom-Carter D, Kondo O, Yasui M, Koyama-Sato M, Inoue M, Kawa K, Rickinson AB, Tierney RJ. Epstein–Barr virus latent gene sequences as geographical markers of viral origin: unique EBNA3 gene signatures identify Japanese viruses as distinct members of the Asian virus family. J Gen Virol 2011; 92:1032-1043. [DOI: 10.1099/vir.0.030023-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polymorphisms in Epstein–Barr virus (EBV) latent genes can identify virus strains from different human populations and individual strains within a population. An Asian EBV signature has been defined almost exclusively from Chinese viruses, with little information from other Asian countries. Here we sequenced polymorphic regions of the EBNA1, 2, 3A, 3B, 3C and LMP1 genes of 31 Japanese strains from control donors and EBV-associated T/NK-cell lymphoproliferative disease (T/NK-LPD) patients. Though identical to Chinese strains in their dominant EBNA1 and LMP1 alleles, Japanese viruses were subtly different at other loci. Thus, while Chinese viruses mainly fall into two families with strongly linked ‘Wu’ or ‘Li’ alleles at EBNA2 and EBNA3A/B/C, Japanese viruses all have the consensus Wu EBNA2 allele but fall into two families at EBNA3A/B/C. One family has variant Li-like sequences at EBNA3A and 3B and the consensus Li sequence at EBNA3C; the other family has variant Wu-like sequences at EBNA3A, variants of a low frequency Chinese allele ‘Sp’ at EBNA3B and a consensus Sp sequence at EBNA3C. Thus, EBNA3A/B/C allelotypes clearly distinguish Japanese from Chinese strains. Interestingly, most Japanese viruses also lack those immune-escape mutations in the HLA-A11 epitope-encoding region of EBNA3B that are so characteristic of viruses from the highly A11-positive Chinese population. Control donor-derived and T/NK-LPD-derived strains were similarly distributed across allelotypes and, by using allelic polymorphisms to track virus strains in patients pre- and post-haematopoietic stem-cell transplant, we show that a single strain can induce both T/NK-LPD and B-cell-lymphoproliferative disease in the same patient.
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Affiliation(s)
- Akihisa Sawada
- Department of Hematology/Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
- Institute for Cancer Studies, University of Birmingham, UK
| | | | - Osamu Kondo
- Department of Hematology/Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Masahiro Yasui
- Department of Hematology/Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Maho Koyama-Sato
- Department of Hematology/Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Masami Inoue
- Department of Hematology/Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Keisei Kawa
- Department of Hematology/Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
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27
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Miles JJ, Bulek AM, Cole DK, Gostick E, Schauenburg AJA, Dolton G, Venturi V, Davenport MP, Tan MP, Burrows SR, Wooldridge L, Price DA, Rizkallah PJ, Sewell AK. Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection. PLoS Pathog 2010; 6:e1001198. [PMID: 21124993 PMCID: PMC2987824 DOI: 10.1371/journal.ppat.1001198] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 10/15/2010] [Indexed: 12/02/2022] Open
Abstract
Despite the ∼10(18) αβ T cell receptor (TCR) structures that can be randomly manufactured by the human thymus, some surface more frequently than others. The pinnacles of this distortion are public TCRs, which exhibit amino acid-identical structures across different individuals. Public TCRs are thought to result from both recombinatorial bias and antigen-driven selection, but the mechanisms that underlie inter-individual TCR sharing are still largely theoretical. To examine this phenomenon at the atomic level, we solved the co-complex structure of one of the most widespread and numerically frequent public TCRs in the human population. The archetypal AS01 public TCR recognizes an immunodominant BMLF1 peptide, derived from the ubiquitous Epstein-Barr virus, bound to HLA-A*0201. The AS01 TCR was observed to dock in a diagonal fashion, grasping the solvent exposed peptide crest with two sets of complementarity-determining region (CDR) loops, and was fastened to the peptide and HLA-A*0201 platform with residue sets found only within TCR genes biased in the public response. Computer simulations of a random V(D)J recombination process demonstrated that both TCRα and TCRβ amino acid sequences could be manufactured easily, thereby explaining the prevalence of this receptor across different individuals. Interestingly, the AS01 TCR was encoded largely by germline DNA, indicating that the TCR loci already comprise gene segments that specifically recognize this ancient pathogen. Such pattern recognition receptor-like traits within the αβ TCR system further blur the boundaries between the adaptive and innate immune systems.
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MESH Headings
- Amino Acid Sequence
- Antigens, Viral/immunology
- CD8-Positive T-Lymphocytes
- Computer Simulation
- Crystallization
- Crystallography, X-Ray
- Cytotoxicity, Immunologic
- HLA-A Antigens/immunology
- HLA-A2 Antigen
- Herpesviridae Infections/immunology
- Herpesviridae Infections/metabolism
- Herpesviridae Infections/virology
- Herpesvirus 4, Human/immunology
- Humans
- Immune Tolerance
- Molecular Sequence Data
- Protein Conformation
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombination, Genetic
- Sequence Homology, Amino Acid
- Surface Plasmon Resonance
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Affiliation(s)
- John J Miles
- Department of Infection, Cardiff University School of Medicine, Heath Park, Cardiff, UK.
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28
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Hassen E, Nahla G, Bouaouina N, Chouchane L. The human leukocyte antigen class I genes in nasopharyngeal carcinoma risk. Mol Biol Rep 2009; 37:119-26. [PMID: 19449168 DOI: 10.1007/s11033-009-9548-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 04/30/2009] [Indexed: 10/20/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a virally associated cancer which is highly prevalent in Southeast Asia and North Africa. Several linkage analysis studies suggested the association of susceptibility HLA (Human Leukocyte Antigen) alleles and haplotypes with NPC development. The HLA system is very polymorphic and according to the ethnic group studied, it has been found to have the capacity to confer susceptibility or resistance to NPC. Our aim was to review the most important described genetic associations of HLA class I in NPC and to comment on the inconsistent associations found in the different NPC incidence areas. We believe that the mechanisms of these associations may involve HLA genes through the differential capacity of each allele to present antigens. However, because HLA genes contain various linked candidate genes, HLA-NPC associations should be carefully interpreted.
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Affiliation(s)
- Elham Hassen
- Faculty of Medicine of Monastir, Molecular Immuno-oncology Laboratory, Monastir University, Monastir, Tunisia.
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29
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Lin X, Gudgeon NH, Hui EP, Jia H, Qun X, Taylor GS, Barnardo MCNM, Lin CK, Rickinson AB, Chan ATC. CD4 and CD8 T cell responses to tumour-associated Epstein-Barr virus antigens in nasopharyngeal carcinoma patients. Cancer Immunol Immunother 2008; 57:963-75. [PMID: 18094968 PMCID: PMC11031094 DOI: 10.1007/s00262-007-0427-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 11/10/2007] [Indexed: 01/14/2023]
Abstract
Nasopharyngeal carcinoma (NPC), an Epstein-Barr virus (EBV)-associated tumour common in Southern Chinese populations, is a potentially important target for T cell-based immunotherapy. The tumour cells are HLA class I- and II-positive and express a limited subset of EBV latent proteins, namely the nuclear antigen EBNA1 and the latent membrane proteins LMP2 and (in some cases) LMP1. To ask whether the tumour develops in the presence of a potentially protective host response or in its absence, we set out to determine the prevailing levels of CD4+ and CD8+ T cell memory to these proteins in NPC patients at tumour diagnosis. We first screened healthy Chinese donors against Chinese strain EBNA1, LMP1 and LMP2 sequences in Elispot assays of interferon-gamma release and identified the immunodominant CD4+ and CD8+ epitope peptides presented by common Chinese HLA alleles. Then, comparing 60 patients with >70 healthy controls on peptide epitope mini-panels, we found that T cell memory to CD4 epitopes in all three proteins was unimpaired in the blood of patients at diagnosis. In most cases NPC patients also showed detectable responses to CD8 epitopes relevant to their HLA type, the one consistent exception being the absence in patients of a B*4001-restricted response to LMP2. We infer that NPC arises in patients whose prevailing levels of T cell memory to tumour-associated EBV proteins is largely intact; the therapeutic goal must therefore be to re-direct the existing memory repertoire more effectively against antigen-expressing tumour cells.
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Affiliation(s)
- Xiaorong Lin
- Sir Y. K. Pao Centre for Cancer, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Nancy H. Gudgeon
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Birmingham, B15 2TT UK
| | - Edwin P. Hui
- Sir Y. K. Pao Centre for Cancer, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hui Jia
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Birmingham, B15 2TT UK
| | - Xue Qun
- Sir Y. K. Pao Centre for Cancer, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Graham S. Taylor
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Birmingham, B15 2TT UK
| | - Martin C. N. M. Barnardo
- Department of Transplant Immunology, Oxford Transplant Centre, University of Oxford, Churchill Hospital, Oxford, UK
| | - C. Kit Lin
- Hong Kong Red Cross Blood Transfusion Service, Kowloon, Hong Kong, China
| | - Alan B. Rickinson
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Birmingham, B15 2TT UK
| | - Anthony T. C. Chan
- Sir Y. K. Pao Centre for Cancer, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong, China
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30
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Midgley RS, Bell AI, McGeoch DJ, Rickinson AB. Latent gene sequencing reveals familial relationships among Chinese Epstein-Barr virus strains and evidence for positive selection of A11 epitope changes. J Virol 2003; 77:11517-30. [PMID: 14557637 PMCID: PMC229270 DOI: 10.1128/jvi.77.21.11517-11530.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epstein-Barr virus (EBV) strains from the highly HLA-A11-positive Chinese population are predominantly type 1 and show a variety of sequence changes (relative to the contemporary Caucasian prototype strain B95.8) in the nuclear antigen EBNA3B sequences encoding two immunodominant HLA-A11 epitopes, here called IVT and AVF. This has been interpreted by some as evidence of immune selection and by others as random genetic drift. To study epitope variation in a broader genomic context, we sequenced the whole of EBNA3B and parts of the EBNA2, 3A, and 3C genes from each of 31 Chinese EBV isolates. At each locus, type 1 viruses showed <2% nucleotide divergence from the B95.8 prototype while type 2 sequences remained even closer to the contemporary African prototype Ag876. However, type 1 isolates could clearly be divided into families based on linked patterns of sequence divergence from B95.8 across all four EBNA loci. Different patterns of IVT and AVF variation were associated with the different type 1 families, and there was additional epitope diversity within families. When the EBNA3 gene sequences of type 1 Chinese strains were subject to computer-based analysis, particular codons within the A11-epitope-coding region were among the few identified as being under positive or diversifying selection pressure. From these results, and the observation that mutant epitopes are consistently nonimmunogenic in vivo, we conclude that the immune selection hypothesis remains viable and worthy of further investigation.
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Affiliation(s)
- R S Midgley
- CRUK Institute for Cancer Studies, University of Birmingham, Birmingham B15 2TT, United Kingdom
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