1
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Wong KW, Hui KF, Lam KP, Kwong DLW, Lung ML, Yang W, Chiang AKS. Meta-analysis of Epstein-Barr virus genomes in Southern Chinese identifies genetic variants and high risk viral lineage associated with nasopharyngeal carcinoma. PLoS Pathog 2024; 20:e1012263. [PMID: 38805547 PMCID: PMC11161099 DOI: 10.1371/journal.ppat.1012263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/07/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Genetic variants in Epstein-Barr virus (EBV) have been strongly associated with nasopharyngeal carcinoma (NPC) in South China. However, different results regarding the most significant viral variants, with polymorphisms in EBER2 and BALF2 loci, have been reported in separate studies. In this study, we newly sequenced 100 EBV genomes derived from 61 NPC cases and 39 population controls. Comprehensive genomic analyses of EBV sequences from both NPC patients and healthy carriers in South China were conducted, totaling 279 cases and 227 controls. Meta-analysis of genome-wide association study revealed a 4-bp deletion downstream of EBER2 (coordinates, 7188-7191; EBER-del) as the most significant variant associated with NPC. Furthermore, multiple viral variants were found to be genetically linked to EBER-del forming a risk haplotype, suggesting that multiple viral variants might be associated with NPC pathogenesis. Population structure and phylogenetic analyses further characterized a high risk EBV lineage for NPC revealing a panel of 38 single nucleotide polymorphisms (SNPs), including those in the EBER2 and BALF2 loci. With linkage disequilibrium clumping and feature selection algorithm, the 38 SNPs could be narrowed down to 9 SNPs which can be used to accurately detect the high risk EBV lineage. In summary, our study provides novel insight into the role of EBV genetic variation in NPC pathogenesis by defining a risk haplotype of EBV for downstream functional studies and identifying a single high risk EBV lineage characterized by 9 SNPs for potential application in population screening of NPC.
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Affiliation(s)
- Ka Wo Wong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kwai Fung Hui
- Department of Pathology, United Christian Hospital, Hong Kong SAR, China
| | - Ki Pui Lam
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Dora Lai-wan Kwong
- Department of Clinical Oncology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maria Li Lung
- Department of Clinical Oncology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Alan K. S. Chiang
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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2
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Chai AWY, Yee SM, Lee HM, Abdul Aziz N, Yee PS, Marzuki M, Wong KW, Chiang AK, Chow LKY, Dai W, Liu TF, Tan LP, Khoo ASB, Lo KW, Lim PV, Rajadurai P, Lightfoot H, Barthorpe S, Garnett MJ, Cheong SC. Establishment and Characterization of an Epstein-Barr Virus-positive Cell Line from a Non-keratinizing Differentiated Primary Nasopharyngeal Carcinoma. CANCER RESEARCH COMMUNICATIONS 2024; 4:645-659. [PMID: 38358347 PMCID: PMC10911800 DOI: 10.1158/2767-9764.crc-23-0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/02/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024]
Abstract
Nasopharyngeal carcinoma (NPC), a cancer that is etiologically associated with the Epstein-Barr virus (EBV), is endemic in Southern China and Southeast Asia. The scarcity of representative NPC cell lines owing to the frequent loss of EBV episomes following prolonged propagation and compromised authenticity of previous models underscores the critical need for new EBV-positive NPC models. Herein, we describe the establishment of a new EBV-positive NPC cell line, designated NPC268 from a primary non-keratinizing, differentiated NPC tissue. NPC268 can undergo productive lytic reactivation of EBV and is highly tumorigenic in immunodeficient mice. Whole-genome sequencing revealed close similarities with the tissue of origin, including large chromosomal rearrangements, while whole-genome bisulfite sequencing and RNA sequencing demonstrated a hypomethylated genome and enrichment in immune-related pathways, respectively. Drug screening of NPC268 together with six other NPC cell lines using 339 compounds, representing the largest high-throughput drug testing in NPC, revealed biomarkers associated with specific drug classes. NPC268 represents the first and only available EBV-positive non-keratinizing differentiated NPC model, and extensive genomic, methylomic, transcriptomic, and drug response data should facilitate research in EBV and NPC, where current models are limited. SIGNIFICANCE NPC268 is the first and only EBV-positive cell line derived from a primary non-keratinizing, differentiated nasopharyngeal carcinoma, an understudied but important subtype in Southeast Asian countries. This model adds to the limited number of authentic EBV-positive lines globally that will facilitate mechanistic studies and drug development for NPC.
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Affiliation(s)
| | - Shi Mun Yee
- Translational Cancer Biology Research Unit, Cancer Research Malaysia, Malaysia
| | - Hui Mei Lee
- Translational Cancer Biology Research Unit, Cancer Research Malaysia, Malaysia
| | - Norazlin Abdul Aziz
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Ministry of Health, Malaysia
- Faculty of Medicine, Universiti Teknologi MARA, Malaysia
| | - Pei San Yee
- Translational Cancer Biology Research Unit, Cancer Research Malaysia, Malaysia
| | - Marini Marzuki
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Ministry of Health, Malaysia
| | - Ka Wo Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P.R. China
| | - Alan K.S. Chiang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P.R. China
| | - Larry Ka-Yue Chow
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P.R. China
| | - Wei Dai
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P.R. China
| | - Teng Fei Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P.R. China
| | - Lu Ping Tan
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Ministry of Health, Malaysia
| | - Alan Soo Beng Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Ministry of Health, Malaysia
- Institute for Research, Development and Innovation and School of Postgraduate Studies, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
- Department of Medical Oncology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, P.R. China
| | | | - Pathmanathan Rajadurai
- Subang Jaya Medical Centre, Malaysia
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Malaysia
| | | | - Syd Barthorpe
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Sok Ching Cheong
- Translational Cancer Biology Research Unit, Cancer Research Malaysia, Malaysia
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Malaysia
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3
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Vafapour Z, Tabatabaie FH, Hosseini SY, Haghighat S, Hashemi SMA, Moattari A, Sarvari J. Sequence variation of the Epstein-Barr virus nuclear antigen 1 (EBNA1) gene in chronic lymphocytic leukemia and healthy volunteer subjects. Arch Virol 2023; 169:1. [PMID: 38063941 DOI: 10.1007/s00705-023-05933-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023]
Abstract
Epstein-Barr virus-related malignancies have been linked to variations in the sequences of EBV genes, notably EBNA1. Therefore, the purpose of this study was to examine the DBD/DD domain and USP7 binding domain sequences at the C-terminus of the EBNA1 gene in patients with chronic lymphocytic leukemia (CLL). This study included 40 CLL patients and 21 healthy volunteers. Using commercial kits, total DNA was extracted from buffy coat samples, and each sample was tested for the presence of the EBV genome. The C-terminus of EBNA1 was then amplified from positive samples, using nested PCR. Sanger sequencing was used to identify mutations in the PCR products, and the results were analyzed using MEGA11 software. The mean ages of CLL patients and healthy individuals were 61.07 ± 10.2 and 59.08 ± 10.3, respectively. In the EBNA-1 amplicons from CLL patients and healthy individuals, 38.5% and 16.7%, respectively, harbored mutations in the DBD/DD domain of the C-terminal region of the EBNA1 gene (P = 0.378). The mutation frequency at locus 97,320 was significantly higher in CLL patients than in healthy individuals (P = 0.039). Three EBV subtypes based on residue 487 were detected. The frequency of alanine, threonine, and valine in both groups was 88, 8, and 4 percent, respectively (P = 0.207). Moreover, all of the isolates from healthy donors had alanine at this position. The findings indicated that the presence of threonine or valine at residue 487 as well as a synonymous substitution at residue 553 in the C-terminal region of EBNA1 might be involved in the pathogenesis of EBV in CLL patients.
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Affiliation(s)
- Zahra Vafapour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Fatemeh Hosseini Tabatabaie
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Shirin Haghighat
- Department of Hematology and Medical Oncology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Jamal Sarvari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran.
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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4
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Su ZY, Siak PY, Leong CO, Cheah SC. The role of Epstein-Barr virus in nasopharyngeal carcinoma. Front Microbiol 2023; 14:1116143. [PMID: 36846758 PMCID: PMC9947861 DOI: 10.3389/fmicb.2023.1116143] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a metastasis-prone malignancy closely associated with the Epstein-Barr virus (EBV). Despite ubiquitous infection of EBV worldwide, NPC incidences displayed predominance in certain ethnic groups and endemic regions. The majority of NPC patients are diagnosed with advanced-stage disease, as a result of anatomical isolation and non-specific clinical manifestation. Over the decades, researchers have gained insights into the molecular mechanisms underlying NPC pathogenesis as a result of the interplay of EBV infection with several environmental and genetic factors. EBV-associated biomarkers were also used for mass population screening for the early detection of NPC. EBV and its encoded products also serve as potential targets for the development of therapeutic strategies and tumour-specific drug delivery. This review will discuss the pathogenic role of EBV in NPC and efforts in exploiting the potential of EBV-associated molecules as biomarkers and therapeutic targets. The current knowledge on the role of EBV and its associated products in NPC tumorigenesis, development and progression will offer a new outlook and potential intervention strategy against this EBV-associated malignancy.
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Affiliation(s)
- Zhi Yi Su
- Faculty of Medicine and Health Sciences, UCSI University, Bandar Springhill, Negeri Sembilan, Malaysia
| | - Pui Yan Siak
- Faculty of Medicine and Health Sciences, UCSI University, Bandar Springhill, Negeri Sembilan, Malaysia
| | - Chee-Onn Leong
- AGTC Genomics Sdn Bhd, Pusat Perdagangan Bandar, Persiaran Jalil 1, Bukit Jalil, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Shiau-Chuen Cheah
- Faculty of Medicine and Health Sciences, UCSI University, Bandar Springhill, Negeri Sembilan, Malaysia
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5
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Ranger-Rogez S. EBV Genome Mutations and Malignant Proliferations. Infect Dis (Lond) 2021. [DOI: 10.5772/intechopen.93194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The Epstein-Barr virus (EBV) is a DNA virus with a relatively stable genome. Indeed, genomic variability is reported to be around 0.002%. However, some regions are more variable such as those carrying latency genes and specially EBNA1, -2, -LP, and LMP1. Tegument genes, particularly BNRF1, BPLF1, and BKRF3, are also quite mutated. For a long time, it has been considered for this ubiquitous virus, which infects a very large part of the population, that particular strains could be the cause of certain diseases. However, the mutations found, in some cases, are more geographically restricted rather than associated with proliferation. In other cases, they appear to be involved in oncogenesis. The objective of this chapter is to provide an update on changes in viral genome sequences in malignancies associated with EBV. We focused on describing the structure and function of the proteins corresponding to the genes mentioned above in order to understand how certain mutations of these proteins could increase the tumorigenic character of this virus. Mutations described in the literature for these proteins were identified by reporting viral and/or cellular functional changes as they were described.
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6
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Thuan LD, Kha ND, Minh NT, Thuy LHA. Novel Patterns of the Epstein-Barr Nuclear Antigen (EBNA-1) V-Val Subtype in EBV-associated Nasopharyngeal Carcinoma from Vietnam. Balkan J Med Genet 2019; 22:61-68. [PMID: 31523622 PMCID: PMC6714338 DOI: 10.2478/bjmg-2019-0011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Epstein-Barr nuclear antigen 1 (EBNA-1) gene, plays a key role in viral infection, immortalization, viral genome replication, transcription and maintenance, and is the frequently detected gene, protein in both latent and lytic stage of Epstein-Barr virus (EBV). Based on the amino acid at position 487, EBNA-1 was classified into five subtypes, including P-Ala, P-Thr, V-Val, V-Pro and V-Leu. In Vietnam, an Asian country with a high incidence, mortality rates of nasopharyngeal carcinoma (NPC), had limited research on the EBNA-1 variation. Therefore, the aim of the current study was to identify the pattern of the EBNA-1 V-Val subtype in Vietnamese NPC patients, for its value further applied in NPC patients. Fifty-eight NPC biopsy samples were collected from local patients, analyzed by nested-polymerase chain reaction (nested-PCR), sequencing and compared to a previous B95-8 prototype sequence. Four EBNA-1 subtypes, including V-Val (35/44, 79.55%), P-Ala (2/44, 4.55%), P-Thr (5/44, 11.36%), and V-Leu (2/44, 4.55%), were observed in 44/58 samples. The sequences of the V-Val subtype were compared to the B95-8 prototype, resulting in five patterns, contained seven consensus changes, including five amino acid changes at positions 487, 499, 502, 524, 594, and two silent changes at residues 520 and 553. Of these, four of five, patterns were identified as novel patterns of the V-Val subtype, showing the different changes of amino acids at positions 492, 528, 529, 553, 585 and 588, by comparison with previous studies of V-Val EBNA-1. Those data suggested the profile of variation patterns of the EBNA-1 gene, related to geographic distribution, in Vietnamese NPC patients.
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Affiliation(s)
- LD Thuan
- Department of Pharmaceutical and Medical Biotechnology, Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam
| | - ND Kha
- Faculty of Biology and Biotechnology, University of Science, Vietnam National University of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - NT Minh
- Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - LHA Thuy
- Department of Pharmaceutical and Medical Biotechnology, Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam
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7
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Zhao MH, Sun L, Li P, Liu L, Luo B, Wang XF. Sequence analysis of Epstein–Barr virus (EBV) BNLF2a gene in malignant hematopathy of Northern China. Future Virol 2019. [DOI: 10.2217/fvl-2018-0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BNLF2a is an early Epstein–Barr virus gene whose protein plays an immune escaping role by inhibiting the transporter associated with antigen processing. To explore the association between BNLF2a gene variations and EBV tumorigenesis, the BNLF2a gene of 259 EBV-positive samples (171 lymphohematopoietic disease samples and 88 throat washings from healthy donors) from northern China were sequenced. On the basis of phylogenetic tree and mutation characteristics of BNLF2a, all specimens were divided into two major genotypes: BNLF2a-A and BNLF2a-B. BNLF2a-A type, similar to the prototype B95-8, was the major subtype in all subpopulations. Healthy donors carried less BNLF2a-A and more BNLF2a-B than donors with lymphohematopoietic disease. The conservation of the BNLF2a gene may be crucial to its function.
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Affiliation(s)
- Meng-He Zhao
- Department of Pathogenic Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, PR China
| | - Lingling Sun
- Department of Pathology, Affiliated Hospital of Qingdao University Medical College, 59 Haier Road, Qingdao, 266003, PR China
| | - Ping Li
- Department of Blood Transfusion, Affiliated Hospital of Qingdao University Medical College, 16 Jiangsu Road, Qingdao, 266003, PR China
| | - Lei Liu
- Department of Laboratory, Qingdao commercial staff hospital, 6 Haipo Road, Qingdao, 266011, Shandong Province, China
| | - Bing Luo
- Department of Pathogenic Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, PR China
| | - Xiao-Feng Wang
- Department of Pathogenic Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, PR China
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8
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Hui KF, Chan TF, Yang W, Shen JJ, Lam KP, Kwok H, Sham PC, Tsao SW, Kwong DL, Lung ML, Chiang AKS. High risk Epstein-Barr virus variants characterized by distinct polymorphisms in the EBER locus are strongly associated with nasopharyngeal carcinoma. Int J Cancer 2019; 144:3031-3042. [PMID: 30536939 DOI: 10.1002/ijc.32049] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
Abstract
Whether certain variants of Epstein-Barr virus (EBV) are linked to the pathogenesis of nasopharyngeal carcinoma (NPC), which shows a marked geographic restriction, remains an unresolved issue. We performed a case-control study comparing genomic sequences of EBV isolated from saliva samples of 142 population carriers with those from primary tumour biopsies derived from 62 patients with NPC of Hong Kong. Cluster analysis discovered five EBV subgroups 1A-C and 2A-B amongst the population carriers in contrast to the predominance of 1A and -B in the majority of NPC. Genome-wide association study (GWAS) identified a panel of NPC-associated single nucleotide polymorphisms (SNPs) and indels in the EBER locus. The most significant polymorphism, which can be found in 96.8% NPC cases and 40.1% population carriers of Hong Kong, is a four-base-deletion polymorphism downstream of EBER2 (EBER-del) from coordinates 7188-7191 (p = 1.91 × 10-7 ). In addition, the predicted secondary structure of EBER2 is altered with likely functional consequence in nearly all NPC cases. Using the SNPs and indels associated with NPC, genetic risk score is assigned for each EBV variant. EBV variants with high genetic risk score are found to be much more prevalent in Hong Kong Chinese than individuals of other geographic regions and in NPC than other EBV-associated cancers. We conclude that high risk EBV variants with polymorphisms in the EBER locus, designated as HKNPC-EBERvar, are strongly associated with NPC. Further investigation of the biological function and potential clinical application of these newly identified polymorphisms in NPC and other EBV-associated cancers is warranted.
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Affiliation(s)
- Kwai Fung Hui
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Tsz Fung Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.,Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Ki Pui Lam
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Hin Kwok
- Centre for Genomic Sciences, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Hong Kong, China
| | - Pak C Sham
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,Centre for Genomic Sciences, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Hong Kong, China
| | - Sai Wah Tsao
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Dora L Kwong
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Maria Li Lung
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alan Kwok Shing Chiang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.,Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China
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9
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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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10
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Triptolide inhibits Epstein-Barr nuclear antigen 1 expression by increasing sensitivity of mitochondria apoptosis of nasopharyngeal carcinoma cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:192. [PMID: 30111354 PMCID: PMC6094928 DOI: 10.1186/s13046-018-0865-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/19/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Epstein-Barr virus (EBV) is widely found in nasopharyngeal carcinoma (NPC) tissue and associated with poor prognosis of patients. EBV nuclear antigen 1 (EBNA1) is expressed in all NPC tumors and plays multiple biological roles in both virus and host cells. Triptolide is a natural product extracted from Tripterygium and shows anti-cancer activities. The goal of this work was to illustrate the anti-cancer effect of triptolide and elucidate a novel anti-apoptotic mechanism of EBNA1 in NPC cells encountered with triptolide. METHODS In the present study, a CCK-8 assay was used to analyze the proliferation of NPC cells treated with triptolide in a dose- and time-dependent ways. Effects of triptolide on NPC cell cycle and apoptosis were investigated by flow cytometric analysis. EBNA1 expression in mRNA and protein levels was determined by quantitative real-time PCR and Western blot, respectively. RESULTS Our results showed that triptolide effectively inhibited proliferation of NPC cells. Triptolide arrested NPC cell cycles in S phase and induced apoptosis through a caspase-9-dependent apoptosis pathway. Low-dose of triptolide reduced the half-life of EBNA1 and significantly decreased EBNA1 expression by promoting the process of proteasome-ubiquitin pathway. Over-expression of EBNA1, which was independent from EBV genome, effectively attenuated the apoptosis induced by triptolide. In addition, triptolide significantly inhibited proliferations of tumors induced by EBV-positive cells in vivo. Furthermore, EBNA1 were expressed in all NPC biopsies of Chinese patients. CONCLUSIONS In summary, our study provides the evidence that triptolide induces EBNA1 degradation and stimulates NPC apoptosis through mitochondria apoptotic pathway. In addition, EBNA1 assists NPC cells to resist triptolide-induced apoptosis through inhibiting caspase-9-dependent apoptotic pathway.
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11
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Wu S, Liu W, Li H, Zhao Z, Yang Y, Xiao H, Song Y, Luo B. Conservation and polymorphism of EBV RPMS1 gene in EBV-associated tumors and healthy individuals from endemic and non-endemic nasopharyngeal carcinoma areas in China. Virus Res 2018; 250:75-80. [PMID: 29665370 DOI: 10.1016/j.virusres.2018.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022]
Abstract
As a member of the BamHI-A rightward transcripts family of the Epstein-Barr virus (EBV), RPMS1 expression has been confirmed in all EBV-associated tumors. However, few studies have investigated the single-nucleotide polymorphisms (SNPs) of RPMS1, and only one SNP site (g155391a) has been reported to be associated with nasopharyngeal carcinoma occurrence. The objective of this study was to investigate the polymorphism of RPMS1 in EBV-associated tumors (gastric carcinoma, nasopharyngeal carcinoma, and lymphoma). In this research, nested-PCR was performed to analyze DNA sequences of 420 EBV-associated samples. Phylogenetic analysis revealed four RPMS1 genotypes (RPMS1-A, RPMS1-B, RPMS1-C, and RPMS1-D). A significant difference (p < 0.05) among northern and southern China samples was observed. Furthermore, there was a significant difference between EBV-associated tumors and healthy controls for RPMS1 (p < 0.05). These findings demonstrated that RPMS1 variation was not only tumor-specific but also geographically restricted in EBV-associated samples.
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Affiliation(s)
- Shuo Wu
- Department of Pathogeny Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China
| | - Wen Liu
- Department of Pathogeny Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China
| | - Hong Li
- Department of Pathology of Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China
| | - Zhenzhen Zhao
- Department of Pathogeny Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China
| | - Yang Yang
- Department of Pathogeny Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China
| | - Hua Xiao
- Department of Pathogeny Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China
| | - Yingying Song
- Department of Pathogeny Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China
| | - Bing Luo
- Department of Pathogeny Biology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China.
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12
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Dheekollu J, Malecka K, Wiedmer A, Delecluse HJ, Chiang AKS, Altieri DC, Messick TE, Lieberman PM. Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency. Oncotarget 2018; 8:7248-7264. [PMID: 28077791 PMCID: PMC5352318 DOI: 10.18632/oncotarget.14540] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 12/26/2016] [Indexed: 12/27/2022] Open
Abstract
Epstein-Barr Virus (EBV) latent infection is a causative co-factor for endemic Nasopharyngeal Carcinoma (NPC). NPC-associated variants have been identified in EBV-encoded nuclear antigen EBNA1. Here, we solve the X-ray crystal structure of an NPC-derived EBNA1 DNA binding domain (DBD) and show that variant amino acids are found on the surface away from the DNA binding interface. We show that NPC-derived EBNA1 is compromised for DNA replication and episome maintenance functions. Recombinant virus containing the NPC EBNA1 DBD are impaired in their ability to immortalize primary B-lymphocytes and suppress lytic transcription during early stages of B-cell infection. We identify Survivin as a host protein deficiently bound by the NPC variant of EBNA1 and show that Survivin depletion compromises EBV episome maintenance in multiple cell types. We propose that endemic variants of EBNA1 play a significant role in EBV-driven carcinogenesis by altering key regulatory interactions that destabilize latent infection.
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Affiliation(s)
| | | | | | | | - Alan K S Chiang
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
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13
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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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14
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Neves M, Marinho-Dias J, Ribeiro J, Sousa H. Epstein-Barr virus strains and variations: Geographic or disease-specific variants? J Med Virol 2016; 89:373-387. [PMID: 27430663 DOI: 10.1002/jmv.24633] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2016] [Indexed: 12/24/2022]
Abstract
The Epstein-Barr Virus (EBV) is associated with the development of several diseases, including infectious mononucleosis (IM), Burkitt's Lymphoma (BL), Nasopharyngeal Carcinoma, and other neoplasias. The publication of EBV genome 1984 led to several studies regarding the identification of different viral strains. Currently, EBV is divided into EBV type 1 (B95-8 strain) and EBV type 2 (AG876 strain), also known as type A and type B, which have been distinguished based upon genetic differences in the Epstein-Barr nuclear antigens (EBNAs) sequence. Several other EBV strains have been described in the past 10 years considering variations on EBV genome, and many have attempted to clarify if these variations are ethnic or geographically correlated, or if they are disease related. Indeed, there is an increasing interest to describe possible specific disease associations, with emphasis on different malignancies. These studies aim to clarify if these variations are ethnic or geographically correlated, or if they are disease related, thus being important to characterize the epidemiologic genetic distribution of EBV strains on our population. Here, we review the current knowledge on the different EBV strains and variants and its association with different diseases. J. Med. Virol. 89:373-387, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marco Neves
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Porto, Portugal.,Faculty of Medicine of University of Porto (FMUP), Porto, Portugal
| | - Joana Marinho-Dias
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto, Porto, Portugal.,Abel Salazar Institute for the Biomedical Sciences of University of Porto (ICBAS-UP), Porto, Portugal
| | - Joana Ribeiro
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Porto, Portugal.,Faculty of Medicine of University of Porto (FMUP), Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Hugo Sousa
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto, Porto, Portugal
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15
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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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16
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Nor Hashim NA, Ramzi NH, Velapasamy S, Alex L, Chahil JK, Lye SH, Munretnam K, Haron MR, Ler LW. Identification of genetic and non-genetic risk factors for nasopharyngeal carcinoma in a Southeast Asian population. Asian Pac J Cancer Prev 2016; 13:6005-10. [PMID: 23464394 DOI: 10.7314/apjcp.2012.13.12.6005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is endemic in Southern Chinese and Southeast Asian populations. Geographical and ethnic clustering of the cancer is due to genetic, environmental, and lifestyle risk factors. This case-control study aimed to identify or confirm both genetic and non-genetic risk factors for NPC in one of the endemic countries, Malaysia. MATERIALS AND METHOD A panel of 768 single-nucleotide polymorphisms (SNPs) previously associated with various cancers and known non-genetic risk factors for NPC were selected and analyzed for their associations with NPC in a case-control study. RESULTS Statistical analysis identified 40 SNPs associated with NPC risk in our population, including 5 documented previously by genome-wide association studies (GWAS) and other case-control studies; the associations of the remaining 35 SNPs with NPC were novel. In addition, consistent with previous studies, exposure to occupational hazards, overconsumption of salt-cured foods, red meat, as well as low intake of fruits and vegetables were also associated with NPC risk. CONCLUSIONS In short, this study confirmed and/or identified genetic, environmental and dietary risk factors associated with NPC susceptibility in a Southeast Asian population.
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Affiliation(s)
- Nikman Adli Nor Hashim
- Molecular Research and Services Laboratory, INFOVALLEY® Life Sciences Sdn. Mines Resort City, Selangor, Malaysia.
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17
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Feng FT, Cui Q, Liu WS, Guo YM, Feng QS, Chen LZ, Xu M, Luo B, Li DJ, Hu LF, Middeldorp JM, Ramayanti O, Tao Q, Cao SM, Jia WH, Bei JX, Zeng YX. A single nucleotide polymorphism in the Epstein-Barr virus genome is strongly associated with a high risk of nasopharyngeal carcinoma. CHINESE JOURNAL OF CANCER 2015; 34:563-72. [PMID: 26675171 PMCID: PMC4699395 DOI: 10.1186/s40880-015-0073-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
Abstract
Background Epstein-Barr virus (EBV) commonly infects the general population and has been associated with nasopharyngeal carcinoma (NPC), which has a high incidence in certain regions. This study aimed to address how EBV variations contribute to the risk of NPC. Methods Using logistic regression analysis and based on the sequence variations at EBV-encoded RPMS1, a multi-stage association study was conducted to identify EBV variations associated with NPC risk. A protein degradation assay was performed to characterize the functional relevance of the RPMS1 variations. Results Based on EBV-encoded RPMS1 variations, a single nucleotide polymorphism (SNP) in the EBV genome (locus 155391: G>A, named G155391A) was associated with NPC in 157 cases and 319 healthy controls from an NPC endemic region in South China [P < 0.001, odds ratio (OR) = 4.47, 95% confidence interval (CI) 2.71–7.37]. The results were further validated in three independent cohorts from the NPC endemic region (P < 0.001, OR = 5.20, 95% CI 3.18–8.50 in 168 cases vs. 241 controls, and P < 0.001, OR = 5.27, 95% CI 4.06–6.85 in 726 cases vs. 880 controls) and a non-endemic region (P < 0.001, OR = 7.52, 95% CI 3.69–15.32 in 58 cases vs. 612 controls). The combined analysis in 1109 cases and 2052 controls revealed that the SNP G155391A was strongly associated with NPC (Pcombined < 0.001, OR = 5.27, 95% CI 4.31–6.44). Moreover, the frequency of the SNP G155391A was associated with NPC incidence but was not associated with the incidences of other EBV-related malignancies. Furthermore, the protein degradation assay showed that this SNP decreased the degradation of the oncogenic RPMS1 protein. Conclusions Our study identified an EBV variation specifically and significantly associated with a high risk of NPC. These findings provide insights into the pathogenesis of NPC and strategies for prevention.
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Affiliation(s)
- Fu-Tuo Feng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Qian Cui
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Wen-Sheng Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Yun-Miao Guo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Qi-Sheng Feng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Li-Zhen Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Miao Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, 266021, Shandong, P. R. China.
| | - Da-Jiang Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Li-Fu Hu
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177, Stockholm, Sweden.
| | - Jaap M Middeldorp
- Department of Pathology, VU University Medical Center, Amsterdam, 1007 MB, The Netherlands.
| | - Octavia Ramayanti
- Department of Pathology, VU University Medical Center, Amsterdam, 1007 MB, The Netherlands.
| | - Qian Tao
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong, 999077, P. R. China.
| | - Su-Mei Cao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Epidemiology, Cancer Prevention Center, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Wei-Hua Jia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Jin-Xin Bei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
| | - Yi-Xin Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, P. R. China. .,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P. R. China.
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18
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Lei H, Li T, Li B, Tsai S, Biggar RJ, Nkrumah F, Neequaye J, Gutierrez M, Epelman S, Mbulaiteye SM, Bhatia K, Lo SC. Epstein-Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations. Sci Rep 2015; 5:16706. [PMID: 26593963 PMCID: PMC4655394 DOI: 10.1038/srep16706] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022] Open
Abstract
Epstein Barr virus (EBV) sequence variation is thought to contribute to Burkitt lymphoma (BL), but lack of data from primary BL tumors hampers efforts to test this hypothesis. We directly sequenced EBV from 12 BL biopsies from Ghana, Brazil, and Argentina, aligned the obtained reads to the wild-type (WT) EBV reference sequence, and compared them with 100 published EBV genomes from normal and diseased people from around the world. The 12 BL EBVs were Type 1. Eleven clustered close to each other and to EBV from Raji BL cell line, but away from 12 EBVs reported from other BL-derived cell lines and away from EBV from NPC and healthy people from Asia. We discovered 23 shared novel nucleotide-base changes in the latent membrane protein (LMP)-1 promoter and gene (associated with 9 novel amino acid changes in the LMP-1 protein) of the 11 BL EBVs. Alignment of this region for the 112 EBV genomes revealed four distinct patterns, tentatively termed patterns A to D. The distribution of BL EBVs was 48%, 8%, 24% and 20% for patterns A to D, respectively; the NPC EBV's were Pattern B, and EBV-WT was pattern D. Further work is needed to investigate the association between EBV LMP-1 patterns with BL.
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Affiliation(s)
- Haiyan Lei
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Tianwei Li
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Bingjie Li
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Shien Tsai
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | | | | | - Janet Neequaye
- Department of Child Health, University of Ghana, Accra, Ghana
| | | | - Sidnei Epelman
- Department of Pediatric Oncology, St Marcelina Hospital, Sao Paolo, Brazil
| | - Sam M. Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Shyh-Ching Lo
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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19
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Sun L, Zhao Z, Liu S, Liu X, Sun Z, Luo B. Sequence Variation Analysis of Epstein-Barr Virus Nuclear Antigen 1 Gene in the Virus Associated Lymphomas of Northern China. PLoS One 2015; 10:e0140529. [PMID: 26460969 PMCID: PMC4604123 DOI: 10.1371/journal.pone.0140529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/28/2015] [Indexed: 12/27/2022] Open
Abstract
Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is the only viral protein expressed in all EBV-positive tumors as it is essential for the maintenance, replication and transcription of the virus genome. According to the polymorphism of residue 487 in EBNA1 gene, EBV isolates can be classified into five subtypes: P-ala, P-thr, V-val, V-leu and V-pro. Whether these EBNA1 subtypes contribute to different tissue tropism of EBV and are consequently associated with certain malignancies remain to be determined. To elucidate the relationship, one hundred and ten EBV-positive lymphoma tissues of different types from Northern China, a non-NPC endemic area, were tested for the five subtypes by nested-PCR and DNA sequencing. In addition, EBV type 1 and type 2 classification was typed by using standard PCR assays across type-specific regions of the EBNA3C genes. Four EBNA1 subtypes were identified: V-val (68.2%, 75/110), P-thrV (15.5%, 17/110), V-leuV (3.6%, 4/110) and P-ala (10.9%, 12/110). The distribution of the EBNA1 subtypes in the four lymphoma groups was not significantly different (p = 0.075), neither was that of the EBV type 1/type 2 (p = 0.089). Compared with the previous data of gastric carcinoma (GC), nasopharyngeal carcinoma (NPC) and throat washing (TW) from healthy donors, the distribution of EBNA1 subtypes in lymphoma differed significantly (p = 0.016), with a little higher frequency of P-ala subtype. The EBV type distribution between lymphoma and the other three groups was significantly different (p = 0.000, p = 0.000, p = 0.001, respectively). The proportion of type 1 and type 2 mixed infections was higher in lymphoma than that in GC, NPC and TW. In lymphomas, the distribution of EBNA1 subtypes in the three EBV types was not significantly different (p = 0.546). These data suggested that the variation patterns of EBNA1 gene may be geographic-associated rather than tumor-specific and the role of EBNA1 gene variations in tumorigenesis needs more extensive and deep explorations.
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Affiliation(s)
- Lingling Sun
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Zhenzhen Zhao
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Song Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Xia Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
- * E-mail:
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20
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The full-length DNA sequence of Epstein Barr virus from a human gastric carcinoma cell line, SNU-719. Virus Genes 2015; 51:329-37. [DOI: 10.1007/s11262-015-1248-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/09/2015] [Indexed: 01/27/2023]
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21
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Shen ZC, Luo B, Chen JN, Chao Y, Shao CK, Liu QQ, Wang Y. High prevalence of the EBER variant EB-8m in endemic nasopharyngeal carcinomas. PLoS One 2015; 10:e0121420. [PMID: 25807550 PMCID: PMC4373760 DOI: 10.1371/journal.pone.0121420] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/01/2015] [Indexed: 01/26/2023] Open
Abstract
Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) are the most highly expressed transcripts in all EBV-associated tumors and are involved in both lymphoid and epithelioid carcinogenesis. Our previous study on Chinese isolates from non-endemic area of nasopharyngeal carcinoma (NPC) identified new EBER variants (EB-8m and EB-10m) which were less common but relatively more frequent in NPC cases than healthy donors. In the present study, we determined the EBER variants in NPC cases and healthy donors from endemic and non-endemic areas of NPC within China and compared the EBER variants, in relation to the genotypes at BamHI F region (prototype F and f variant), between population groups and between two areas. According to the phylogenetic tree, four EBER variants (EB-6m, EB-8m, EB-10m and B95-8) were identified. EB-6m was dominant in all population groups except for endemic NPC group, in which EB-8m was dominant. EB-8m was more common in endemic NPC cases (82.0%, 41/50) than non-endemic NPC cases (33.7%, 32/95) (p<0.0001), and it was also more frequent in healthy donors from endemic area (32.4%, 24/74) than healthy donors from non-endemic area (1.1%, 1/92) (p<0.0001). More importantly, the EB-8m was more prevalent in NPC cases than healthy donors in both areas (p<0.0001). The f variant, which has been suggested to associate with endemic NPC, demonstrated preferential linkage with EB-8m in endemic isolates, however, the EB-8m variant seemed to be more specific to NPC isolates than f variant. These results reveal high prevalence of EBER EB-8m variant in endemic NPC cases, suggesting an association between NPC development and EBV isolates carrying EB-8m variant. Our finding identified a small healthy population group that shares the same viral strain which predominates in NPC cases. It could be interesting to carry extensive cohort studies following these individuals to evaluate the risk to develop NPC.
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Affiliation(s)
- Zhi-chao Shen
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, People’s Republic of China
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, People’s Republic of China
| | - Jian-ning Chen
- Department of Pathology, The Third Affiliated Hospitals of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yan Chao
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People’s Republic of China
| | - Chun-kui Shao
- Department of Pathology, The Third Affiliated Hospitals of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Qian-qian Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, People’s Republic of China
| | - Yun Wang
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, People’s Republic of China
- * E-mail:
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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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Chao M, Wang HN, Lu YJ, Chang YS, Yu JS. The V-val subtype Epstein-Barr virus nuclear antigen 1 promotes cell survival after serum withdrawal. Oncol Rep 2014; 33:958-66. [PMID: 25434292 DOI: 10.3892/or.2014.3625] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/03/2014] [Indexed: 11/06/2022] Open
Abstract
Epstein-Barr virus (EBV) can establish latent infection and has been associated with various human cancers. Epstein-Barr nuclear antigen 1 (EBNA1) is the only viral protein that is expressed in all EBV-associated malignant tissues. The N- and C-terminal domains of EBNA1, which are connected by internal glycine/alanine-rich short repeat sequences of various sizes, show sequence divergence across EBV strains isolated from around the world. At least five subtypes have been described, according to the amino acid at residue 487: P-ala, P-thr, V-val, V-pro, and V-leu. Whether the variations of EBNA-1 contribute to the pathogenesis of EBV or simply reflect the geographical distribution of EBV remain to be investigated. Furthermore, the cell effects conferred by EBNA1 subtypes that differ from that of the B95.8 prototype, which belongs to the P-ala subtype, remain to be elucidated. In this study, PCR was amplified with the full-length V-val EBNA1 gene from the CG3 cell line, an EBV-carrying lymphoblastoid cell line derived from a Taiwanese chronic myeloid leukemia patient. Plasmids expressing His-tagged EBNA1 fusion proteins in E. coli were constructed and used to raise antibodies in rabbit. The V-val EBNA1 gene was then cloned into a eukaryotic expression vector and successfully expressed in the transfected cultured cells. Expression of V-val EBNA1 rendered 293 cells able to undergo serum‑independent cell proliferation, providing them with anti-apoptotic abilities, which are two characteristics of cancer cells. These data suggested that use of EBNA1 originally derived from tumor cells, rather than the more commonly utilized prototype, when investigating the potential role of EBNA1 in the oncogenesis of EBV-associated malignancies, is crucial.
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Affiliation(s)
- Mei Chao
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan, Tao-Yang 333, Taiwan R.O.C
| | - Hsiao-Ning Wang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan, Tao-Yang 333, Taiwan R.O.C
| | - Yi Jin Lu
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan, Tao-Yang 333, Taiwan R.O.C
| | - Yu-Sun Chang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan, Tao-Yang 333, Taiwan R.O.C
| | - Jau-Song Yu
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yang 333, Taiwan R.O.C
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25
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Bernig T, Richter N, Volkmer I, Staege MS. Functional analysis and molecular characterization of spontaneously outgrown human lymphoblastoid cell lines. Mol Biol Rep 2014; 41:6995-7007. [PMID: 25037273 DOI: 10.1007/s11033-014-3587-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 07/05/2014] [Indexed: 01/14/2023]
Abstract
In vitro, the infection of human B-cells with the lymphotropic gammaherpesvirus Epstein-Barr virus (EBV) induces formation of permanently growing lymphoblastoid cell lines (LCL). In a spontaneously outgrown LCL (cell line CSIII), we detected nucleotide sequence variations of the EBV nuclear antigen 1 (EBNA1) RNA that was different from the reference sequence of EBNA1 in the prototypic EBV strain B95-8. In the present study, we molecularly and functionally characterized this virus isolate in comparison to LCL with the prototypic nucleotide sequence. Although we detected high functional similarity between CSIII and the other LCL, our data suggest that the lytic cycle might be ineffective in the CSIII LCL. DNA microarray analysis indicated that RNA binding motif, single stranded interacting protein 1 (RBMS1), which is typically expressed in latency III of EBV to prevent the lytic cycle, was the most overexpressed gene in CSIII LCL.
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Affiliation(s)
- Toralf Bernig
- Department of Pediatrics, Children's Cancer Research Centre, Martin Luther University Halle-Wittenberg, Ernst-Grube Str. 40, D-06097, Halle, Germany
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26
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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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Liu YC, Chen Z, Neller MA, Miles JJ, Purcell AW, McCluskey J, Burrows SR, Rossjohn J, Gras S. A molecular basis for the interplay between T cells, viral mutants, and human leukocyte antigen micropolymorphism. J Biol Chem 2014; 289:16688-98. [PMID: 24759101 DOI: 10.1074/jbc.m114.563502] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations within T cell epitopes represent a common mechanism of viral escape from the host protective immune response. The diverse T cell repertoire and the extensive human leukocyte antigen (HLA) polymorphism across populations is the evolutionary response to viral mutation. However, the molecular basis underpinning the interplay between HLA polymorphism, the T cell repertoire, and viral escape is unclear. Here we investigate the T cell response to a HLA-B*35:01- and HLA-B*35:08-restricted (407)HPVGEADYFEY(417) epitope from Epstein-Barr virus and naturally occurring variants at positions 4 and 5 thereof. Each viral variant differently impacted on the epitope's flexibility and conformation when bound to HLA-B*35:08 or HLA-B*35:01. We provide a molecular basis for understanding how the single residue polymorphism that discriminates between HLA-B*35:01/08 profoundly impacts on T cell receptor recognition. Surprisingly, one viral variant (P5-Glu to P5-Asp) effectively changed restriction preference from HLA-B*35:01 to HLA-B*35:08. Collectively, our study portrays the interplay between the T cell response, viral escape, and HLA polymorphism, whereby HLA polymorphism enables altered presentation of epitopes from different strains of Epstein-Barr virus.
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Affiliation(s)
- Yu Chih Liu
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michelle A Neller
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - Anthony W Purcell
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Scott R Burrows
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - Jamie Rossjohn
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN Wales, United Kingdom, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie Gras
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
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28
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Lei H, Li T, Hung GC, Li B, Tsai S, Lo SC. Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology. BMC Genomics 2013; 14:804. [PMID: 24252203 PMCID: PMC3882885 DOI: 10.1186/1471-2164-14-804] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 11/12/2013] [Indexed: 01/31/2023] Open
Abstract
Background We conducted genomic sequencing to identify Epstein Barr Virus (EBV) genomes in 2 human peripheral blood B lymphocytes that underwent spontaneous immortalization promoted by mycoplasma infections in culture, using the high-throughput sequencing (HTS) Illumina MiSeq platform. The purpose of this study was to examine if rapid detection and characterization of a viral agent could be effectively achieved by HTS using a platform that has become readily available in general biology laboratories. Results Raw read sequences, averaging 175 bps in length, were mapped with DNA databases of human, bacteria, fungi and virus genomes using the CLC Genomics Workbench bioinformatics tool. Overall 37,757 out of 49,520,834 total reads in one lymphocyte line (# K4413-Mi) and 28,178 out of 45,335,960 reads in the other lymphocyte line (# K4123-Mi) were identified as EBV sequences. The two EBV genomes with estimated 35.22-fold and 31.06-fold sequence coverage respectively, designated K4413-Mi EBV and K4123-Mi EBV (GenBank accession number KC440852 and KC440851 respectively), are characteristic of type-1 EBV. Conclusions Sequence comparison and phylogenetic analysis among K4413-Mi EBV, K4123-Mi EBV and the EBV genomes previously reported to GenBank as well as the NA12878 EBV genome assembled from database of the 1000 Genome Project showed that these 2 EBVs are most closely related to B95-8, an EBV previously isolated from a patient with infectious mononucleosis and WT-EBV. They are less similar to EBVs associated with nasopharyngeal carcinoma (NPC) from Hong Kong and China as well as the Akata strain of a case of Burkitt’s lymphoma from Japan. They are most different from type 2 EBV found in Western African Burkitt’s lymphoma.
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Affiliation(s)
- Haiyan Lei
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, NIH Building 29B, Rm, 1NN06, 29 Lincoln Dr,, 20892-4555 Bethesda, MD, USA.
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29
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Senyuta N, Yakovleva L, Goncharova E, Scherback L, Diduk S, Smirnova K, Maksimovich D, Gurtsevitch V. Epstein-barr virus latent membrane protein 1 polymorphism in nasopharyngeal carcinoma and other oral cavity tumors in Russia. J Med Virol 2013; 86:290-300. [DOI: 10.1002/jmv.23729] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Natalia Senyuta
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
| | - Larissa Yakovleva
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
| | - Elena Goncharova
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
| | - Liana Scherback
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
| | - Sergey Diduk
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
| | - Ksenia Smirnova
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
| | - Dmitry Maksimovich
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
| | - Vladimir Gurtsevitch
- Laboratory of Viral Carcinogenicity; N.N. Blokhin Cancer Research Center; Moscow Russia
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Fan Q, He JF, Wang QR, Cai HB, Sun XG, Zhou XX, Qin HD, Shugart YY, Jia WH. Functional polymorphism in the 5'-UTR of CR2 is associated with susceptibility to nasopharyngeal carcinoma. Oncol Rep 2013; 30:11-6. [PMID: 23612877 PMCID: PMC3729234 DOI: 10.3892/or.2013.2421] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/18/2013] [Indexed: 12/27/2022] Open
Abstract
Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) is a squamous cell cancer endemic in Southern China and Southeast Asia. It has been shown that inflammatory and immune responses during EBV infection contribute to the development of NPC. The complement receptor 2 (CR2) gene plays central roles during inflammatory and immune responses and, therefore, is a good candidate susceptibility gene for NPC. We performed PCR-based sequencing to identify multiple single-nucleotide polymorphisms (SNPs) within the exon regions of the CR2 gene in a Cantonese population. Two SNPs were screened in 528 NPC patients and 408 normal individuals to perform a case-control study matched according to age, gender and residence. Furthermore, we cloned the entire 5′-UTR and entire CR2 promoter into a luciferase report system and compared the luciferase activities between the different allelic constructs. A SNP in the 5′-UTR of CR2 (24 T/C, rs3813946) showed a significant association (P<0.01) with NPC in the Cantonese population studied. The subjects were categorized into 2 age groups: group 1, age ≤45 years and group 2, age >45 years. In group 1, the allelic frequencies of 24 T/C in the patients were significantly different from those of the controls (P=0.0034). The odds ratio (OR=1.81) also indicated a higher risk of NPC in individuals who carried the minor allele C. All constructs exerted allelic differences on luciferase activities, but only the susceptible allele +24C construct showed increased activity. Our findings implicate CR2 as a susceptibility gene for NPC and suggest that enhanced CR2 expression may be involved in the oncogenesis and development of NPC.
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Affiliation(s)
- Qin Fan
- College of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, P.R. China
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31
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Gourzones C, Busson P, Raab-Traub N. Epstein-Barr Virus and the Pathogenesis of Nasopharyngeal Carcinomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013. [DOI: 10.1007/978-1-4614-5947-7_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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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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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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34
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Wang Y, Wang XF, Sun ZF, Luo B. Unique variations of Epstein-Barr virus-encoded BARF1 gene in nasopharyngeal carcinoma biopsies. Virus Res 2012; 166:23-30. [PMID: 22406129 DOI: 10.1016/j.virusres.2012.02.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 12/11/2022]
Abstract
The Epstein-Barr virus (EBV) BamHI-A rightward frame 1 (BARF1) gene is frequently expressed in EBV-associated epithelial malignancies and involves in oncogenicity and immunomodulation. To characterize the variations of BARF1 gene in different populations, the sequences of BARF1 gene in Northern Chinese nasopharyngeal carcinoma (NPC), EBV-associated gastric carcinoma (EBVaGC) and healthy donors were analyzed. The correlation of BARF1 variation with polymorphisms of BamHI F fragment (type F and f variants) and EBV-coded viral interleukin-10 (vIL-10) gene (B95-8 and SPM patterns) was also explored. Two major subtypes of BARF1 gene, designated as B95-8 and V29A, were identified. B95-8 subtype had identical amino acid sequence to B95-8 and was the dominant subtype among the EBV isolates from Northern China. V29A subtype, with one consistent amino acid change at residue 29 (V→A) and several nucleotide changes, showed higher frequency in NPC cases (25.3%, 20/79) than in EBVaGC cases (0/45) or healthy donors (4.3%, 2/46) (NPC vs. EBVaGC: P=0.0001; NPC vs. healthy donor: P=0.004). A preferential linkage between BamHI F and BARF1/vIL-10 polymorphisms was found. Type f isolates was specially correlated with the V29A/SPM genotype in NPC isolates and type f/V29A/SPM was preferentially found in NPC. BARF1/c-fms homology domain, transforming domain and cytotoxic T lymphocyte (CTL) epitopes of BARF1 were highly conserved in most isolates, suggesting the important role of BARF1 in virus infection and the potential usefulness in EBV-targeting immunotherapy of EBV-associated tumors. The relatively higher prevalence of type f/V29A/SPM strains in NPC may also suggest the association between these variations in multiple viral genes and NPC.
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Affiliation(s)
- Yun Wang
- Department of Medical Microbiology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao 266021, China
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35
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Ai J, Xie Z, Liu C, Huang Z, Xu J. Analysis of EBNA-1 and LMP-1 variants in diseases associated with EBV infection in Chinese children. Virol J 2012; 9:13. [PMID: 22236445 PMCID: PMC3269356 DOI: 10.1186/1743-422x-9-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 01/11/2012] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND In China, primary EBV infection occurs during childhood with seroprevalence reaching about 100% by 10 years of age. There are few studies on EBV variants in diseases associated with EBV infection in Chinese children. In this study, we investigated the diversity of the EBV genes (EBNA-1 and LMP-1) and the relationship between EBV variants and the clinical phenotypes in diseases associated with EBV infections in Chinese pediatric cases. RESULTS The frequencies of EBV type I in the IM, HLH and HL samples were 98.4%, 100% and 95.8%, respectively. Three known EBNA-1 variants were identified, including V-val (all were V-val-v1 sub-variant), P-thr' and V-Leu (MT). The frequency of V-val-v1 was 98.6% in the IM samples, 100% in the HLH samples and 97.1% in the HL samples. There were no significant differences of the distribution of EBNA-1 variants between IM, HLH and HL samples (P > 0.05). Three known LMP-1 variants, including China 1, China 2 and Med, were identified and China 1 was predominant in all groups (IM 88.6%, HLH 100% and HL 100%). The frequency of del-LMP-1 was 88.6% in the IM samples, 100% in the HLH samples and 96.0% in the HL samples. There were no significant differences in the frequency of del-LMP-1 between the IM, HLH and HL samples (P > 0.05). The frequency of XhoI loss was 90.6% in the IM samples, 100% in the HLH samples and 100% in the HL samples, with no significant difference in frequency (P > 0.05). In the EBV type I strain, V-val-v1 variant (EBNA-1) was linked with China1 variant (LMP-1) in 88.9% of the IM samples, 100% of the HLH samples and 80.0% of the HL samples in this study. CONCLUSIONS Type I EBV was the most prevalent subtype EBV in Chinese pediatric cases and V-val-v1 (EBNA-1) and China1 (LMP-1) variants were the most dominant variants. There was a strong linkage between V-val-v1 (EBNA-1) variant and China1 (LMP-1) variant in type I EBV. The sequence variation in EBV genes may represent a geographic polymorphism since no preferential associations were found between specific EBV variants and specific diseases in this study.
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Affiliation(s)
- Junhong Ai
- Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
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Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology. J Virol 2011; 85:11291-9. [PMID: 21880770 DOI: 10.1128/jvi.00823-11] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV)-encoded molecules have been detected in the tumor tissues of several cancers, including nasopharyngeal carcinoma (NPC), suggesting that EBV plays an important role in tumorigenesis. However, the nature of EBV with respect to genome width in vivo and whether EBV undergoes clonal expansion in the tumor tissues are still poorly understood. In this study, next-generation sequencing (NGS) was used to sequence DNA extracted directly from the tumor tissue of a patient with NPC. Apart from the human sequences, a clinically isolated EBV genome 164.7 kb in size was successfully assembled and named GD2 (GenBank accession number HQ020558). Sequence and phylogenetic analyses showed that GD2 was closely related to GD1, a previously assembled variant derived from a patient with NPC. GD2 contains the most prevalent EBV variants reported in Cantonese patients with NPC, suggesting that it might be the prevalent strain in this population. Furthermore, GD2 could be grouped into a single subtype according to common classification criteria and contains only 6 heterozygous point mutations, suggesting the monoclonal expansion of GD2 in NPC. This study represents the first genome-wide analysis of a clinical isolate of EBV directly extracted from NPC tissue. Our study reveals that NGS allows the characterization of genome-wide variations of EBV in clinical tumors and provides evidence of monoclonal expansion of EBV in vivo. The pipeline could also be applied to the study of other pathogen-related malignancies. With additional NGS studies of NPC, it might be possible to uncover the potential causative EBV variant involved in NPC.
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Lorenzetti MA, Altcheh J, Moroni S, Moscatelli G, Chabay PA, Preciado MV. EBNA1 sequences in Argentinean pediatric acute and latent Epstein-Barr virus infection reflect circulation of novel South American variants. J Med Virol 2010; 82:1730-8. [PMID: 20827771 DOI: 10.1002/jmv.21871] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Epstein-Barr virus (EBV) is related to the development of lymphomas and is also the etiological agent for infectious mononucleosis (IM). Sequence variation of the EBNA1 gene, consistently expressed in all EBV-positive cells, has been widely studied. Based on the amino acid at codon 487 five major EBNA1 variants have been described, two closely related prototypic variants (P-ala and P-thr) and three variant sequences (V-leu, V-val, and V-pro). Sub-variants were then further classified based on mutations other than the originally described. While several studies proposed associations with tumors and/or anatomical compartments, others argued in favor of a geographical distribution of these variants. In the present study, EBNA1 variants in 11 pediatric patients with IM and 19 pediatric EBV lymphomas from Argentina were compared as representatives of benign and malignant infection in children, respectively. A 3-month follow-up study of EBNA1 variants in peripheral blood cells and in oral secretions of patients with IM was performed. A new V-ala variant which includes five V-ala sub-variants and three new V-leu sub-variants was described. These data favor the geographical association hypothesis since no evidence for a preferential compartment distribution of EBNA1 variants and sub-variants was found. This is the first study to characterize EBNA1 variants in pediatric patients with infection mononucleosis worldwide.
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Affiliation(s)
- Mario Alejandro Lorenzetti
- Molecular Biology Laboratory, Pathology Division, Ricardo Gutiérrez Children Hospital, Buenos Aires, Argentina
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Gras S, Chen Z, Miles JJ, Liu YC, Bell MJ, Sullivan LC, Kjer-Nielsen L, Brennan RM, Burrows JM, Neller MA, Khanna R, Purcell AW, Brooks AG, McCluskey J, Rossjohn J, Burrows SR. Allelic polymorphism in the T cell receptor and its impact on immune responses. ACTA ACUST UNITED AC 2010; 207:1555-67. [PMID: 20566715 PMCID: PMC2901058 DOI: 10.1084/jem.20100603] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for this phenomenon is undefined. We examined the T cell response to an HLA-B*3501-restricted epitope (HPVGEADYFEY) from Epstein-Barr virus (EBV), which is frequently dominated by a TRBV9*01(+) public TCR (TK3). However, the common allelic variant TRBV9*02, which differs by a single amino acid near the CDR2beta loop (Gln55-->His55), was never used in this response. The structure of the TK3 TCR, its allelic variant, and a nonnaturally occurring mutant (Gln55-->Ala55) in complex with HLA-B*3501(HPVGEADYFEY) revealed that the Gln55-->His55 polymorphism affected the charge complementarity at the TCR-peptide-MHC interface, resulting in reduced functional recognition of the cognate and naturally occurring variants of this EBV peptide. Thus, polymorphism in the TCR loci may contribute toward variability in immune responses and the outcome of infection.
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Affiliation(s)
- Stephanie Gras
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Wang Y, Liu X, Xing X, Cui Y, Zhao C, Luo B. Variations of Epstein-Barr virus nuclear antigen 1 gene in gastric carcinomas and nasopharyngeal carcinomas from Northern China. Virus Res 2009; 147:258-64. [PMID: 19941915 DOI: 10.1016/j.virusres.2009.11.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 11/17/2009] [Accepted: 11/17/2009] [Indexed: 10/20/2022]
Abstract
The Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1), the only viral protein consistently expressed in all EBV-associated tumors, is classified into five distinct subtypes: P-ala, P-thr, V-leu, V-val and V-pro based on the signature changes at amino acid residue 487. By now, whether the EBNA1 subtypes preferentially associate with particular malignancies or represent geographical polymorphism remains controversial. In China, most studies of the EBNA1 variations focused on nasopharyngeal carcinoma (NPC) in endemic area, among which some suggested the V-val subtype is preferentially associated with NPC. To characterize the variations of EBNA1 in NPC non-endemic area in China and to explore the association of EBNA1 variations with EBV-associated gastric carcinoma (EBVaGC) and NPC, the C-terminal sequences of EBNA1 were analyzed for 41 EBVaGC, 41 NPC biopsies and 55 throat washing (TW) samples from healthy donors in Northern China. Three major patterns of the EBNA1 variations, V-val, P-thrV and V-leuV, were observed, and V-val was the most common subtype in all the three groups, followed by P-thrV and V-leuV. The distribution of the EBNA1 subtypes among EBVaGC, NPC and healthy donors was not significantly different (P>0.05). In addition, preferential linkages between EBNA1 subtypes and EBNA3C variants were found to exist. There was no evidence that particular EBNA1 subtypes are preferentially associated with EBVaGC or NPC in Northern China, suggesting that EBNA1 gene variations are geographically restricted rather than tumor-specific polymorphisms.
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Affiliation(s)
- Yun Wang
- Department of Medical Microbiology, Qingdao University Medical College, 38 Dengzhou Road, Qingdao, 266021, China
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40
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Ayadi W, Karray-Hakim H, Feki L, Khabir A, Boudawara T, Ghorbel A, Daoud J, Frikha M, Hammami A. IgA antibodies against the Epstein-Barr nuclear antigen1 as a valuable biomarker for the diagnosis of nasopharyngeal carcinoma in Tunisian patients. J Med Virol 2009; 81:1412-21. [DOI: 10.1002/jmv.21532] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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41
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Chang CM, Yu KJ, Mbulaiteye SM, Hildesheim A, Bhatia K. The extent of genetic diversity of Epstein-Barr virus and its geographic and disease patterns: a need for reappraisal. Virus Res 2009; 143:209-21. [PMID: 19596032 DOI: 10.1016/j.virusres.2009.07.005] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 06/30/2009] [Accepted: 07/02/2009] [Indexed: 12/12/2022]
Abstract
Epstein-Barr virus (EBV) is a ubiquitous, gamma-1 lymphotrophic virus etiologically linked to nasopharyngeal carcinoma (NPC), endemic to Southern China, and Burkitt lymphoma (BL), endemic to equatorial Africa, both of which are rare elsewhere in the world. Why EBV is associated with different malignancies in different geographic regions remains puzzling and may be related to EBV genotypic variability through specific disease and geographic associations. We review the literature on sequence variation in EBV genes, focusing on LMP-1, EBNA-1, and BZLF-1 and their distribution by geography and disease. Given the limitations of current studies, definitive conclusions regarding the link between EBV genotypes, disease and geography are not possible. We suggest that the true extent of EBV diversity is likely to be greater than is currently recognized. Additional studies conducted in carefully selected populations, that are sufficiently powered to provide robust estimates, and that utilize testing approaches that permit full characterization of viral diversity are needed to further our understanding of patterns of EBV genetic variation and their association with malignancies in different regions.
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Affiliation(s)
- Cindy M Chang
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, 6120 Executive Blvd., EPS 7074, Rockville, MD 20892, USA.
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42
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Li DJ, Bei JX, Mai SJ, Xu JF, Chen LZ, Zhang RH, Yu XJ, Hong MH, Zeng YX, Kang T. The dominance of China 1 in the spectrum of Epstein-Barr virus strains from Cantonese patients with nasopharyngeal carcinoma. J Med Virol 2009; 81:1253-60. [PMID: 19475622 DOI: 10.1002/jmv.21503] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nasopharyngeal carcinoma is a disease with a remarkable geographic and ethnic distribution, and has a high incidence in southern China. Infection with Epstein-Barr virus (EBV) is an important contributing factor. The profile of EBV strains in Cantonese patients from Guangdong, the nasopharyngeal carcinoma endemic region in southern China, is described on the sequence variations in latent membrane protein 1 carboxyl-terminus. The results show that China 1 was the dominant EBV strain detected in both the tumor biopsies and samples of throat washings, whereas multiple strains, including China 1, China 2, B95-8, and Med, were detected in blood samples. In addition, a new strain named China 4 was found in blood samples. These findings suggest that the host population is susceptible to the predominant China 1 strain in the nasopharyngeal carcinoma endemic region of China, but its relationship with the host remains to be characterized further.
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Affiliation(s)
- Da-Jiang Li
- State Key Laboratory of Oncology in Southern China, Guangzhou, China
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43
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Do NV, Ingemar E, Phi PTP, Jenny A, Chinh TT, Zeng Y, Hu L. A major EBNA1 variant from Asian EBV isolates shows enhanced transcriptional activity compared to prototype B95.8. Virus Res 2007; 132:15-24. [PMID: 18096263 DOI: 10.1016/j.virusres.2007.10.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Revised: 10/10/2007] [Accepted: 10/12/2007] [Indexed: 11/16/2022]
Abstract
Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) has an instrumental role in maintaining EBV latent infection by controlling EBV episome replication and regulating viral transcription. It is a ubiquitously expressed protein during latent viral infection and in EBV-associated tumors. The EBNA1 C-terminus interacts functionally with the Qp and Cp that control viral gene expression in latency I/II and III, respectively. EBNA1 has been classified into five subtypes due to sequence variation in the DNA-interacting C-terminus. By DNA sequence analysis of its C-terminus, we detected a main sub-variant (V-val-v1) of EBNA1 with valine located in both positions 487 and 528 from matched samples including NPC biopsies and peripheral blood taken from Vietnamese (9), Chinese (12) NPC patients and healthy donors (5). In the FR-region of oriP from nine NPC biopsies from Vietnam we also frequently found substitutions, deletions and variable numbers of repeats. Using a luciferase reporter system, EBNA1 and FR both derived from Asian isolates induced higher transcriptional activity than those from B95-8 virus.
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Affiliation(s)
- Nguyen-Van Do
- Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet, S-171 77 Stockholm, Sweden.
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44
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Provenzano M, Selleri S, Jin P, Wang E, Werden R, Slezak S, Adams SD, Panelli MC, Leitman SF, Stroncek DF, Marincola FM. Comprehensive epitope mapping of the Epstein-Barr virus latent membrane protein-2 in normal, non tumor-bearing individuals. Cancer Immunol Immunother 2007; 56:1047-63. [PMID: 17124584 PMCID: PMC11031044 DOI: 10.1007/s00262-006-0246-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 10/17/2006] [Indexed: 10/23/2022]
Abstract
Latent membrane protein (LMP)-2 is one of the Epstein-Barr virus (EBV)-encoded proteins consistently expressed by nasopharyngeal carcinoma (NPC). EBV-transformed lymphoblastoid cell lines (LCL) have been used in patients with NPC to induce LMP-2-recognizing T cell lines which have been in turn utilized for protein-wide mapping of T cell epitopes. However, comprehensive mapping of naturally recognized LMP-2 epitopes in non tumor-bearing individuals has not been reported. Here, we applied a low sensitivity epitope-defining technique for the identification of LMP-2 CTL responses detectable ex vivo in EBV-experienced individuals. This screening tool has been previously validated by analyzing memory CTL responses to Flu, cytomegalovirus (CMV), and the melanoma associated antigen gp100/Mel17. Peripheral blood monocytes (PBMC) from ten Caucasian and ten Chinese individuals were stimulated ex vivo with pools of nonamer (9-mer) peptides overlapping in a stepwise fashion each single amino acid of the LMP-2 sequence. No obvious differences were observed between the immune response of the two ethnic groups save for those related to the divergence in the ethnic prevalence of HLA haplotypes. Several novel and known LMP-2 epitopes were identified. Reactivity toward at least one LMP-2 epitope was detected in 18 of the 20 donors but no prevalent human leukocyte antigen (HLA)/epitope combination was observed confirming that LMP-2 reactivity in the context of common HLA alleles is more pleiotropic than that of FLU and CMV. We believe that the usefulness of these epitopes occurring naturally in non-cancer bearing patients as reagents for the immunization of patients with early or advanced stage NPC deserves further evaluation.
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Affiliation(s)
- Maurizio Provenzano
- Immune Oncology Section, Department of Surgery, University Hospital ZLF, Hebelstrasse 20, 4031 Basel, Switzerland
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Silvia Selleri
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
- Department of Human Morphology, Universita’ degli Studi di Milano, via Mangiagalli 31, 20133 Milano, Italy
| | - Ping Jin
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ena Wang
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Rosemary Werden
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Stephanie Slezak
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon D. Adams
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Monica C. Panelli
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Susan F. Leitman
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - David F. Stroncek
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Francesco M. Marincola
- Department of Transfusion Medicine, Building 10, Room 1C711, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
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Abstract
A nasofaringe é a parte mais superior das vias aéreas superiores. Seu limite superior é a base do osso esfenóide e occipital, situa-se anteriormente às duas primeiras vértebras cervicais e à frente do clivo. Seus limites laterais são formados pelas margens do músculo constritor superior da faringe e pela fáscia faringobasilar, recessos faríngeos, toro tubário e tuba auditiva. O limite inferior é um plano horizontal que passa pelo palato duro e pelo músculo palatofaríngeo. Anteriormente, comunica-se com a cavidade nasal via coana posterior. Mede cerca de 2,0 cm de diâmetro ântero-posterior e cerca de 4,0 cm de extensão crânio-caudal. O carcinoma de células escamosas compreende aproximadamente 70% a 98% de todas as neoplasias malignas da nasofaringe em adultos. Este tipo de tumor apresenta alta incidência na população asiática, sendo mais comum entre os homens e o terceiro mais comum entre as mulheres. A manifestação clínica do carcinoma da nasofaringe depende do tamanho da lesão e da sua localização, sendo que as lesões de pequenas dimensões são geralmente assintomáticas. A tomografia computadorizada e a ressonância magnética desempenham papel essencial e complementar no estadiamento e no tratamento dos pacientes portadores de câncer da nasofaringe.
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46
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Fan Q, Jia WH, Zhang RH, Yu XJ, Chen LZ, Feng QS, Zeng YX. Association of pIgR polymorphisms with nasopharyngeal carcinoma. Chin J Cancer Res 2006. [DOI: 10.1007/s11670-006-0168-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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47
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Puchhammer-Stöckl E, Görzer I. Cytomegalovirus and Epstein-Barr virus subtypes—The search for clinical significance. J Clin Virol 2006; 36:239-48. [PMID: 16697698 DOI: 10.1016/j.jcv.2006.03.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Accepted: 03/23/2006] [Indexed: 11/19/2022]
Abstract
Cytomegalovirus (CMV) as well as Epstein Barr virus (EBV) genomes include regions which show in part substantial polymorphisms. Characterization of several polymorphic regions led to the identification of various CMV and EBV subtypes. Within the last years there have been undertaken numerous efforts to find out whether the diverse subtypes differentially contribute to clinical manifestations. However, although some associations have been described so far between a certain virus subtype and the development of individual diseases these analyses were greatly complicated by the huge genomic background of CMV and EBV, by the large variety of individual host-virus relations and by differences in the geographic or demographic subtype distribution. In addition, it was shown meanwhile that a substantial proportion of virus infections is due to mixed infections with different subtypes. In this review we will give an overview of the current knowledge concerning the clinical significance of individual CMV and EBV subtypes, defined by characterization of selected polymorphisms. In addition, we also focus on recent analyses which show that infection with mixed virus subtype populations may be disadvantageous compared to single virus subtype infections.
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48
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Zeng MS, Li DJ, Liu QL, Song LB, Li MZ, Zhang RH, Yu XJ, Wang HM, Ernberg I, Zeng YX. Genomic sequence analysis of Epstein-Barr virus strain GD1 from a nasopharyngeal carcinoma patient. J Virol 2006; 79:15323-30. [PMID: 16306603 PMCID: PMC1316000 DOI: 10.1128/jvi.79.24.15323-15330.2005] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To date, the only entire Epstein-Barr virus (EBV) genomic sequence available in the database is the prototype B95.8, which was derived from an individual with infectious mononucleosis. A causative link between EBV and nasopharyngeal carcinoma (NPC), a disease with a distinctly high incidence in southern China, has been widely investigated. However, no full-length analysis of any substrain of EBV from this area has been reported. In this study, we analyzed the entire genomic sequence of an EBV strain from a patient with NPC in Guangdong, China. This EBV strain was termed GD1 (Guangdong strain 1), and the full-length sequence of GD1 was submitted to the GenBank database. The assigned accession number is AY961628. The entire GD1 sequence is 171,656 bp in length, with 59.5% G+C content and 40.5% A+T content. We detected many sequence variations in GD1 compared to prototypical strain B95.8, including 43 deletion sites, 44 insertion sites, and 1,413 point mutations. Furthermore, we evaluated the frequency of some of these GD1 mutations in Cantonese NPC patients and found them to be highly prevalent. These findings suggest that GD1 is highly representative of the EBV strains isolated from NPC patients in Guangdong, China, an area with the highest incidence of NPC in the world. Furthermore, these findings provide the second full-length sequence analysis of any EBV strain as well as the first full-length sequence analysis of an NPC-derived EBV strain.
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Affiliation(s)
- Mu-Sheng Zeng
- State Key Laboratory of Oncology in Southern China, Guangzhou 510060, China
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