Conserved mutation of Epstein-Barr virus-encoded BamHI-A Rightward Frame-1 (BARF1) gene in Indonesian nasopharyngeal carcinoma
© Hutajulu et al; licensee BioMed Central Ltd. 2010
Received: 8 July 2010
Accepted: 19 September 2010
Published: 19 September 2010
BamHI-A rightward frame-1 (BARF1) is a carcinoma-specific Epstein-Barr virus (EBV) encoded oncogene. Here we describe the BARF1 sequence diversity in nasopharyngeal carcinoma (NPC), other EBV-related diseases and Indonesian healthy EBV carriers in relation to EBV genotype, viral load and serology markers. Nasopharyngeal brushings from 56 NPC cases, blood or tissue from 15 other EBV-related disorders, spontaneous B cell lines (LCL) from 5 Indonesian healthy individuals and several prototype EBV isolates were analysed by PCR-direct sequencing.
Most NPC isolates revealed specific BARF1 nucleotide changes compared to prototype B95-8 virus. At the protein level these mutations resulted in 3 main substitutions (V29A, W72G, H130R), which are not considered to cause gross tertiary structure alterations in the hexameric BARF1 protein. At least one amino acid conversion was detected in 80.3% of NPC samples compared to 33.3% of non-NPC samples (p < 0.001) and 40.0% of healthy LCLs (p = 0.074). NPC isolates also showed more frequent codon mutation than non-NPC samples. EBV strain typing revealed most isolates as EBV type 1. The viral load of either NPC or non-NPC samples was high, but only in non- NPC group it related to a particular BARF1 variant. Serology on NPC sera using IgA/EBNA-1 ELISA, IgA/VCA-p18 ELISA and immunoblot score showed no relation with BARF1 sequence diversity (p = 0.802, 0.382 and 0.058, respectively). NPC patients had variable antibody reactivity against purified hexameric NPC-derived BARF1 irrespective of the endogenous BARF1 sequence.
The sequence variation of BARF1 observed in Indonesian NPC patients and controls may reflect a natural selection of EBV strains unlikely to be predisposing to carcinogenesis. The conserved nature of BARF1 may reflect an important role in EBV (epithelial) persistence.
Epstein-Barr virus (EBV) is a human gamma-herpes virus that establishes persistent infection of B lymphocytes in more than 90% of the human adult population [1, 2]. EBV is associated with a variety of lymphocytic cell malignancies including Burkitt lymphoma, Hodgkin's Disease, non-Hodgkin lymphoma, and post-transplant and AIDS-associated lymphoproliferative disorders as well as epithelial cell malignancies such as nasopharyngeal carcinoma (NPC) and gastric carcinoma, reflecting its dual cell tropism .
The vast majority of NPC cases, in particular the prevalent undifferentiated WHO type-III, is 100% related to EBV infection. In this type of NPC, EBV is present in all tumour cells with active expression of distinct viral coding and non coding genes . The etiological role of EBV in NPC pathogenesis is consistently reflected by the presence of clonal EBV genomes in premalignant and malignant nasopharyngeal lesions  and the expression of viral proteins . NPC develops in parallel with characteristic IgA and IgG antibody responses to EBV proteins which are detectable at early and even preclinical stage of disease [6–8]. Moreover, abnormal EBV DNA loads and viral mRNA are present in nasopharyngeal brushings, whereas elevated EBV DNA loads are detectable in the circulation of most patients at the time of NPC diagnosis [7, 9–11].
Two types of EBV have been identified, which can be discriminated by genomic difference in a subset of latent genes encoding EBV nuclear antigen 2 (EBNA-2), EBNA-3A, -3B, and -3C [12, 13]. EBV type 1, which is predominantly detected in Asian NPC patients, has a greater efficiency of B lymphocyte transformation than EBV type 2 , and this difference may associate with divergence in the EBNA-2 sequences [15, 16].
EBV gene expression between and within tumors is highly variable. Each EBV-associated malignancy is characterized by a distinct viral gene expression profile, although EBNA-1, EBERs, and BARTs are found in all EBV-related tumors . Of the 86 genes encoded by EBV genome , two are considered as viral oncogenes, i.e. LMP1 and BARF1, both having tumorigenic activity in an epithelial background [2, 18–20].
LMP1 is detected only in 50-90% of NPC tumors with heterogenous expression [21–23]. LMP1 gene with a 30 bp deletion (del-LMP1) at nucleotide positions 168256-168285 (codons 346-355) compared to the B95-8 EBV prototype is found in a higher frequency of Asian NPC cases [24, 25]. In addition, EBV del-LMP 1 is associated with increased NPC tumorigenicity in nude mice . More recently, additional amino acid substitutions have been described for LMP1, but the functional consequences remain unclear [27, 28].
BARF1-encoded protein was found to be expressed in more than 85% NPC biopsies and its mRNA is consistently expressed [10, 29–31]. BARF1 protein forms a hexameric structure that is actively secreted and may act as immunomodulator through homology with the colony stimulating factor receptor c-fms, binding CSF-1 (M-CSF) [17, 30–35]. BARF1 has mitogenic properties and can induce oncogenic transformation in rodent fibroblasts [18, 19, 35] and human B lymphocytic line [36, 37]. Overexpression of BARF1 in EBV-infected epithelial cells leads to enhanced tumor formation in nude mice  and its immortalization potency has been demonstrated in monkey kidney primary epithelial cells . Moreover, the BARF1 gene is consistently transcribed in EBV-positive gastric cancer in the absence of LMP1 [31, 39]. Thus, BARF1 would then be more pivotal for NPC oncogenesis than the LMP1 protein. However, in contrast to LMP1 which has been widely explored, study of BARF1 sequence variation is still limited.
Therefore in the present study we aimed to determine whether BARF1 gene has sequence diversity in NPC. To verify its association with NPC, sequence analysis in other EBV-related disorders and in spontaneous lymphoblastoid cell lines (LCL) established from healthy Indonesian blood donors was also defined. To identify whether BARF1 variation has an influence on tumor biology, EBV genotype (EBNA-2 subtype), EBV DNA load, and serology pattern were analysed. Finally, we studied the immunogenic properties of NPC-derived BARF1 as a purified hexameric protein.
Most of NPC isolates display nucleotide and amino acid changes
In the present study we have sequenced the complete BARF1 gene from 56 NPC brushing samples,15 non-NPC EBV-related tissue or blood, 5 spontaneous LCL from healthy EBV-seropositive individuals and several NPC-derived and non-NPC reference EBV strains. The EBV genome of B95-8 was used as the prototype EBV strain. The sequence of BARF1 gene derived from the B95-8 transformed LCL JY was identical to that of the B95-8 sequence from the database (GeneBank No. V01555). Prototype GD1 and AG876 strains also revealed an identical BARF1 sequence compared to B95-8. The C666-1 cell line showed 1 silent mutation at position of 165545 (T to C). The C15 tumor line displayed 4 nucleotide mutations, one at position of 165589 (T to C) leading to V29A conversion, and 3 silent mutations at position of 165677 (G to A), 165944 (C to T), and 166136 (C to T). The C17 tumor line did not demonstrate any nucleotide exchange compared to the B95-8 prototype.
The point nucleotide mutations and amino acid changes observed in the BARF1 gene sequence from 56 NPC patients, 15 other EBV-related disorders, and 5 healthy individuals (one isolate might show more than one mutation).
(n = 56)
(n = 15)
(n = 5)
T → A
S → T
C → T
T → C
V → A
A → G
T → G
W → G
T → C
C → T
T → C
C → T
S → F
A → G
H → R
C → T
Most of non-NPC EBV samples and healthy LCLs did not exhibit any nucleotide change and the sequences were similar to the B95-8 genome. Some isolates (33.3% of non-NPC and 40.0% of healthy carriers) showed 2-6 nucleotide mutations leading to 2 specific codon exchanges. These converting amino acids were identical to those of NPC majority (V29A and H130R).
Proportion of NPC cases based on sequence diversity (number of amino acid conversion) when compared to other EBV-related diseases.
Number of amino acid conversion
Frequency (N) for sample of NPC and other EBV-related diseases
3 and 4
At amino acid level the tree was divided into several branches with the common mutations at codon 29 and 130. The group with most of non-NPC and healthy samples in term of their similarity to the sequence of B95-8, GD1 and AG876 contained only few NPC isolates. In contrary, majority of NPC were included in other branches along with a small number of non-NPC and Indonesian healthy LCLs characterizing the occurence of more mutations and diversities. One NPC (NPC-20) and 3 PTLD isolates (PTLD-2, PTLD-6, and PTLD-7) were put in a separated branch from other isolates revealing same codon conversions (V29A and H130R) because they had less overall nucleotide mutations. Seven NPC isolates were grouped together as the fact of having 3 mutations. Two of them (NPC-16 and NPC-44) had further separation than the other 5 as they presented one more rare mutation.
In the NPC lines, C666-1 cell line had 1 silent mutation and was grouped together with the EBV genome prototypes, most of non-NPC and healthy samples, and few of NPC isolates at both the phylogenetic tree. In this group the C17 tumor line was also classified since it exhibited identical BARF1 gene sequence to B95-8. The C15 tumor line, which showed 4 nucleotide exchanges, was clustered with some PTLD isolates at nucleotide tree. At amino acid level 1 NPC sample joined this small cluster, which was separated from most of NPC samples.
Structural analysis of BARF1 amino acid substitutions
Correlation of BARF1 sequence variation with viral and diagnostic parameters
To determine whether BARF1 variation might associate with a particular EBV genotype, we performed a classic EBV genotype analysis for the EBNA-2 gene [13, 40]. The EBV-positive JY (B95-8) DNA was used as positive control for EBV type 1 (250 bp in length) while Jijoye DNA was used as positive control for EBV type 2 (300 bp in length). EBV type 1 was detected in 55/56 (98.2%) of NPC cases and 14/15 (93.3%) of other EBV-related disorders, respectively. One NPC sample showed mixed-type infection and 1 non-NPC sample contained EBV type 2. No correlation was found between the presence of BARF1 variant to the EBV genotype, although the number of type 2 isolates was too small to allow statistical analysis.
Because BARF1 variation might have an effect on NPC tumor behaviour or EBV activity associating with the malignant process, we analysed possible correlations between BARF1 sequence variation and biological markers reflecting NPC disease progression. Most NPC samples were obtained from patients with advanced disease (tumor, nodul >2). No relation was found between the level of BARF1 variation and tumor, nodul or metastase-stage (data not shown).
BARF1 is a putative EBV-encoded oncogene, predominantly and abundantly expressed in EBV-associated carcinoma, but not in EBV-driven lymphomas [30, 39, 41]. To characterize genetic diversity of the EBV-encoded BARF1 oncogene, we analysed BARF1 nucleotide sequences in various EBV-positive clinical specimens. Since BARF1 is especially expressed in epithelial tumor cells, the focus was on EBV-driven NPC tumors. This study is the first to describe in detail the sequence variation of the BARF1 genotype in NPC, non-NPC EBV isolates, and healthy carriers.
A total of 11 nucleotide changes were found among NPC isolates, most of them being silent mutations. Five mutations led to amino acid changes, mostly yielding conserved mutations of V29A (valine to alanine) and H130R (histidine to arginine). Zhang et al.  reported variants of BARF1 gene on EBV cell lines from EBV-associated T/NK-cell lymphoma showing change of G to A at the position of 165554, change of T to C at 165589, and change of T to C at 165545. Only nucleotide mutation on 165589 (T to C) was similar to most of the sequences in our isolates. We did not find any isolate exhibiting mutation on other two nucleotides identified by that study.
Analysis of BARF1 gene in NPC and non-NPC EBV-related disorders showed a significant correlation between variant BARF1 and NPC susceptibility (p < 0.001). Interestingly, the Dutch-Caucasian NPC case (named NPC-56-NL in figure 1) also revealed a mutated BARF1 sequence. In further analysis difference in mutation frequency showed significant difference between NPC and European non-NPC group in particular the existence of 2 (p < 0.001) and 3-4 codon mutations (p = 0.030). However, no difference was demonstrated between NPC and regional EBV isolates in spontaneous LCL cultured directly from the arm of healthy Indonesian EBV carriers (p = 0.074). This indicates that mutant BARF1 EBV is prevalent in the endemic NPC population in Indonesia. Furthermore, BARF1 variants with 2 amino acid changes (V29A and H130R) most commonly detected in EBV isolates from the NPC group which indicates this to be the dominant strain in Indonesian NPC. The similarity to EBV strains found in healthy Indonesian individuals supports the view that this represents a geographic-associated distribution of EBV variants rather than a specific oncogenic strain. Moreover, the EBV-positive NPC cell line C666-1 obtained from a Chinese NPC case  and NPC tumor line C17 of European origin  were in the same phylogenetic branch with EBV genome prototype B95-8. Another NPC tumor line derived from North-African origin, C15 , even though demonstrating the V29A codon conversion, was also separated from most of the Indonesian NPC samples. Therefore, grouping most Indonesian NPC isolates apart from these NPC lines, as well as Chinese NPC prototype GD1, indicates that Indonesian NPC evolved independently from NPC strains from different geographic origins.
Several studies on LMP1 genetic variation argued that the genetic diversity in LMP1 gene may lead to potential immune evasion of infected host cells [45–47]. Another study showed a greater oncogenic potential of LMP1 variants with a 30 bp C-terminal deletions . The overall conserved character of the BARF1 gene suggests the importance of BARF1 function for virus-driven immortalization and escape strategies in an epithelial context. This is in line with the low variability of other lytic cycle proteins, like the viral IL10 encoded in BCRF1  and the major envelope protein gp350/220 encoded in BLLF1 . The limited overall sequence diverged at the protein level in different EBV isolates suggests BARF1 to play an important role in epithelial persistence during natural viral infection in man.
The functional consequence of any mutation in BARF1 gene presented in this study is not known yet. Probably these will be minimal because the mutations are rather conserved. Detailed functional analysis of BARF1 protein is now underway. Our preliminary data indicate that the Indonesian variant BARF1 (V29A and H130R) is rapidly secreted from human epithelial cells, has a stable hexameric structure and binds M-CSF (CSF-1) with high affinity (Hoebe et al., unpublished data). Therefore a contribution of the observed amino acid substitutions to altered protein functions and oncogenesis is considered unlikely, but this remains to be determined in further studies.
Our ongoing studies indicate that the natural hexameric BARF1 is a protein of low immunogenicity relative to other EBV proteins and largely escapes humoral immunity. However, when present, anti-BARF1 antibody responses are formed irrespective of the sequence of the endogenous BARF1 in a particular patient. This argues against major influences in the tertiary structure imposed by the observed mutations and is in line with the conserved characteristics of the amino acid substitutions. Further studies are needed to reveal potential subtle influences of BARF1 sequence variation on its oncogenic or pathogenic properties that might predispose to NPC development.
EBV type 1 and type 2 differ in geographic distributions and among patient populations. We found that nearly 100% of our subjects contain EBV type 1, either from Asian (Indonesian) or European background. It has been recorded that EBV type 1 is predominated in Asia NPC (86.5-95.0%), while EBV type 2 is rarely detected (4.0-13.5%) [24, 25, 50]. Our NPC samples showed even less EBV type 2 and in a form of mixed type (1.7%). We did not find an association between EBNA-2 subtypes and BARF1 sequence variation.
Quantitative analysis of EBV DNA levels in brushing in the NPC group indicated no trend or differrence when having a BARF1 variant. In term of antibody response against EBV, all serology assays assessing the abundance or diversity of antibody responses to EBV latent or lytic antigens revealed no significant differences relating to the presence of BARF1 mutations.
The present study revealed that Indonesian NPC-derived EBV strains exhibit BARF1 genetic variation relative to the B95-8 prototype which may contribute to a biological role for BARF1 in NPC development. In term of EBV genotype, viral load, and antibody reactivity to EBV there was no correlation between presence of single or multiple mutation(s) or none, suggesting no effect of BARF1 mutation of the biological markers associating with EBV carcinogenesis in NPC. The silent or conserved nature of most mutations and comparison to indirect disease markers suggests these variations are determined by the geographical prevalence and have minor biological effects on NPC development. The evolutionary conservation of BARF1 sequence and structure points to an important role for BARF1 protein in EBV biology.
Materials and methods
Patients and controls
Fifty-five NPC patients were recruited from Dr. Sardjito Teaching Hospital, Universitas Gadjah Mada, Yogyakarta, Indonesia. NPC diagnosis was based on pathological assessment tumor biopsy specimens based on WHO criteria, as detailed before [6, 51]. All cases were in advanced stages. Approval of the local medical ethical committee was obtained. We also included 1 NPC patient identified at VU University Medical Center, Amsterdam, The Netherlands.
As controls, whole blood or tumor tissue of other EBV-related diseases (n = 15) were collected. This non-NPC group consisted of post-transplant lymphoproliferative disease (PTLD) (n = 7), acquired immune deficiency syndrome (n = 4), Burkitt's lymphoma (n = 1), non-Hodgkin lymphoma (n = 1), infectious mononucleosis (n = 1), and gastric cancer (n = 1). All non-NPC EBV-related patients were Caucasians. In order to define BARF1 variation in the general population, 5 spontaneous LCLs established from peripheral blood mononuclear cells of healthy EBV-seropositive individuals from Indonesian background, were also included. These spontaneous LCL lines were obtained by culturing fresh blood B-lymphocytes in the presence of 1 mM cyclosporine-A. NPC xenograft samples C15 and C17 were a gift from Dr. Pierre Busson (Inst. Gustave Roussy, Villejuif, France) . EBV positive cell lines B95-8 and JY (EBV-1 prototype), Jijoye (EBV-2 prototype) and spontaneous LCLs were cultured in RPMI-1640 medium (Nissui Pharmaceutical Co., Tokyo, Japan) and the EBV positive NPC cell line C666-1  was cultured in DMEM/Ham's F12 medium, all with penicillin (100 IU/ml), streptomycin (100 μg/ml), and 10% fetal bovine serumin a CO2 incubator at 37°C.
Genomic DNA from NPC patients was obtained from nasopharyngeal brushings performed by experienced Ear, Nose, and Throat specialists. In all cases, the nasopharyngeal (NP) brush sample was taken prior to the biopsy in patients with suspected NPC, and both were sampled from the same site, as defined by nasendoscopy, exactly as described before . In total, 56 NP brush samples were obtained from patients with subsequently biopsy-proven NPC. Genomic DNA from other non-NPC EBV-related patients were obtained either from formalin fixed paraffin-embedded tissues from archival cases or from peripheral blood [9, 52].
EBV DNA was isolated from 1 ml of lysed brushings, blood or tissue samples by silica-based extraction [9, 10, 53]. Nucleic acids were eluted in 100 μl of which 5 μl was used in subsequent DNA amplification assays. All reagents for nucleic acid isolation were obtained from BioMerieux (Boxtel, The Netherlands).
Primer sequences were derived from the B95-8 prototype sequence [GeneBank accession No. V01555]. We designed two pairs of primers for sequence analysis of BARF1 in a double PCR procedure. The outer sequences were BARF1-F1 (forward): 5'-TCCTCACAAACACAGAATCTG-3' (165364-165384) and BARF1-R4 (reverse): 5'-ACGAGTCGCGAGGCTATC-3' (166229-166246) amplified the full 882 bp BARF1 sequence in a first PCR step and the the inner primers BARF1-F6 (forward): 5'-GAGTGGCCTTTCAGGGGCTTC-3' (165711-165734) and BARF1-R5 (reverse): 5'-GTGGCCTTTCAGGGGCTTC-3' (165845-165866) combined with F1 and R4 were subsequently used for generating two PCR amplicons with an overlap of 155 basepairs. BARF1 amplification was performed in a final volume of 25 μl of a master mix sample solution containing 1.5 mM MgCl2, 200 μM dNTPs, 1 U of Taq DNA polymerase, and 10 pmol each of forward and reverse primers. The EBV B95-8 transformed LCL, JY, was used as positive control. The cycling parameters were 94°C for 5 min, 45 cycles of 94°C for 1 min, followed by 54°C for 1 min; 72°C for 1 min; and a 7 min hold at 72°C. After amplification, the PCR products were purified using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany) and 2 μl DNA was used for sequencing. PCR direct sequencing of BARF1 was carried out using BigDye Terminator version 3.1. (Applied Biosystems, Foster City, CA, USA) with 2 μl of each sample and 2 pmol of each of the corresponding primers. Each reaction was analysed on ABI PRISM 310 Genetic Analyzer (Applied Biosystems) and partly by external commercial party (Baseclear, Leiden, The Netherlands). Data were assembled and edited using Chromas Lite software (Technelysium Pty Ltd). The acquired BARF1 sequence then was aligned and compared to the combined Raji and B95-8 prototype as the wild type of EBV genome in BLAST (National Center for Biotechnology Information: NCBI; http://www.ncbi.nlm.nih.gov).
To analyse the phylogenetic relationship within the EBV sequence samples, the BARF1 sequence was aligned from B95-8, GD1 [Genbank No. AY961628], AG876 [Genbank No. NC009334], NPC lines and all BARF1 variants. The sequences were aligned and the distances between each sample were determined with the ClustalW home page. A phylogenetic tree was assembled from these matrices by the neighbor-joining method using the Phylogenetic Tree Printer (Phylodendron: http://iubio.bio.indiana.edu/treeapp/).
Definition of EBV type 1 or type 2 was determined by nested-PCR [13, 40]. The first PCR reaction amplified a common region of EBNA-2 followed by two separate nested reactions amplifying distinctive regions. DNA was amplified in 25 μl reactions containing 1.5 mM MgCl2, gelatin 0.001%, 0.3 μM of each primer, 1 U of Taq Platinum DNA polymerase (Invitrogen) and 1 μl of first reaction for nested-PCR. Cycling conditions: First reaction: 94°C 2 min, 35 cycles of 94°C 1 min, 52°C 90 sec,72°C 4 min, followed by 72°C for 10 min. Nested reaction: 94°C, 2 min, 35 cycles of 94°C 30 sec, 52°C 1 min, 72°C 2 min, followed by 72°C for 10 min. The EBV-positive JY and Jijoye were used as positive control for type 1 and type 2 PCR assays, respectively. PCR reactions were performed at least twice, in a 9800 Fast Thermal Cycler (Applied Biosystems). After PCR assay, the amplified products were subjected to electrophoresis in 2% agarose gel (Sigma), stained with ethidium bromide, and visualized under ultra violet illumination. The amplicons of EBV type 1 and type 2 were 250 bp and 300 bp in length, respectively.
EBV DNA load quantification by quantitative real-time PCR
The EBV DNA load in brushings was determined by a quantitative LightCycler (LC) real-time PCR that targets a highly conserved 213-bp region of EBNA-1 . The primers used in this assay were QP1 and QP2, and the fluorigenic internal hybridization probes were EBNA LCN and EBNA FLN (TIB MolBiol, Berlin, Germany). Real-time PCR reagents were obtained from Roche Diagnostics (Almere, The Netherlands). Ten fold dilutions of spectrophotometrically quantified plasmid DNA containing the EBNA-1 target sequence were used to create a standard curve. PCR runs were conducted in a mixture of 20 μl containing 20 pmol of each primer, 4 pmol of each probe, 2 μl of LightCycler Fast Start DNA master hybridization probe reaction mixture, 4 mM MgCl2, and 5 μl of plasmid DNA or clinical specimen DNA. Amplification was conducted for 45 cycles of 10 sec at 95°C, 10 sec at 55°C, and 10 sec at 72°C. Then PCR samples were cooled to 40°C.
In all NPC patients and controls EBV specific IgA reactivity was quantitatively assessed by a synthetic peptide based enzyme-linked immunosorbent assay (ELISA) for immunodominant epitopes derived from EBNA-1 and VCA-p18 (BFRF3) . IgG seroreactivity against EBV was assessed by immunoblotting by using the nuclear fraction of HH514.c16 cells, which were chemically induced to express the viral early and capsid antigens. Immunoblots were scored semiquantitatively from 1 (weakest) to 4 (strongest), with reference to several control samples and monoclonal antibodies analysed in parallel as described elsewhere .
IgG reactivity against BARF1 was studied by ELISA using sera of EBV negative and EBV positive healthy donors as well as NPC patients. The antigen for ELISA consisted of affinity chromatography-purified native hexameric NPC-derived BARF1 protein expressed in human HEK293 cells (Hoebe et al., manuscript submitted). In short, 10 μg/ml BARF1 protein was coated in 0.05 M Na2CO3 pH 9.6 overnight at 4°C. Serum dilution and incubation conditions were standardized as described before .
Chi-square test and Fischer's exact test were performed to analyse the frequency of mutation in NPC cases, non-NPC EBV-related diseases and healthy individuals. Differences between diagnostic parameters and sequence variations were tested using one-way analysis of variance (ANOVA) (EBV DNA load) and Mann-Whitney U-test (serology). Computations were done using the statistical software SPSS version 15.0.
We gratefully acknowledge Nuffic/Netherland Fellowship Program (NFP-PhD 08/36) and Dutch Cancer Society (KWF IN2004-17). This study was partly supported by Institute for Research and Community Services Universitas Gadjah Mada Indonesia (year 2007 and 2008). We also thank Harijadi for pathological assistance, Jarir Atthobari for statistical advice and Nicholas Tarbouriech for creating the image of the BARF1 molecular structure.
- Cohen JI, Lekstrom K: Epstein-Barr virus BARF1 protein is dispensable for B-cell transformation and inhibits alpha interferon secretion from mononuclear cells. J Virol. 1999, 73 (9): 7627-7632.PubMedPubMed CentralGoogle Scholar
- Young LS, Rickinson AB: Epstein-Barr virus: 40 years on. Nat Rev Cancer. 2004, 4 (10): 757-768. 10.1038/nrc1452.PubMedView ArticleGoogle Scholar
- Thompson MP, Kurzrock R: Epstein-Barr virus and cancer. Clin Cancer Res. 2004, 10 (3): 803-821. 10.1158/1078-0432.CCR-0670-3.PubMedView ArticleGoogle Scholar
- Middeldorp JM, Brink AA, van den Brule AJ, Meijer CJ: Pathogenic roles for Epstein-Barr virus (EBV) gene products in EBV-associated proliferative disorders. Crit Rev Oncol Hematol. 2003, 45 (1): 1-36. 10.1016/S1040-8428(02)00078-1.PubMedView ArticleGoogle Scholar
- Pathmanathan R, Prasad U, Sadler R, Flynn K, Raab-Traub N: Clonal proliferations of cells infected with Epstein-Barr virus in preinvasive lesions related to nasopharyngeal carcinoma. N Engl J Med. 1995, 333 (11): 693-698. 10.1056/NEJM199509143331103.PubMedView ArticleGoogle Scholar
- Fachiroh J, Schouten T, Hariwiyanto B, Paramita DK, Harijadi A, Haryana SM, Ng MH, Middeldorp JM: Molecular diversity of Epstein-Barr virus IgG and IgA antibody responses in nasopharyngeal carcinoma: a comparison of Indonesian, Chinese, and European subjects. J Infect Dis. 2004, 190 (1): 53-62. 10.1086/421245.PubMedView ArticleGoogle Scholar
- Kondo S, Horikawa T, Takeshita H, Kanegane C, Kasahara Y, Sheen TS, Sato H, Furukawa M, Yoshizaki T: Diagnostic value of serum EBV-DNA quantification and antibody to viral capsid antigen in nasopharyngeal carcinoma patients. Cancer Sci. 2004, 95 (6): 508-513. 10.1111/j.1349-7006.2004.tb03241.x.PubMedView ArticleGoogle Scholar
- Ji MF, Wang DK, Yu YL, Guo YQ, Liang JS, Cheng WM, Zong YS, Chan KH, Ng SP, Wei WI, et al.: Sustained elevation of Epstein-Barr virus antibody levels preceding clinical onset of nasopharyngeal carcinoma. Br J Cancer. 2007, 96 (4): 623-630. 10.1038/sj.bjc.6603609.PubMedPubMed CentralView ArticleGoogle Scholar
- Stevens SJ, Verkuijlen SA, Hariwiyanto B, Fachiroh J, Paramita DK, Tan IB, Haryana SM, Middeldorp JM: Diagnostic value of measuring Epstein-Barr virus (EBV) DNA load and carcinoma-specific viral mRNA in relation to anti-EBV immunoglobulin A (IgA) and IgG antibody levels in blood of nasopharyngeal carcinoma patients from Indonesia. J Clin Microbiol. 2005, 43 (7): 3066-3073. 10.1128/JCM.43.7.3066-3073.2005.PubMedPubMed CentralView ArticleGoogle Scholar
- Stevens SJ, Verkuijlen SA, Hariwiyanto B, Paramita DK, Fachiroh J, Adham M, Tan IB, Haryana SM, Middeldorp JM: Noninvasive diagnosis of nasopharyngeal carcinoma: nasopharyngeal brushings reveal high Epstein-Barr virus DNA load and carcinoma-specific viral BARF1 mRNA. Int J Cancer. 2006, 119 (3): 608-614. 10.1002/ijc.21914.PubMedView ArticleGoogle Scholar
- Yang X, Goldstein AM, Chen CJ, Rabkin CS, Chen JY, Cheng YJ, Hsu WL, Sun B, Diehl SR, Liu MY, et al.: Distribution of Epstein-Barr viral load in serum of individuals from nasopharyngeal carcinoma high-risk families in Taiwan. Int J Cancer. 2006, 118 (3): 780-784. 10.1002/ijc.21396.PubMedView ArticleGoogle Scholar
- van Baarle D, Hovenkamp E, Kersten MJ, Klein MR, Miedema F, van Oers MH: Direct Epstein-Barr virus (EBV) typing on peripheral blood mononuclear cells: no association between EBV type 2 infection or superinfection and the development of acquired immunodeficiency syndrome-related non-Hodgkin's lymphoma. Blood. 1999, 93 (11): 3949-3955.PubMedGoogle Scholar
- Hassan R, White LR, Stefanoff CG, de Oliveira DE, Felisbino FE, Klumb CE, Bacchi CE, Seuanez HN, Zalcberg IR: Epstein-Barr virus (EBV) detection and typing by PCR: a contribution to diagnostic screening of EBV-positive Burkitt's lymphoma. Diagn Pathol. 2006, 1: 17-10.1186/1746-1596-1-17.PubMedPubMed CentralView ArticleGoogle Scholar
- Brooks JM, Croom-Carter DS, Leese AM, Tierney RJ, Habeshaw G, Rickinson AB: Cytotoxic T-lymphocyte responses to a polymorphic Epstein-Barr virus epitope identify healthy carriers with coresident viral strains. J Virol. 2000, 74 (4): 1801-1809. 10.1128/JVI.74.4.1801-1809.2000.PubMedPubMed CentralView ArticleGoogle Scholar
- Cohen JI, Wang F, Mannick J, Kieff E: Epstein-Barr virus nuclear protein 2 is a key determinant of lymphocyte transformation. Proc Natl Acad Sci USA. 1989, 86 (23): 9558-9562. 10.1073/pnas.86.23.9558.PubMedPubMed CentralView ArticleGoogle Scholar
- Rickinson AB, Young LS, Rowe M: Influence of the Epstein-Barr virus nuclear antigen EBNA 2 on the growth phenotype of virus-transformed B cells. J Virol. 1987, 61 (5): 1310-1317.PubMedPubMed CentralGoogle Scholar
- Tarbouriech N, Ruggiero F, de Turenne-Tessier M, Ooka T, Burmeister WP: Structure of the Epstein-Barr virus oncogene BARF1. J Mol Biol. 2006, 359 (3): 667-678. 10.1016/j.jmb.2006.03.056.PubMedView ArticleGoogle Scholar
- Wei MX, Ooka T: A transforming function of the BARF1 gene encoded by Epstein-Barr virus. EMBO J. 1989, 8 (10): 2897-2903.PubMedPubMed CentralGoogle Scholar
- Sheng W, Decaussin G, Sumner S, Ooka T: N-terminal domain of BARF1 gene encoded by Epstein-Barr virus is essential for malignant transformation of rodent fibroblasts and activation of BCL-2. Oncogene. 2001, 20 (10): 1176-1185. 10.1038/sj.onc.1204217.PubMedView ArticleGoogle Scholar
- Seto E, Ooka T, Middeldorp J, Takada K: Reconstitution of nasopharyngeal carcinoma-type EBV infection induces tumorigenicity. Cancer Res. 2008, 68 (4): 1030-1036. 10.1158/0008-5472.CAN-07-5252.PubMedView ArticleGoogle Scholar
- Young LS, Dawson CW, Clark D, Rupani H, Busson P, Tursz T, Johnson A, Rickinson AB: Epstein-Barr virus gene expression in nasopharyngeal carcinoma. J Gen Virol. 1988, 69 (Pt 5): 1051-1065. 10.1099/0022-1317-69-5-1051.PubMedView ArticleGoogle Scholar
- Fahraeus R, Fu HL, Ernberg I, Finke J, Rowe M, Klein G, Falk K, Nilsson E, Yadav M, Busson P, et al.: Expression of Epstein-Barr virus-encoded proteins in nasopharyngeal carcinoma. Int J Cancer. 1988, 42 (3): 329-338. 10.1002/ijc.2910420305.PubMedView ArticleGoogle Scholar
- Khabir A, Karray H, Rodriguez S, Rose M, Daoud J, Frikha M, Boudawara T, Middeldorp J, Jlidi R, Busson P: EBV latent membrane protein 1 abundance correlates with patient age but not with metastatic behavior in north African nasopharyngeal carcinomas. Virol J. 2005, 2: 39-10.1186/1743-422X-2-39.PubMedPubMed CentralView ArticleGoogle Scholar
- Hu LF, Zabarovsky ER, Chen F, Cao SL, Ernberg I, Klein G, Winberg G: Isolation and sequencing of the Epstein-Barr virus BNLF-1 gene (LMP1) from a Chinese nasopharyngeal carcinoma. J Gen Virol. 1991, 72 (Pt 10): 2399-2409. 10.1099/0022-1317-72-10-2399.PubMedView ArticleGoogle Scholar
- Chen XY, Pepper SD, Arrand JR: Prevalence of the A and B types of Epstein-Barr virus DNA in nasopharyngeal carcinoma biopsies from southern China. J Gen Virol. 1992, 73 (Pt 2): 463-466. 10.1099/0022-1317-73-2-463.PubMedView ArticleGoogle Scholar
- Li SN, Chang YS, Liu ST: Effect of a 10-amino acid deletion on the oncogenic activity of latent membrane protein 1 of Epstein-Barr virus. Oncogene. 1996, 12 (10): 2129-2135.PubMedGoogle Scholar
- Edwards RH, Sitki-Green D, Moore DT, Raab-Traub N: Potential selection of LMP1 variants in nasopharyngeal carcinoma. J Virol. 2004, 78 (2): 868-881. 10.1128/JVI.78.2.868-881.2004.PubMedPubMed CentralView ArticleGoogle Scholar
- Mainou BA, Raab-Traub N: LMP1 strain variants: biological and molecular properties. J Virol. 2006, 80 (13): 6458-6468. 10.1128/JVI.00135-06.PubMedPubMed CentralView ArticleGoogle Scholar
- Decaussin G, Sbih-Lammali F, de Turenne-Tessier M, Bouguermouh A, Ooka T: Expression of BARF1 gene encoded by Epstein-Barr virus in nasopharyngeal carcinoma biopsies. Cancer Res. 2000, 60 (19): 5584-5588.PubMedGoogle Scholar
- Hayes DP, Brink AA, Vervoort MB, Middeldorp JM, Meijer CJ, van den Brule AJ: Expression of Epstein-Barr virus (EBV) transcripts encoding homologues to important human proteins in diverse EBV associated diseases. Mol Pathol. 1999, 52 (2): 97-103. 10.1136/mp.52.2.97.PubMedPubMed CentralView ArticleGoogle Scholar
- Seto E, Yang L, Middeldorp J, Sheen TS, Chen JY, Fukayama M, Eizuru Y, Ooka T, Takada K: Epstein-Barr virus (EBV)-encoded BARF1 gene is expressed in nasopharyngeal carcinoma and EBV-associated gastric carcinoma tissues in the absence of lytic gene expression. J Med Virol. 2005, 76 (1): 82-88. 10.1002/jmv.20327.PubMedView ArticleGoogle Scholar
- Comeau MR, Johnson R, DuBose RF, Petersen M, Gearing P, VandenBos T, Park L, Farrah T, Buller RM, Cohen JI, et al.: A poxvirus-encoded semaphorin induces cytokine production from monocytes and binds to a novel cellular semaphorin receptor, VESPR. Immunity. 1998, 8 (4): 473-482. 10.1016/S1074-7613(00)80552-X.PubMedView ArticleGoogle Scholar
- Strockbine LD, Cohen JI, Farrah T, Lyman SD, Wagener F, DuBose RF, Armitage RJ, Spriggs MK: The Epstein-Barr virus BARF1 gene encodes a novel, soluble colony-stimulating factor-1 receptor. J Virol. 1998, 72 (5): 4015-4021.PubMedPubMed CentralGoogle Scholar
- Cohen JI: The biology of Epstein-Barr virus: lessons learned from the virus and the host. Curr Opin Immunol. 1999, 11 (4): 365-370. 10.1016/S0952-7915(99)80062-4.PubMedView ArticleGoogle Scholar
- Sall A, Caserta S, Jolicoeur P, Franqueville L, de Turenne-Tessier M, Ooka T: Mitogenic activity of Epstein-Barr virus-encoded BARF1 protein. Oncogene. 2004, 23 (28): 4938-4944. 10.1038/sj.onc.1207607.PubMedView ArticleGoogle Scholar
- Wei MX, Moulin JC, Decaussin G, Berger F, Ooka T: Expression and tumorigenicity of the Epstein-Barr virus BARF1 gene in human Louckes B-lymphocyte cell line. Cancer Res. 1994, 54 (7): 1843-1848.PubMedGoogle Scholar
- Sheng W, Decaussin G, Ligout A, Takada K, Ooka T: Malignant transformation of Epstein-Barr virus-negative Akata cells by introduction of the BARF1 gene carried by Epstein-Barr virus. J Virol. 2003, 77 (6): 3859-3865. 10.1128/JVI.77.6.3859-3865.2003.PubMedPubMed CentralView ArticleGoogle Scholar
- Wei MX, de Turenne-Tessier M, Decaussin G, Benet G, Ooka T: Establishment of a monkey kidney epithelial cell line with the BARF1 open reading frame from Epstein-Barr virus. Oncogene. 1997, 14 (25): 3073-3081. 10.1038/sj.onc.1201128.PubMedView ArticleGoogle Scholar
- zur Hausen A, Brink AA, Craanen ME, Middeldorp JM, Meijer CJ, van den Brule AJ: Unique transcription pattern of Epstein-Barr virus (EBV) in EBV-carrying gastric adenocarcinomas: expression of the transforming BARF1 gene. Cancer Res. 2000, 60 (10): 2745-2748.PubMedGoogle Scholar
- van Baarle D, Hovenkamp E, Dukers NH, Renwick N, Kersten MJ, Goudsmit J, Coutinho RA, Miedema F, van Oers MH: High prevalence of Epstein-Barr virus type 2 among homosexual men is caused by sexual transmission. J Infect Dis. 2000, 181 (6): 2045-2049. 10.1086/315521.PubMedView ArticleGoogle Scholar
- Brink AA, Meijer CJ, Nicholls JM, Middeldorp JM, van den Brule AJ: Activity of the EBNA1 promoter associated with lytic replication (Fp) in Epstein-Barr virus associated disorders. Mol Pathol. 2001, 54 (2): 98-102. 10.1136/mp.54.2.98.PubMedPubMed CentralView ArticleGoogle Scholar
- Zhang Y, Ohyashiki JH, Takaku T, Shimizu N, Ohyashiki K: Transcriptional profiling of Epstein-Barr virus (EBV) genes and host cellular genes in nasal NK/T-cell lymphoma and chronic active EBV infection. Br J Cancer. 2006, 94 (4): 599-608. 10.1038/sj.bjc.6602968.PubMedPubMed CentralView ArticleGoogle Scholar
- Cheung ST, Huang DP, Hui AB, Lo KW, Ko CW, Tsang YS, Wong N, Whitney BM, Lee JC: Nasopharyngeal carcinoma cell line (C666-1) consistently harbouring Epstein-Barr virus. Int J Cancer. 1999, 83 (1): 121-126. 10.1002/(SICI)1097-0215(19990924)83:1<121::AID-IJC21>3.0.CO;2-F.PubMedView ArticleGoogle Scholar
- Busson P, Ganem G, Flores P, Mugneret F, Clausse B, Caillou B, Braham K, Wakasugi H, Lipinski M, Tursz T: Establishment and characterization of three transplantable EBV-containing nasopharyngeal carcinomas. Int J Cancer. 1988, 42 (4): 599-606. 10.1002/ijc.2910420422.PubMedView ArticleGoogle Scholar
- Saechan V, Mori A, Mitarnun W, Settheetham-Ishida W, Ishida T: Analysis of LMP1 variants of EBV in Southern Thailand: evidence for strain-associated T-cell tropism and pathogenicity. J Clin Virol. 2006, 36 (2): 119-125. 10.1016/j.jcv.2006.01.018.PubMedView ArticleGoogle Scholar
- Nagamine M, Takahara M, Kishibe K, Nagato T, Ishii H, Bandoh N, Ogino T, Harabuchi Y: Sequence variations of Epstein-Barr virus LMP1 gene in nasal NK/T-cell lymphoma. Virus Genes. 2007, 34 (1): 47-54. 10.1007/s11262-006-0008-5.PubMedView ArticleGoogle Scholar
- Tang YL, Lu JH, Cao L, Wu MH, Peng SP, Zhou HD, Huang C, Yang YX, Zhou YH, Chen Q, et al.: Genetic variations of EBV-LMP1 from nasopharyngeal carcinoma biopsies: potential loss of T cell epitopes. Braz J Med Biol Res. 2008, 41 (2): 110-116. 10.1590/S0100-879X2008000200006.PubMedView ArticleGoogle Scholar
- Kanai K, Satoh Y, Yamanaka H, Kawaguchi A, Horie K, Sugata K, Hoshikawa Y, Sata T, Sairenji T: The vIL-10 gene of the Epstein-Barr virus (EBV) is conserved in a stable manner except for a few point mutations in various EBV isolates. Virus Genes. 2007, 35 (3): 563-569. 10.1007/s11262-007-0153-5.PubMedView ArticleGoogle Scholar
- Kawaguchi A, Kanai K, Satoh Y, Touge C, Nagata K, Sairenji T, Inoue Y: The evolution of Epstein-Barr virus inferred from the conservation and mutation of the virus glycoprotein gp350/220 gene. Virus Genes. 2009, 38 (2): 215-223. 10.1007/s11262-008-0323-0.PubMedView ArticleGoogle Scholar
- Tiwawech D, Srivatanakul P, Karalak A, Ishida T: Association between EBNA2 and LMP1 subtypes of Epstein-Barr virus and nasopharyngeal carcinoma in Thais. J Clin Virol. 2008, 42 (1): 1-6. 10.1016/j.jcv.2007.11.011.PubMedView ArticleGoogle Scholar
- Fachiroh J, Paramita DK, Hariwiyanto B, Harijadi A, Dahlia HL, Indrasari SR, Kusumo H, Zeng YS, Schouten T, Mubarika S, et al.: Single-assay combination of Epstein-Barr Virus (EBV) EBNA1- and viral capsid antigen-p18-derived synthetic peptides for measuring anti-EBV immunoglobulin G (IgG) and IgA antibody levels in sera from nasopharyngeal carcinoma patients: options for field screening. J Clin Microbiol. 2006, 44 (4): 1459-1467. 10.1128/JCM.44.4.1459-1467.2006.PubMedPubMed CentralView ArticleGoogle Scholar
- van Beek J, zur Hausen A, Klein Kranenbarg E, van de Velde CJ, Middeldorp JM, van den Brule AJ, Meijer CJ, Bloemena E: EBV-positive gastric adenocarcinomas: a distinct clinicopathologic entity with a low frequency of lymph node involvement. J Clin Oncol. 2004, 22 (4): 664-670. 10.1200/JCO.2004.08.061.PubMedView ArticleGoogle Scholar
- Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noordaa J: Rapid and simple method for purification of nucleic acids. J Clin Microbiol. 1990, 28 (3): 495-503.PubMedPubMed CentralGoogle Scholar
- Stevens SJ, Verkuijlen SA, Brule AJ, Middeldorp JM: Comparison of quantitative competitive PCR with LightCycler-based PCR for measuring Epstein-Barr virus DNA load in clinical specimens. J Clin Microbiol. 2002, 40 (11): 3986-3992. 10.1128/JCM.40.11.3986-3992.2002.PubMedPubMed CentralView ArticleGoogle Scholar
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