Epstein-Barr virus DNA in nasopharyngeal biopsies

Higher incidence of nasopharyngeal carcinoma in some regions in the world confers for interplay between genetic factors and external stimuli

Nasopharyngeal carcinoma (NPC) is a rare variety of head and neck cancers. The risk factors include three major causes: genetic factors, viral infection, and environmental and dietary factors. The types of NPC show strong ethnic and geographic variations. The keratinizing and non-keratinizing types are prevalent in the lower incidence regions like North America and Europe; whereas the undifferentiated type is mostly found in the regions with higher incidences like China, North Africa, Arctic, and Nagaland of North-East India. These suggest a possible major role of the internal genetic factors for generation and promotion of this disease. Viral infections might accelerate the process of carcinogenesis by helping in cellular proliferation and loss of apoptosis. Diet and other environmental factors promote these neoplastic processes and further progression of the disease occurs.

Genome-wide profiling of Epstein-Barr virus integration by targeted sequencing in Epstein-Barr virus associated malignancies

Rationale: Epstein-Barr virus (EBV) is associated with multiple malignancies with expression of viral oncogenic proteins and chronic inflammation as major mechanisms contributing to tumor development. A less well-studied mechanism is the integration of EBV into the human genome possibly at sites which may disrupt gene expression or genome stability.

Methods: We sequenced tumor DNA to profile the EBV sequences by hybridization-based enrichment. Bioinformatic analysis was used to detect the breakpoints of EBV integrations in the genome of cancer cells.

Results: We identified 197 breakpoints in nasopharyngeal carcinomas and other EBV-associated malignancies. EBV integrations were enriched at vulnerable regions of the human genome and were close to tumor suppressor and inflammation-related genes. We found that EBV integrations into the introns could decrease the expression of the inflammation-related genes, TNFAIP3, PARK2, and CDK15, in NPC tumors. In the EBV genome, the breakpoints were frequently at oriP or terminal repeats. These breakpoints were surrounded by microhomology sequences, consistent with a mechanism for integration involving viral genome replication and microhomology-mediated recombination.

Conclusion: Our finding provides insight into the potential of EBV integration as an additional mechanism mediating tumorigenesis in EBV associated malignancies.

Genome-wide Analysis of Epstein-Barr Virus (EBV) Integration and Strain in C666-1 and Raji Cells

EBV is a key risk factor for many malignancy diseases such as nasopharyngeal carcinoma (NPC) and Burkitt lymphoma (BL). EBV integration has been reported, but its scale and impact to cancer development is remains unclear. C666-1 (NPC cell line) and Raji (BL cell line) are commonly studied EBV-positive cancer cells. A rare few EBV integration sites in Raji were found in previous research by traditional methods. To deeply survey EBV integration, we sequenced C666-1 and Raji whole genomes by the next generation sequencing (NGS) technology and a total of 909 breakpoints were detected in the two cell lines. Moreover, we observed that the number of integration sites was positive correlated with the total amount of chromosome structural variations (SVs) and copy number structural variations (CNVs), and most breakpoints located inside or nearby genome structural variations regions. It suggested that host genome instability provided an opportunity for EBV integration on one hand and the integration aggravated host genome instability on the other hand. Then, we respectively assembled the C666-1 and Raji EBV strains which would be useful resources for EBV-relative studies. Thus, we report the most comprehensive characterization of EBV integration in NPC cell and BL cell, and EBV shows the wide range and random integration to increase the tumorigenesis. The NGS provides an incomparable level of resolution on EBV integration and a convenient approach to obtain viral strain compared to any research technology before.

Glucocorticoids activate Epstein Barr virus lytic replication through the upregulation of immediate early BZLF1 gene expression

Psychological stress-associated immune dysregulation has been shown to disrupt the steady-state expression and reactivate latent herpes viruses. One such virus is the Epstein Barr virus (EBV), which is associated with several human malignancies. EBV infects >90% of people living in North America and persists for life in latently infected cells. Although several studies have shown that glucocorticoids (GCs) can directly induce reactivation of the latent virus, the mechanism of stress hormone involvement in the control of EBV gene expression is not well understood. In this study, we tested the hypothesis that GCs can induce the latent EBV genome to lytically replicate through the induction of the EBV immediate early gene BZLF1 which encodes the lytic transactivator protein ZEBRA. We show a dose-dependent upregulation of BZLF1 mRNA expression by hydrocortisone (HC) and dexamethasone (Dex) in Daudi cells, an EBV genome positive Burkitt's lymphoma cell line, and Dex-induction of the early gene products BLLF3 (encoding for the EBV dUTPase) and BALF5 (encoding for the EBV DNA polymerase). We show that Daudi cells express glucocorticoid receptors (GR) that mediate Dex-dependent upregulation of BZLF1 mRNA levels. This effect was inhibited by both the glucocorticoid receptor antagonist RU486 and by cycloheximide. The results suggest that GCs, in addition to inducing stress-related immune dysregulation, can mediate latent EBV reactivation through the induction of the BZLF1 gene.

Distribution and phenotype of Epstein-Barr virus-infected cells in human pharyngeal tonsils

Although Epstein-Barr virus (EBV) is often found in human tonsils, it remains to be precisely determined in what cells and microenvironment the virus is present. Although generally regarded as a B lymphotropic virus, EBV is associated with non-B-cell tumors, for example, NK/T-cell lymphoma, carcinoma, and leiomyosarcoma. To provide a basis for understanding the origin and biology of EBV-infected non-B cells, the immunophenotype of all EBV-infected cells in reactive human tonsils was determined by subjecting tonsil sections to dual/triple EBER in situ hybridization and immunohistochemistry with monoclonal antibodies to T cells (CD3, CD4, CD8, CCR3), B cells (CD20), plasma cells (CD138), natural killer (NK) cells (PEN5), and epithelial cells (cytokeratin), as well as frozen section immunostaining with antibodies to EBV latent proteins EBNA1, EBNA2, LMP1, and EBV early protein BZLF1. Most tonsils contained nearly equal numbers of EBNA1- and LMP1-positive cells (latency program) while only a few contained EBNA2-positive cells (growth program). More than 1000 EBER-positive cells from six tonsils were detected in the interfollicular zone (59%), tonsillar crypts (26%), and follicles (15%). Most (82%) EBER-positive cells are CD20-positive B cells, 7% are CD3-positive T cells, and 11% are cells of indeterminate lineage, often with plasmacytoid morphology. However, no EBER-positive plasma cells were identified. Rare EBER-positive NK cells and EBER/BZLF1-positive epithelial cells were identified. The direct demonstration of EBV within rare T cells, NK cells, and epithelial cells in reactive human tonsils provide a basis for further understanding of the origin of EBV-associated tumors of non-B-cell type.

Improved Accuracy of Detection of Nasopharyngeal Carcinoma by Combined Application of Circulating Epstein–Barr Virus DNA and Anti-Epstein–Barr Viral Capsid Antigen IgA Antibody

Background: Circulating Epstein–Barr viral (EBV) DNA and anti-EBV capsid antigen IgA (IgA VCA) represent two of the most sensitive peripheral blood markers of nasopharyngeal carcinoma (NPC), but direct comparative studies of these two markers are lacking.

Methods: The sensitivities and specificities of IgA-VCA and EBV DNA for diagnosis of NPC were determined in 139 new cases of NPC and 178 healthy individuals, respectively. EBV DNA was also assessed in 36 healthy family members identified as having false-positive IgA-VCA results at a screening clinic. EBV DNA was measured by a real-time quantitative PCR assay with a detection limit of 60 copies/mL. IgA-VCA was measured by semiquantitative indirect immunofluorescent method; a titer ≥1/10 was taken as positive.

Results: The sensitivities of EBV DNA and IgA-VCA for diagnosis of NPC were 95% (95% confidence interval, 91–98%) and 81% (73–87%), respectively. The combined marker panel had an overall sensitivity (positive result by either marker) of 99%. The concentrations of both markers showed dependence on cancer stage. The specificities of EBV DNA and IgA-VCA were 98% (96–99%) and 96% (91–98%), respectively. Among 36 healthy family members with false-positive IgA-VCA results, three-fourths had undetectable EBV DNA, whereas the others had increased EBV DNA concentrations that were significantly lower than in NPC patients.

Conclusions: For diagnosis of NPC, EBV DNA identifies almost all false-negative IgA-VCA cases and gives a 99% diagnostic sensitivity when combined with IgA-VCA. In the screening setting, EBV DNA identifies three-fourths of false-positive IgA-VCA cases. The selective application of EBV DNA in an IgA-VCA-based screening protocol could improve screening accuracy with only moderate increases in cost.

Detection of Epstein-Barr virus and subsets of lymphoid cells in adenoid tissue of children under 2 years of age

Epstein-Barr virus (EBV) has been closely associated with undifferentiated nasopharyngeal carcinoma (NPC) and T/NK nasal non Hodgkin lymphoma. Nevertheless, the presence of EBV in non neoplastic lymphoid tissue of the nasopharynx has been rarely investigated. In a previous study by our group, using in situ hybridization to detect EBV in adenoids of children (2-13 years old) resected because of nasal obstruction due to hypertrophy, we found EBV genome in 72% of the cases. It was now intended to study the frequency of EBV expression in adenoids from children that underwent surgical removal, belonging to a lower age group (1-2 years old). It was also intended to establish which lymphoid subsets are involved in this infection. Adenoidal paraffin sections from 21 patients aged 1-2 years old (mean 1.6 years), 15 males and six females were submitted to double labeling: in situ hybridization with EBER 1/2 probes to detect EBV and immunohistochemistry to determine the lymphocyte typing of EBV-positive cells (CD20 for B-lymphocytes, CD3 for T-lymphocytes and CD56 and CD57 for NK-cells). Among 21 patients, seven showed positive lymphoid cells for EBV (33%). In almost all cases, EBV-positive cells were also CD20-positive. Some EBV-positive cells showed no labeling with any of the lymphoid markers, but in no instance they were positive for CD3, CD56 or CD57. This study confirms the preferential infection of B-lymphocytes by EBV, which in some instances can down regulate the expression of CD20.

Nasopharyngeal swab and PCR for the screening of nasopharyngeal carcinoma in the endemic area: a good supplement to the serologic screening

BACKGROUND

Nasopharyngeal carcinoma (NPC) is a common head and neck cancer in Taiwan. Early detection is the best way to improve survival for this disease. A prospective study was designed to assess the feasibility of a new screening method for NPC by use of polymerase chain reaction (PCR) based on the close association of NPC and Epstein-Barr virus (EBV).

METHODS

One hundred thirty-three different tissues from nasopharynx, nose, and sinus were investigated by use of PCR to check for the presence of EBV genome. Subsequently, from April 1996 to March 1997, 55 patients were enrolled in a prospective screening study. All patients underwent nasopharyngeal swabs before biopsy. Polymerase chain reaction detection of EBV genome was conducted on swab samples. Anti-EBV viral capsid antigen (VCA) in IgA and IgG class were checked at the same visit.

RESULTS

The EBV genome was present in 91.4% (85/93) of NPC tissues and in 25.0% (10/40) of non-NPC tissues (p < .001, chi2 test). Of the 55 swabs, 49 (89.1%) specimens obtained enough cells for PCR examination. Thirty of these 49 patients were pathologically proved NPC. The presence of EBV were 86.7% (26/30) in NPC group and 42.1% (8/19) in non-NPC group. The sensitivity and specificity were 86.7% and 57.9%, respectively, which were similar to those of serologic method (87.5% and 43.5%) when the cut-off point was set at anti-VCA IgG > or = 160 and IgA > or = 10. Combining both methods elevates the specificity to 84.2%.

CONCLUSIONS

The sensitivity of this PCR screening method is similar to that of the serologic method. Combining both methods can greatly increase the specificity, indicating this new method is a good supplement to the serologic screening of this endemic disease.

Role of Epstein-Barr virus in fine-needle aspirates of metastatic neck nodes in the diagnosis of nasopharyngeal carcinoma

BACKGROUND

The patient with nasopharyngeal carcinoma (NPC) frequently is initially seen with regional node dissemination. Preliminary investigations suggest that the presence of Epstein-Barr virus (EBV) genomes in neck metastases from an occult primary may be diagnostic and predictive of NPC. The goal of this study was to test this proposition.

METHODS

The polymerase chain reaction (PCR) was used to detect the presence of EBV DNA in fine-needle aspirate (FNA) samples obtained from malignant neck nodes. Control samples were obtained from other locations in the head and neck.

PATIENTS

The patients in this study were evaluated at the Toronto Princess Margaret Hospital, a province-wide tertiary-care cancer treatment center. Of the 23 patients evaluated with malignant neck masses, 6 had NPC, 5 patients had metastatic squamous cell carcinoma of an unknown primary, and 12 patients served as controls with other known head and neck carcinomas. One of the patients initially diagnosed as an unknown primary later demonstrated NPC. FNA specimens were also obtained from 24 normal parotid, submandibular, or thyroid glands for comparison.

RESULTS

In the samples with sufficient DNA for analysis, EBV was detected in 5 of 5 neck nodes from patients with known NPC. EBV was also detected in the neck node of a patient who went on to develop NPC and in a cervical node from 1 of 2 patients in whom the primary tumor remained unknown. None of the evaluable control neck nodes of FNA controls from other sites demonstrated EBV.

CONCLUSIONS

These results demonstrate the utility of NPC-diagnostic EBV gene amplification in FNA samples of neck metastases and suggest that the presence of the EBV genome in FNA samples of neck nodes is predictive of the presence of NPC.

Epstein-Barr virus DNA detection in gingival tissues of patients undergoing surgical extractions

The main oral manifestation of Epstein-Barr virus (EBV) infection is hairy leukoplakia, a lesion associated with the acquired immunodeficiency syndrome (AIDS) and occasionally in other immunocompromised patients. However, the recent literature describes the presence of viral genome in clinically normal oral tissues. The purpose of this work was to investigate these occult EBV infections in gingival epithelium. The Southern blot method with 32P-radiolabelled DNA probes under stringent conditions was applied to 20 interproximal gingival papillae specimens and revealed homologous EBV sequences in 4 of 10 AIDS patients as well as in 4 of 10 HIV negative patients. In order to determine whether EBV has a predilection for the gingival tissues, samples of nasal, laryngeal and oral mucosa, other than gingival mucosa, were collected from 10 HIV-negative patients undergoing surgical treatment for a variety of clinical conditions. None of these extra-periodontal mucosal specimens contained homologous EBV DNAs, except an edentulous palatal gingival specimen. With the present detection of EBV DNAs in the gingival tissues of patients undergoing surgical extractions, it would be of interest to investigate more systematically these subclinical infections in order to determine their exact implications in oral disease.

Detection of EBV DNA in post-nasal space biopsy tissue from asymptomatic EBV-seropositive individuals

The association between EBV and nasopharyngeal carcinoma (NPC) has been well documented although the precise role of the virus in the genesis of the tumour is not understood. We undertook this study to examine the prevalence of EBV infection in nasopharyngeal tissue obtained from 33 healthy individuals not considered to be at risk of developing NPC. Using polymerase chain amplification (PCR) and in situ hybridization we have identified EBV DNA in 70% (23/33) of the tissues examined. Our data demonstrate that EBV is present at the site of tumour development in the low-risk population and by inference that the virus is also present before the onset of disease in the high-risk group. This survey supports the concept of NPC pathogenesis as a multifactorial process.

Detection of occult nasopharyngeal primary tumours by means of in situ hybridization

Detection of nasopharyngeal carcinoma primaries in patients presenting with neck node metastases may sometimes demand considerable efforts. By using the 'in situ hybridization' technique, we manage to identify the Epstein-Barr virus in neck metastases secondary to nasopharyngeal carcinomas. We propose that such identification in neck node metastases where the primary lesion is unknown indicates a nasopharyngeal primary.

Two epithelial tumor cell lines (HNE-1 and HONE-1) latently infected with Epstein-Barr virus that were derived from nasopharyngeal carcinomas

Two epithelial tumor cell lines were established from biopsy specimens of nasopharyngeal carcinomas (NPC). The specimens were taken from poorly differentiated squamous cell carcinomas of the nasopharynx. The tissues were prepared for cell culture and eventually two continuous epithelial cell lines were obtained and designated HONE-1 and HNE-1. Light and electron microscopic examination of these two cell lines demonstrated cells with an epithelial morphology including the presence of desmosomes. The HNE-1 cell line has been passaged more than 100 times and the HONE-1 cell line has been passaged more than 90 times. It was found that early-passage uncloned HNE-1 cells (passage 23) could be superinfected with the B95-8 and NPC-EBV isolates as demonstrated by the induction of Epstein-Barr virus (EBV)-specific early antigen(s) in a small percentage of the cells; HONE-1 cells could also be superinfected with EBV. Southern blot analysis detected EBV DNA in samples from uncloned HNE-1 cells at passages 12, 17, 21, 27, and 35. However, by passage 45, EBV DNA could no longer be detected in HNE-1 cells by Southern blot analysis. The EBV genome was detected in parental HONE-1 cells at subculture 9 and in clone 40 cells up to passage 40 thus far. When HNE-1 cells were examined for the expression of the EBV-encoded nuclear antigen (EBNA) at passage 12, only about 10% of the cells were found to be positive. The percentage of EBNA-positive HNE-1 cells decreased as the cells were passaged. A similar loss of EBNA was observed in uncloned HONE-1 cells, but not in HONE-1 clone 40 cells. In clone 40, which has been passaged 40 times thus far, 85-90% of the cells are still EBNA-positive. The data suggest that EBV genome-positive HNE-1 and HONE-1 cells were lost as the cells were cultivated in vitro and that cloning the cells at an early passage level may be critical in maintaining EBV genome-positive epithelial NPC cells. These EBV genome-positive epithelial NPC cell lines will be useful for studying the association of EBV and NPC.