Pretreatment with restriction enzyme or bovine serum albumin for effective PCR amplification of Epstein-Barr virus DNA in DNA extracted from paraffin-embedded gastric carcinoma tissue

Epstein-Barr Virus-Infected Malignant T/NK-Cell Lymphoma in a Patient with Hypersensitivity to Mosquito Bites

We report an autopsy case of Epstein-Barr virus (EBV)-infected malignant lymphoma in a young male who had hypersensitivity to mosquito bites. The autopsy revealed multiple confluent lymphoma lesions in the lungs, and on the right leg irregular-shaped skin ulcers were seen. The left pleural effusion also contained a large number of lymphoma cells. The lymphoma cells were determined as T/NK-cell type cells by immunohistochemistry. EBV DNA was detected most intensively in the lungs and EBV-encoded small RNAs-positive lymphoma cells were also observed in the lungs at a high frequency. EBV latent membrane protein-1 expression and a high Ki-67 labeling indices were noted in the lymphoma cells of the lung lesions. These findings indicate that the development of the malignant lymphoma was associated with the proliferation of EBV-infected lymphoma cells, and the cells that infiltrated the whole the body, especially the lungs, caused the patient's death.

The use of bovine serum albumin to improve the RT-qPCR detection of foodborne viruses rinsed from vegetable surfaces

AIMS

To demonstrate that produce rinsates used for RT-qPCR detection of foodborne viruses may cause significant PCR inhibition and propose a means to reduce its impact on sensitivity.

METHODS AND RESULTS

Here, it is shown that rinsing and concentration from spinach and precut lettuce have the potential to generate RNA extracts that are inhibitory to RT-qPCRs assembled from commercial kits for the detection of norovirus GII (NoV GII), hepatitis A virus (HAV), hepatitis E virus (HEV), rotavirus (RV) and feline calicivirus (FCV) as sample process control. It is further shown that the addition of bovine serum albumin (BSA) to those reactions restored a positive signal in all cases. The effect of BSA was dependent upon the primer/probe combination. Moreover, two of the detection systems (FCV and HAV) strongly benefited from the addition of BSA even in the absence of PCR inhibitors.

CONCLUSIONS

BSA was shown to restore positive signals in five different RT-qPCR systems that were otherwise completely inhibited by produce rinsate extracts. It is therefore suggested to consider the addition of BSA to RT-qPCRs for the detection of foodborne viruses when inhibition is observed.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study clearly demonstrates the potency of PCR inhibitors generated during routine virus concentration from produce and that it can be alleviated by the addition of BSA to the RT-qPCRs. Although used elsewhere, the addition of BSA to PCRs is not a common practice in this growing field of research.

Epstein-Barr virus as a marker of biological aggressiveness in breast cancer

Purpose:

Although a potential role of the Epstein-Barr virus (EBV) in the pathogenesis of breast cancer (BC) has been underlined, results remain conflicting. Particularly, the impact of EBV infection on biological markers of BC has received little investigation.

Methods:

In this study, we established the frequency of EBV-infected BC using real-time quantitative PCR (RT–PCR) in 196 BC specimens. Biological and pathological characteristics according to EBV status were evaluated.

Results:

EBV DNA was present in 65 of the 196 (33.2%) cases studied. EBV-positive BCs tended to be tumours with a more aggressive phenotype, more frequently oestrogen receptor negative (P=0.05) and with high histological grade (P=0.01). Overexpression of thymidine kinase activity was higher in EBV-infected BC (P=0.007). The presence of EBV was weakly associated with HER2 gene amplification (P=0.08).

Conclusion:

Our study provides evidence for EBV-associated BC undergoing distinct carcinogenic processes, with more aggressive features.

Detection and location of Helicobacter pylori in human gastric carcinomas

AIM: To define the infection status of Helicobacter pylori in 109 patients with gastric cancers and H pylori localization in gastric carcinoma tissues in South China.

METHODS: The incidence of H pylori infection in gastric carcinomas was estimated by polymerase chain reaction (PCR), simultaneously; both morphological features and the localization of H pylori in gastric carcinomas were demonstrated by Warthin-Starry (WS) staining. The relationships between H pylori infection and the clinical-pathologic factors of gastric carcinomas were analyzed by software SPSS10.0.

RESULTS: H pylori was found in 42 (39.03%) and 58 (53.21%) cases of 109 patients with gastric carcinomas by PCR and WS, respectively. H pylori infection rate detected in gastric carcinomas by WS was higher than that by PCR (χ² = 9.735, P<0.005<0.01). WS stain showed that H pylori existed in the gastric antrum mucus, mucosal gland of normal tissues adjacent to gastric carcinomas and the gland, mucus pool of cancer tissues. The positive rate of H pylori in normal tissues adjacent to carcinomas was higher than that in cancer tissues (χ² = 15.750, P<0.005<0.01). No significant differences in age, sex, site, histological types and lymph node metastasis were found between H pylori-positive gastric carcinomas and H pylori-negative cases by both methods, but there were statistically significant differences of H pylori positive rate between early and advanced stage of gastric carcinomas (χ² = 4.548 or 5.922, P = 0.033 or 0.015<0.05).

CONCLUSION: These results suggested that H pylori infection might play a certain role in the early stage of carcinogenesis of human gastric mucosa epithelia.

Detection of Mycobacterium tuberculosis complex by PCR in hospital air samples

Tuberculosis remains a health problem in many developed countries. After the development of a sedimentation method, a semi-quantitative approach for bioaerosol monitoring of Mycobacterium tuberculosis based on polymerase chain reaction (PCR) was adapted for direct detection in air. Bovine serum albumin was added to override airborne environmental particle PCR inhibitors. The method gave positive results in hospital rooms where tubercular pneumonia patients were hospitalized during the first days after their diagnosis.

The inhibitory effect of pentobarbitone on reverse transcription-PCR

Pentobarbitone sodium (Sodium 5-ethyl-5[1-methylbutyl]-pentobarbitone) is a short-acting barbiturate that is commonly used to euthanase animals. As part of our studies into the molecular genetics of copper toxicosis in Bedlington terrier dogs, reverse-transcription (RT)-PCR was noted to always fail on RNA samples collected from livers of dogs sacrificed by pentobarbitone injection. When samples were collected without pentobarbitone, however, RT-PCR was always successful. We suspected the possible inhibition by pentobarbitone sodium of either reverse transcriptase or Taq polymerase. In vitro studies showed that pentobarbitone interference of PCR occurred at >4 microg/microl. To identify if pentobarbitone produced competitive inhibition, each components (Taq polymerase, MgCl(2), dNTP, etc.) of the PCR was individually altered. However, inhibition still persisted, suggesting that multiple PCR components may be affected. Also it was shown that pentobarbitone interference was not dependent on the PCR product size. Simple dilution of pentobarbitone contaminated DNA solutions, and the addition of bovine serum albumin (BSA) to the PCR mix overcame pentobarbitone interference. In vivo, PCR by pentobarbitone was found to be compounded by high DNA concentration and pentobarbitone contamination. In addition, both high DNA concentration and pentobarbitone contamination could be overcome through dilution and the addition of BSA. Further work is required to quantify pentobarbitone concentration in the liver-extracted DNA and RNA samples before this inhibition effect on PCR can be fully elucidated.

Characterization of Epstein-Barr virus infection in a human signet ring cell gastric carcinoma cell line, HSC-39

In order to study the mechanism of Epstein-Barr virus (EBV) infection in gastric carcinoma cells, we characterized the EBV infection in signet ring cell line HSC-39, derived from a human gastric carcinoma. HSC-39 cells were highly susceptible to cell-free EBV infection by Akata and P3HR-1 EBV strains. EBV nuclear antigen (EBNA) and EBV-encoded small RNA (EBER) were detected in the infected cells. Akata and P3HR-1 EBV-infected cell clones were isolated by a limiting dilution technique. The Akata and P3HR-1 EBV-infected clones differed from each other in morphology and growth patterns. Akata EBV-infected clones had lower growth rates than did P3HR-1 EBV-infected clones in both liquid and soft agar mediums. Both the infected HSC-39 cells and the clones expressed EBNA1 and EBER, but did not express EBNA2, latent membrane protein (LMP) 1 and LMP2A. The Q promoter (p), but not the Cp/Wp for EBNA transcription, was active in the infected HSC-39 cells and all clones. No lytic infection was observed in either infected parental cells or any clones. Uninfected HSC-39 cells did not express a principal EBV receptor CD21; however, Akata but not P3HR-1 EBV-infected clones expressed low levels of CD21 mRNA. These results demonstrate that the cellular phenotypes of HSC-39 cells are altered by EBV infection in strain-specific manner. We propose the HSC-39 cell line as a model target for the study of the mechanism and significance of EBV infection in gastric carcinoma.

Epstein-Barr virus DNA is detected in peripheral blood mononuclear cells of EBV-seronegative infants with infectious mononucleosis-like symptoms

We demonstrated Epstein-Barr virus (EBV) DNA in peripheral blood mononuclear cells (PBMCs) from infants with infectious mononucleosis- (IM) like symptoms. Thirteen of the 17 patients did not have EBV antibodies; however, EBV DNA was detected in 8 PBMC from the 13 seronegative patients by PCR. The 4 patients were retested in 6-12 months later. Three patients were still seronegative; however EBV DNA wasnot detected. One patient seroconverted and EBV DNA could still be detected. The transcript of EBNA1 was detected in one patient, but neither EBNA2 nor LMP2A were detected in all PBMC from the 4 tested patients. Type 1 EBV DNA was detected in 5 PBMC of 7 tested patients, and type 2 EBV DNA was detected in type 1 positive PBMC of one patient as well. The IL-1 beta polymorphism that is reported to be one of the immunological factors of EBV seronegativity revealed no difference in IM-like patients. These results indicated that EBV infection occurs in EBV-seronegative IM-like infants; however, the modes of infection are clearly different from IM.

Epstein-Barr virus DNA is detected in peripheral blood mononuclear cells of EBV-seronegative infants with infectious mononucleosis-like symptoms

We demonstrated Epstein-Barr virus (EBV) DNA in peripheral blood mononuclear cells (PBMCs) from infants with infectious mononucleosis- (IM) like symptoms. Thirteen of the 17 patients did not have EBV antibodies; however, EBV DNA was detected in 8 PBMC from the 13 seronegative patients by PCR. The 4 patients were retested in 6-12 months later. Three patients were still seronegative; however EBV DNA wasnot detected. One patient seroconverted and EBV DNA could still be detected. The transcript of EBNA1 was detected in one patient, but neither EBNA2 nor LMP2A were detected in all PBMC from the 4 tested patients. Type 1 EBV DNA was detected in 5 PBMC of 7 tested patients, and type 2 EBV DNA was detected in type 1 positive PBMC of one patient as well. The IL-1 beta polymorphism that is reported to be one of the immunological factors of EBV seronegativity revealed no difference in IM-like patients. These results indicated that EBV infection occurs in EBV-seronegative IM-like infants; however, the modes of infection are clearly different from IM.

Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat

The full potential of diagnostic PCR is limited, in part, by the presence of inhibitors in complex biological samples that reduce the amplification efficiency. Therefore, different pre-PCR treatments are being used to reduce the effects of PCR inhibitors. The aim of the present study was to investigate the effects of 16 amplification facilitators to enhance DNA amplification in the presence of blood, feces, or meat. Different concentrations of amplification facilitators and inhibitory samples were added to PCR mixtures containing rTth or Taq DNA polymerase. The addition of 0.6% (wt/vol) bovine serum albumin to reaction mixtures containing Taq DNA polymerase reduced the inhibitory effect of blood and allowed DNA amplification in the presence of 2% instead of 0.2% (vol/vol) blood. Furthermore, the addition of bovine serum albumin (BSA) to reaction mixtures containing feces or meat enhanced the amplification capacities of both polymerases. Taq DNA polymerase was able to amplify DNA in the presence of 4% instead of 0.4% (vol/vol) feces and 4% instead of 0.2% (vol/vol) meat, and rTth was able to amplify DNA in the presence of 4% instead of 0.4% (vol/vol) feces and 20% instead of 2% (vol/vol) meat. The single-stranded DNA binding T4 gene 32 protein (gp32) had a relieving effect similar to that of BSA, except when it was added to PCR mixtures of rTth containing meat and of Taq DNA polymerase containing feces. The relieving effects of betaine and a cocktail of proteinase inhibitors were more sample specific. The addition of 11.7% (wt/vol) betaine allowed Taq DNA polymerase to amplify DNA in the presence of 2% (vol/vol) blood, while the addition of proteinase inhibitors allowed DNA amplification by both polymerases in the presence of 4% (vol/vol) feces. When various combinations of betaine, BSA, gp32, and proteinase inhibitors were tested, no synergistic or additive effects were observed. The effects of facilitators on real-time DNA synthesis instead of conventional PCR were also studied.

Tumorigenesis of Epstein-Barr virus-positive epithelial cell lines derived from gastric tissues in the SCID mouse

To study the tumorigenesis of Epstein-Barr virus (EBV)-positive epithelial cell lines GT38 and GT39 derived from human gastric tissues, we inoculated these cells under the skin of severe combined immunodeficient (SCID) mice. The development of tumors was observed in each of the mice about 2 months after the inoculation. The tumors were diagnosed with undifferentiated carcinoma by hematoxylin/eosin staining. EBV-encoded small RNA1 was detected in the paraffin-embedded tumor sections. The tumor cells had human chromosome. The circular, but not linear, EBV DNA was detected in the tumors. The molecular sizes of EBV DNA termini were the same as that of the inoculated GT38 or GT39 cells. The expressions of EBV nuclear antigen 2 and latent membrane protein 1 reduced in the tumors. Transcripts of BamHI C and W promoters in latency III were detected in the tumors and the cultured cells in vitro. The tumor cells were passaged from one SCID mouse to other SCID mice and to cultures in vitro. This is the first evidence that the EBV-positive epithelial cell lines produced tumors in the SCID mouse.

Rapid differentiation of Borrelia garinii from Borrelia afzelii and Borrelia burgdorferi sensu stricto by LightCycler fluorescence melting curve analysis of a PCR product of the recA gene

To differentiate the Borrelia burgdorferi sensu lato genospecies, LightCycler real-time PCR was used for the fluorescence (SYBR Green I) melting curve analysis of borrelial recA gene PCR products. The specific melting temperature analyzed is a function of the GC/AT ratio, length, and nucleotide sequence of the amplified product. A total of 32 DNA samples were tested. Of them three were isolated from B. burgdorferi reference strains and 16 were isolated from B. burgdorferi strains cultured from Ixodes ricinus ticks; 13 were directly isolated from nine human biopsy specimens and four I. ricinus tick midguts. The melting temperature of B. garinii was 2 degrees C lower than that of B. burgdorferi sensu stricto and B. afzelii. Melting curve analysis offers a rapid alternative for identification and detection of B. burgdorferi sensu lato genospecies.

Detection of Epstein-Barr virus in salivas and throat washings in healthy adults and children

It is well known that Epstein-Barr virus (EBV) is excreted from oral regions in the patients with infectious mononucleosis. We analyzed the prevalence of EBV in saliva and throat washings from healthy people in Japan by the polymerase chain reaction assay. EBV DNA was detected in 43 (90%) of the 48 throat washings from healthy adults (21 to 57 years old) and in 35 (38%) of the 93 salivas from healthy children (0 to 6 years old). The percentages of the EBV DNA-positive ratio in salivas increased in proportion relative to the increase of the children's ages. EBV type 1 was predominant and was detected in 86 and 94% of adults and children, respectively. Umbilical cord lymphocytes were transformed by some throat washings from EBV seropositive donors. EBV DNA was detected in throat washings from two healthy adults whose EBV antibody was not detected. In both cases, higher amounts of EBV DNA were detected in their peripheral blood mononuclear cells than in those of other, EBV antibody-positive donors. These results demonstrated the incidence of EBV excretion in oral regions of healthy individuals in Japan and defined a novel type of EBV infection in healthy adults.