A semiquantitative PCR method (SQ-PCR) to measure Epstein–Barr virus (EBV) load: its application in transplant patients

Semi-Quantitative RT-PCR: An Effective Method to Explore the Regulation of Gene Transcription Level Affected by Environmental Pollutants

Semi-quantitative reverse transcription and polymerase chain reaction (sqRT-PCR) is a simple and specific method for quantitative RNA in recent years. The relative quantity of a specific mRNA in the samples can be inferred by reverse transcription of mRNA into cDNA, and PCR amplification and determination of the quantity of PCR products. The semi-quantitative analysis is carried out under a fixed number of PCR cycles, and the total RNA concentration is kept in the exponential phase of the PCR. The method is to use a housekeeping gene (usually actin, GAPDH, and EF1α) as a reference standard in treated and control organisms to observe the expression of the interested genes (upregulated or downregulated) in toxicology. In this chapter, we describe a step-by-step method for determining the differential regulation of target genes in organisms exposed to environmental pollutants.

Epstein-Barr virus load in transplant patients: Early detection of post-transplant lymphoproliferative disorders

High levels of circulating EBV load are used as a marker of post-transplant lymphoproliferative disorders (PTLD). There is no consensus regarding the threshold level indicative of an increase in peripheral EBV DNA. The aim of the study was to clinically validate a developed EBV quantification assay for early PTLD detection. Transversal study: paired peripheral blood mononuclear cells (PBMC), plasma and oropharyngeal lymphoid tissue (OLT) from children undergoing a solid organ transplant with (n=58) and without (n=47) PTLD. Retrospective follow-up: 71 paired PBMC and plasma from recipients with (n=6) and without (n=6) PTLD history. EBV load was determined by real-time PCR. The diagnostic ability to detect all PTLD (categories 1-4), advanced PTLD (categories 2-4) or neoplastic PTLD (categories 3 and 4) was estimated by analyzing the test performance at different cut-off values or with a load variation greater than 0.5log units. The higher diagnostic performance for identifying all, advanced or neoplastic PTLD, was achieved with cut-off values of 1.08; 1.60 and 2.47log EBVgEq/10(5) PBMC or 2.30; 2.60; 4.47loggEq/10(5) OLT cells, respectively. EBV DNA detection in plasma showed high specificity but low (all categories) or high (advanced/neoplastic categories) sensitivity for PTLD identification. Diagnostic performance was greater when: (1) a load variation in PBMC or plasma was identified; (2) combining the measure of EBV load in PBMC and plasma. The best diagnostic ability to identify early PTLD stages was achieved by monitoring EBV load in PBMC and plasma simultaneously; an algorithm was proposed.

Post-transplant lymphoproliferative disorders: from epidemiology to pathogenesis-driven treatment

Post-transplant lymphoproliferative disorders (PTLDs) represent the most severe complication of both solid organ and hematopoietic stem cell transplantation. The Epstein-Barr Virus (EBV) is the main driver of PTLD, particularly those occurring early after transplantation. EBV-driven malignancies are associated with selective expression of latent viral proteins, but uncontrolled lytic replication may favor early phases of cell transformation. Besides immunodepression, persistent immune activation and chronic inflammation play an important role in both virus reactivation and expansion of EBV-infected B cells. EBV-induced immortalization requires the expression of telomerase. TERT, the rate-limiting component of the telomerase complex, is central in the switch from the lytic to the latent viral program, and TERT inhibition induces the EBV lytic cycle and cell death. Immunotherapy and combination of EBV lytic cycle inducers with antiviral drugs are promising strategies to improve the treatment of PTLD patients. This review is aimed at providing an update on the intriguing association between EBV and PTLD, mainly focusing on cases arising after kidney and liver transplantation, which account for the vast majority of transplants.

Duplex realtime PCR method for Epstein-Barr virus and human DNA quantification: its application for post-transplant lymphoproliferative disorders detection

INTRODUCTION

The quantification of circulating Epstein-Barr virus (EBV) DNA is used to monitor transplant patients as an early marker of Post-Transplant Lymphoproliferative Disorders (PTLD). So far no standardized methodology exists for such determination.

OBJECTIVE

Our purpose was to develop and validate a real-time PCR assay to quantify EBV DNA in clinical samples from transplant recipients.

METHODS

A duplex real-time PCR method was developed to amplify DNA from EBV and from a human gene. The EBV load was determined in peripheral blood mononuclear cells (PBMC), plasma and oropharyngeal tissue from 64 non-transplanted patients with lymphoid-hypertrophy (Non-Tx), 47 transplant recipients without PTLD (Tx), 54 recipients with PTLD (Tx-PTLD), and 66 blood donors (BD). WinPEPI, version 11.14 software was used for statistical analysis.

RESULTS

Analytical validation: the intra and inter-assays variation coefficients were less than 4.5% (EBV-reaction) and 3% (glyceraldehyde 3-phosphate dehydrogenase - GAPDH reaction). Linear ranges comprised 10(7)-10 EBV genome equivalents (gEq) (EBV-reaction) and 500,000-32 human gEq (GAPDH-reaction). The detection limit was 2.9 EBV gEq (EBV-reaction). Both reactions showed specificity. Application to clinical samples: higher levels of EBV were found in oropharyngeal tissue from transplanted groups with and without PTLD, compared to Non-Tx (p<0.05). The EBV load in PBMC from the groups of BD, Non-Tx, Tx and Tx-PTLD exhibited increasing levels (p<0.05). In BD, PBMC and plasma, EBV loads were undetectable.

CONCLUSIONS

The performance of the assay was suitable for the required clinical application. The assay may be useful to monitor EBV infection in transplant patients, in particular in laboratories from low-income regions that cannot afford to use commercial assays.

Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius

Aspergillus carbonarius accumulates xylitol when it grows on D-xylose. In fungi, D-xylose is reduced to xylitol by the NAD(P)H-dependent xylose reductase (XR). Xylitol is then further oxidized by the NAD(+)-dependent xylitol dehydrogenase (XDH). The cofactor impairment between the XR and XDH can lead to the accumulation of xylitol under oxygen-limiting conditions. Most of the XRs are NADPH dependent and contain a conserved Ile-Pro-Lys-Ser motif. The only known naturally occurring NADH-dependent XR (from Candida parapsilosis) carries an arginine residue instead of the lysine in this motif. In order to overcome xylitol accumulation in A. carbonarius a Lys-274 to Arg point mutation was introduced into the XR with the aim of changing the specificity toward NADH. The effect of the genetic engineering was examined in fermentation for citric acid production and xylitol accumulation by using D-xylose as the sole carbon source. Fermentation with the mutant strain showed a 2.8-fold reduction in xylitol accumulation and 4.5-fold increase in citric acid production compared to the wild-type strain. The fact that the mutant strain shows decreased xylitol levels is assumed to be associated with the capability of the mutated XR to use the NADH generated by the XDH, thus preventing the inhibition of XDH by the high levels of NADH and ensuring the flux of xylose through the pathway. This work shows that enhanced production of citric acid can be achieved using xylose as the sole carbon source by reducing accumulation of other by-products, such as xylitol.

Analyzing abundance of mRNA molecules with a near-infrared fluorescence technique

This study describes a simple method for analyzing the abundance of mRNA molecules in a total DNA sample. Due to the dependence on the near-infrared fluorescence technique, this method is named near-infrared fluorescence gene expression detection (NIRF-GED). The procedure has three steps: (1) isolating total RNA from detected samples and reverse-transcription into cDNA with a biotin-labeled oligo dT; (2) hybridizing cDNA to oligonucleotide probes coupled to a 96-well microplate; and (3) detecting biotins with NIRF-labeled streptavidin. The method was evaluated by performing proof-in-concept detections of absolute and relative expressions of housekeeping and NF-κB target genes in HeLa cells. As a result, the absolute expression of three genes, Ccl20, Cxcl2, and Gapdh, in TNF-α-uninduced HeLa cells was determined with a standard curve constructed on the same microplate, and the relative expression of five genes, Ccl20, Cxcl2, Il-6, STAT5A, and Gapdh, in TNF-α-induced and -uninduced HeLa cells was measured by using NIRF-GED. The results were verified by quantitative PCR (qPCR) and DNA microarray detections. The biggest advantage of NIRF-GED over the current techniques lies in its independence of exponential or linear amplification of nucleic acids. Moreover, NIRF-GED also has several other benefits, including high sensitivity as low as several fmols, absolute quantification in the range of 9 to 147 fmols, low cDNA consumption similar to qPCR template, and the current medium throughput in 96-well microplate format and future high throughput in DNA microarray format. NIRF-GED thus provides a new tool for analyzing gene transcripts and other nucleic acid molecules.

Therapeutic options in post-transplant lymphoproliferative disorders

Post-transplantation lymphoproliferative disorders (PTLD) are the second most frequent malignancies after solid organ transplantation and cover a wide spectrum ranging from polyclonal early lesions to monomorphic lymphoma. Available treatment modalities include immunosuppression reduction, immunotherapy with anti-B-cell monoclonal antibodies, chemotherapy, antiviral therapy, cytotoxic T-cell therapy as well as surgery and irradiation. Owing to the small number of cases and the heterogeneity of PTLD, current treatment strategies are mostly based on case reports and small, often retrospective studies. Moreover, many studies on the treatment of PTLD have involved a combination of different treatment options, complicating the evaluation of individual treatment components. However, there has been significant progress over the last few years. Three prospective phase II trials on the efficacy of rituximab monotherapy have shown significant complete remission rates without any relevant toxicity. A prospective, multicenter, international phase II trial evaluating sequential treatment with rituximab and CHOP-based chemotherapy (cyclophosphamide, doxorubicin, vincristine, prednisone) is ongoing and preliminary results have been promising. Cytotoxic T-cell therapy targeting Epstein-Barr virus (EBV)-infected B cells has shown low toxicity and high efficacy in a phase II trial and will be a future therapeutic option at specialized centers. Here, we review the currently available data on the different treatment modalities with a focus on PTLD following solid organ transplantation in adult patients.

Significance of Epstein-Barr virus (EBV) load and Interleukin-10 in post-transplant lymphoproliferative disorders

The complex relationship between EBV, IL-10 and lymphomagenesis has been widely investigated and several studies have highlighted the diagnostic value of EBV DNA copies and serum IL-10, that may be considered as tumor markers. Notwithstanding the great number of data published in the last few years on the behavior of EBV DNA copies in the peripheral blood of transplanted patients, a threshold value significant for impending or overt post-transplant lymphoproliferative disorder (PTLD) has not yet been defined. Too many factors, both technical and clinicopathological, may affect the results of clinical studies, making their comparison difficult. On the contrary, although the role of IL-10 in PTLDs has been well documented, a sufficient number of studies exploring sensitivity and specificity of serum IL-10 measurement is lacking. The aim of this review is to summarise data on EBV load quantification and serum IL-10 detection in transplanted patients, providing clinicians with wide and useful information in order to improve bedside management of transplanted patients with regard to PTLDs occurrence and treatment.

[Infections in immunosuppressed patients]

Molecular biology techniques represent a major advance in the microbiologic diagnosis of infectious diseases, since these methods are able to detect etiological microorganisms with high sensitivity. Moreover, these procedures can also establish prognostic and therapeutic efficacy markers with a sufficiently short turnaround time for the results to have a real impact on the clinical management of immunosuppressed patients. However, these techniques still have substantial limitations that should be solved in the near future: lack of standardization, inter- and intra-assay variability, the difficulty of comparing results among different laboratories and low positive predictive value, due to their high sensitivity, leading to problems in the interpretation of results. The present article reviews the usefulness of molecular biology techniques in the diagnosis and clinical management of infectious diseases caused by human cytomegalovirus, Epstein-Barr virus, human herpes viruses 6 and 7, JC and BK viruses, Toxoplasma gondii and Pneumocystis jiroveci in immunosuppressed patients.

Post-transplant lymphoproliferative disorder after pediatric liver transplantation: characteristics and outcome

Post-Transplant Lymphoproliferative Disorder (PTLD) is a life threatening complication in organ transplant recipients. Risk factors include primary Epstein-Barr virus infection, intensity of immunosupression and cytomegalovirus infection.

OBJECTIVES

To evaluate the incidence, clinical presentation, risk factors, histopathologic appearance and outcome of pediatric liver recipients with PTLD at our institution.

METHOD

Retrospective, descriptive and observational analysis. Between November 1992 and December 2005, 383 liver transplants were performed. The diagnosis of PTLD was based on clinical history and physical examination and confirmed by histologic appearance and immunohistologic staining. Knowles' classification was used for histopathologic diagnosis.

RESULTS

The incidence of PTLD was 5.7% (n: 22p). The average onset after tansplantation (OLT) was 24.9 months. Clinical manifestations were malaise, anorexia, fever of more than 3 days, peripheral adenopathy, tonsillar hypertrophy, abdominal mass, hepatosplenomegaly, snoring, interstitial pulmonary infiltrate, G.T.-tract bleeding, rash, submaxilar mass. Histopathologic diagnosis were Plasmocytic Hyperplasia (n: 10), Polymorphic Lymphoproliferative Disorder (n: 8), Non-Hodgkin Lymphoma (n: 4). Mortality was 18%.

CONCLUSION

The clinical presentations were protean and not specific. A high index of suspicion is important for early diagnosis as it correlates with more benign lesions and more favorable outcume. The lower mortality rate in our series is concordant with that reported in more recent articles.

Epstein-Barr virus polymerase chain reaction-negative stage IV post-transplant lymphoproliferative disorder in a heart transplant patient treated with rituximab

Post-transplant lymphoproliferative disorder (PTLD) is often associated with Epstein-Barr virus (EBV). However, in this report, we describe a heart transplant recipient with pathologically proven EBV-positive PTLD with undetectable virus by polymerase chain reaction. The patient had remission after anti-CD20 antibody treatment early after transplantation.

Circulating Epstein-Barr virus (EBV) in HIV-infected patients and its relation with primary brain lymphoma

OBJECTIVE

To analyze Epstein-Barr virus (EBV) load at different HIV infection stages and its relation with brain lymphoma.

DESIGN

A cross-sectional study was conducted on 172 HIV-infected individuals: 62 asymptomatic HIV carriers (group A), 30 HIV progressors (group B), 73 AIDS patients (group C), seven AIDS patients with brain lymphoma (group C-BL); and 26 blood donors (group BD) as healthy carriers. EBV load was measured in peripheral blood mononuclear cells (PBMC) and plasma samples using a semi-quantitative PCR method.

RESULTS

PBMC-EBV levels in HIV-infected patients were higher than in the blood donors (p<0.05). No differences in PBMC-EBV loads were found in groups A, B, or C (p>0.05), while the C-BL group had significantly lower levels (p<0.05). Similar PBMC-EBV loads were seen in HIV-infected patients with CD4+ T cell counts higher than 50/mm(3) (p>0.05), while significantly lower levels were found in cases with less than 50 cells/mm(3) (p<0.05). In all HIV-infected patients, plasma-EBV load was lower than, or similar to, PBMC-EBV load, unlike 2/7 HIV-positive brain lymphoma patients.

CONCLUSIONS

During HIV infection PBMC-EBV load rises in comparison to healthy carriers, but decreases when immunosuppression progresses and CD4+ T cell count becomes <50/mm(3). Circulating EBV is mainly cell-associated in the HIV-infected population. Neither PBMC-EBV nor plasma-EBV loads would be useful to diagnose brain lymphoma in AIDS patients.

Epstein–Barr viral load in whole blood of adults with posttransplant lymphoproliferative disorder after solid organ transplantation does not correlate with clinical course

Posttransplant lymphoproliferative disease (PTLD) is closely linked to primary Epstein-Barr virus (EBV) infection. A defect of EBV specific cellular immunity is postulated to play a pivotal role in the etiology of PTLD, but there is some debate as to whether EBV load in the peripheral blood of transplant patients predicts onset of PTLD or relapse after treatment. The current prospective, single-center study was undertaken to investigate the impact of therapy on EBV load in adult patients with PTLD. Fifteen patients with PTLD after solid organ transplantation were included and of these, seven had EBV-associated PTLD. All 15 patients received Rituximab as primary therapy. In cases of treatment failure or relapse after Rituximab treatment, patients received polychemotherapy according to the cyclophosphamide, vincristine, doxorubicin, and prednisone regimen. At onset of PTLD, the median EBV load in the peripheral blood of patients was higher in EBV-associated PTLD than PTLD with no associated EBV infection. After Rituximab therapy, four of seven patients with EBV-associated PTLD achieved long-lasting complete remissions. However, in two of these patients, EBV load increased to reach levels as high as those recorded at onset of PTLD. Another patient showed a dramatic decline of EBV load after the first dose of Rituximab while suffering from progressive disease. The other patient relapsed after Rituximab monotherapy, but his viral load stayed low. In total, discordance in EBV load and clinical course was observed in five of the seven patients with EBV-associated PTLD. We conclude that in adult patients with PTLD, EBV load does not correlate with treatment response and is not suitable as a predictive marker for PTLD relapse.