QUADAS-C: A Tool for Assessing Risk of Bias in Comparative Diagnostic Accuracy Studies.

Comparative diagnostic test accuracy studies assess and compare the accuracy of 2 or more tests in the same study. Although these studies have the potential to yield reliable evidence regarding comparative accuracy, shortcomings in the design, conduct, and analysis may bias their results. The currently recommended quality assessment tool for diagnostic test accuracy studies, QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies-2), is not designed for the assessment of test comparisons. The QUADAS-C (Quality Assessment of Diagnostic Accuracy Studies-Comparative) tool was developed as an extension of QUADAS-2 to assess the risk of bias in comparative diagnostic test accuracy studies. Through a 4-round Delphi study involving 24 international experts in test evaluation and a face-to-face consensus meeting, an initial version of the tool was developed that was revised and finalized following a pilot study among potential users. The QUADAS-C tool retains the same 4-domain structure of QUADAS-2 (Patient Selection, Index Test, Reference Standard, and Flow and Timing) and comprises additional questions to each QUADAS-2 domain. A risk-of-bias judgment for comparative accuracy requires a risk-of-bias judgment for the accuracy of each test (resulting from QUADAS-2) and additional criteria specific to test comparisons. Examples of such additional criteria include whether participants either received all index tests or were randomly assigned to index tests, and whether index tests were interpreted with blinding to the results of other index tests. The QUADAS-C tool will be useful for systematic reviews of diagnostic test accuracy addressing comparative questions. Furthermore, researchers may use this tool to identify and avoid risk of bias when designing a comparative diagnostic test accuracy study.

Could Changing the DNA Methylation Landscape Promote the Destruction of Epstein-Barr Virus-Associated Cancers?

DNA methylation at CpG motifs provides an epigenetic route to regulate gene expression. In general, an inverse correlation between DNA hypermethylation at CpG motifs and gene expression is observed. Epstein Barr-virus (EBV) infects people and the EBV genome resides in the nucleus where either its replication cycle initiates or it enters a long-term latency state where the viral genome becomes hypermethylated at CpG motifs. Viral gene expression shows a largely inverse correlation with DNA hypermethylation. DNA methylation occurs through the action of DNA methyl transferase enzymes: writer DNA methyl transferases add methyl groups to specific regions of unmethylated DNA; maintenance DNA methyl transferases reproduce the pattern of DNA methylation during genome replication. The impact of DNA methylation is achieved through the association of various proteins specifically with methylated DNA and their influence on gene regulation. DNA methylation can be changed through altering DNA methyl transferase activity or through the action of enzymes that further modify methylated CpG motifs. Azacytidine prodrugs that are incorporated into CpG motifs during DNA replication are recognized by DNA methyl transferases and block their function resulting in hypomethylation of DNA. EBV-associated cancers have hypermethylated viral genomes and many carcinomas also have highly hypermethylated cellular genomes. Decitabine, a member of the azacytidine prodrug family, reactivates viral gene expression and promotes the recognition of lymphoma cells by virus-specific cytotoxic T-cells. For EBV-associated cancers, the impact of decitabine on the cellular genome and the prospect of combining decitabine with other therapeutic approaches is currently unknown but exciting.

Is EBV Associated with Breast Cancer in Specific Geographic Locations?

Epstein-Barr virus (EBV) is a virus that establishes a life-long infection in people, and infection with EBV is nearly ubiquitous by adulthood. EBV was identified from biopsy material from a child with Burkitt's lymphoma (BL) in sub-Saharan Africa. EBV has a well-characterised role in the development of some cancers, notably, Burkitt's lymphoma (BL), Hodgkin's disease (HD), gastric carcinoma (GC), and nasopharyngeal carcinoma (NPC). Links have also been made between EBV and breast cancer (BC), but these have been controversial. For all EBV-associated cancers, the ubiquitous nature of infection with EBV, contrasted with the relatively rare development of cancer, highlights a problem of determining whether EBV is an aetiological agent of cancer. In addition, the geographic distributions of some EBV-associated cancers point to contributions from additional co-factors. Recent meta-analyses of the incidence of EBV within BC biopsies has revealed that the diversity in the conclusions remain, however, they also show more of an association between EBV and BC biopsies in some study locations. Here, we review the evidence linking EBV with BC, and conclude that the evidence for the presence of EBV in BC biopsies is concentrated in specific geographic regions but is currently insufficient to provide a causal link. We pose some questions that could help to resolve the question of whether EBV contributes to BC and probe the contribution EBV might make to the aetiology of BC.

Interaction sites of the Epstein-Barr virus Zta transcription factor with the host genome in epithelial cells.

Epstein-Barr virus (EBV) is present in a state of latency in infected memory B-cells and EBV-associated lymphoid and epithelial cancers. Cell stimulation or differentiation of infected B-cells and epithelial cells induces reactivation to the lytic replication cycle. In each cell type, the EBV transcription and replication factor Zta (BZLF1, EB1) plays a role in mediating the lytic cycle of EBV. Zta is a transcription factor that interacts directly with Zta response elements (ZREs) within viral and cellular genomes. Here we undertake chromatin-precipitation coupled to DNA-sequencing (ChIP-Seq) of Zta-associated DNA from cancer-derived epithelial cells. The analysis identified over 14 000 Zta-binding sites in the cellular genome. We assessed the impact of lytic cycle reactivation on changes in gene expression for a panel of Zta-associated cellular genes. Finally, we compared the Zta-binding sites identified in this study with those previously identified in B-cells and reveal substantial conservation in genes associated with Zta-binding sites.

A Comparison of Patient-Reported Outcome Measures of Quality of Life By Dialysis Modality in the Treatment of Kidney Failure: A Systematic Review.

BACKGROUND: There is an increasing demand to incorporate patient-reported outcome measures (PROMs) such as quality of life (QOL) in decision-making when selecting a chronic dialysis modality. OBJECTIVE: To compare the change in QOL over time among similar patients on different dialysis modalities to provide unique and novel insights on the impact of dialysis modality on PROMs. DESIGN: Systematic reviews, randomized controlled trials, and nonrandomized controlled trials were examined via a comprehensive search strategy incorporating multiple bibliographic databases. SETTING: Data were extracted from relevant studies from January 1, 2000 to December 31, 2019 without limitations on country of study conduction. PATIENTS: Eligible studies included adults (≥18 years) with end-stage kidney disease of any cause who were prescribed dialysis treatment (either as lifetime treatment or bridge to transplant). MEASUREMENTS: The 5 comparisons were peritoneal dialysis (PD) vs in-center hemodialysis (ICHD), home hemodialysis (HHD) vs ICHD, HHD modalities compared with one another, HHD vs PD, and self-care ICHD vs traditional nurse-based ICHD. METHODS: Included studies compared adults on different dialysis modalities with repeat measures within individuals to determine changes in QOL between dialysis modalities (in-center or home dialysis). Methodological quality was assessed by the Scottish Intercollegiate Guidelines Network (SIGN 50) checklist. A narrative synthesis was conducted, synthesizing the direction and size of any observed effects across studies. RESULTS: Two randomized controlled trials and 9 prospective cohort studies involving a combined total of 3711 participants were included. Comparing PD and ICHD, 5 out of 9 studies found significant differences (P < .05) favoring PD in the change of multiple QOL domains, including "physical component score," "role of social component score," "cognitive status," "role limitation due to emotional function," "role limitation due to physical function," "bodily pain," "burden of kidney disease," "effects of kidney disease on daily life," "symptoms/problems," "sexual function," "finance," and "patient satisfaction." Conversely, 3 of these studies demonstrated statistically significant differences (P < .05) favoring ICHD in the domains of "role limitation due to physical function," "general health," "support from staff," "sleep quality," "social support," "health status," "social interaction," "body image," and "overall health." Comparing HHD and ICHD, significant differences (P < .05) favoring HHD for the QOL domains of "general health," "burden of kidney disease," and the visual analogue scale were reported. LIMITATIONS: Our study is constrained by the small sample sizes of included studies, as well as heterogeneity among both study populations and validated QOL scales, limiting inter-study comparison. CONCLUSIONS: We identified differences in specific QOL domains between dialysis modalities that may aid in patient decision-making based on individual priorities. TRIAL REGISTRATION: PROSPERO Registration Number: CRD42016046980. PRIMARY FUNDING SOURCE: The original research for this study was derived from the Canadian Agency for Drugs and Technologies in Health (CADTH) 2017 optimal use report, titled "Dialysis Modalities for the Treatment of End-Stage Kidney Disease: A Health Technology Assessment." The CADTH receives funding from Canada's federal, provincial, and territorial governments, with the exception of Quebec.

CONTEXTE: On observe une demande croissante pour intégrer des mesures des résultats déclarées par les patients (MRDP) comme la qualité de vie (QDV) dans la prise de décision quant à la modalité de dialyse. OBJECTIF: Comparer l'évolution de la QDV chez des patients de profils similaires, mais utilisant différentes modalités de dialyse, pour fournir un éclairage nouveau sur l'incidence de la modalité sur les MRDP. TYPE D'ÉTUDE: Des revues systématiques et des essais contrôlés avec ou sans répartition aléatoire ont été examinés dans le cadre d'une stratégie de recherche globale incorporant plusieurs bases de données bibliographiques. CONCEPTION: Les données ont été extraites des études pertinentes entre le 1er janvier 2000 et le 31 décembre 2019 sans limitation relativement à l'origine (pays) de l'étude. SUJETS: Les études admissibles portaient sur des adultes atteints d'insuffisance rénale terminale (toutes causes) auxquels un traitement de dialyse avait été prescrit, soit comme traitement à vie, soit en attendant une transplantation. MESURES: Ont été comparées 1) la dialyse péritonéale [DP] vs l'hémodialyse en centre [HDC]; 2) l'hémodialyse à domicile [HDD] vs l'HDC; 3) les modalités d'HDD les unes aux autres; 4) l'HDD vs la DP; et 5) l'HDC autogérée vs l'HDC traditionnelle sous supervision d'une infirmière. MÉTHODOLOGIE: Les études incluses comparaient des adultes sous différentes modalités de dialyse et comportaient des mesures répétées permettant d'observer des changements dans la QDV selon la modalité (en centre ou à domicile). La qualité méthodologique a été évaluée avec la grille d'évaluation du Scottish Intercollegiate Guidelines Network (SIGN 50). Une synthèse narrative a été réalisée pour résumer la direction et l'ampleur de tous les effets observés dans les différentes études. RÉSULTATS: Ont été inclus deux essais contrôlés à répartition aléatoire et neuf études de cohorte prospectives (3 711 patients au total). En comparant la DP à l'HDC, cinq des neufs études rapportaient des différences significatives (P<0,05) favorisant la DP dans plusieurs aspects de la QDV, notamment quant au « score de la composante physique ¼, au « rôle du score de la composante sociale ¼, à « l'état cognitif ¼, à la « limitation dans les activités quotidiennes en raison des aspects émotionnels ¼, à la « limitation dans les activités quotidiennes en raison des aspects physiques ¼, à la « douleur physique ¼, au « fardeau de la néphropathie ¼, aux « conséquences de la néphropathie sur la QDV ¼, aux « symptômes/problèmes ¼, à la « fonction sexuelle ¼, aux « conséquences financières ¼ et à la « satisfaction du patient ¼. En revanche, trois de ces études montraient des différences statistiquement significatives (P<0,05) favorisant l'HDC dans les aspects suivants: « limitation dans les activités quotidiennes en raison des aspects physiques ¼, « état de santé général ¼, « soutien du personnel soignant ¼, « qualité du sommeil ¼, « soutien social ¼, « état de santé ¼, « interactions sociales ¼, « image corporelle ¼ et « état de santé global ¼. En comparant l'HDD et l'HDC, des différences significatives (P<0,05) favorisant l'HDD ont été rapportées en ce qui concerne « l'état de santé général ¼, le « fardeau de la néphropathie ¼ et l'échelle visuelle analogique. LIMITES: L'étude est limitée par la faible taille des échantillons des études incluses, ainsi que par l'hétérogénéité des populations et des échelles validées pour la mesure de la QDV, ce qui restreint les comparaisons entre les études. CONCLUSION: Des différences significatives touchant certains aspects propres à la qualité de vie ont été observées entre les différentes modalités de dialyse. Ces observations pourraient orienter une prise de décision en fonction des priorités individuelles des patients.

Identifying the Cellular Interactome of Epstein-Barr Virus Lytic Regulator Zta Reveals Cellular Targets Contributing to Viral Replication.

The human gammaherpesvirus Epstein-Barr virus (EBV) (human herpesvirus 4 [HHV4]) infects most adults and is an important contributor to the development of many types of lymphoid and epithelial cancers. Essential contributions of viral genes to viral replication are known, but the potential contributions of cell genes are less well delineated. A key player is the viral protein Zta (BZLF1, ZEBRA, or Z). This sequence-specific DNA-binding protein can disrupt EBV latency by driving the transcription of target genes and by interacting with the EBV lytic origin of replication. Here, we used an unbiased proteomics approach to identify the Zta-interactome in cells derived from Burkitt's lymphoma. Isolating Zta and associated proteins from Burkitt's lymphoma cells undergoing EBV replication, followed by tandem mass tag (TMT) mass spectrometry, resulted in the identification of 39 viral and cellular proteins within the Zta interactome. An association of Zta with the cellular protein NFATc2 was validated in independent experiments. Furthermore, the ability of Zta to attenuate the activity of an NFAT-dependent promoter was shown, which suggests a functional consequence for the association. The expression of Zta is itself regulated through NFAT activity, suggesting that Zta may contribute to a feedback loop that would limit its own expression, thus aiding viral replication by preventing the known toxic effects of Zta overexpression.IMPORTANCE Epstein-Barr virus infects most people across the world and causes several kinds of cancer. Zta is an important viral protein that makes the virus replicate by binding to its DNA and turning on the expression of some genes. We used a sensitive, unbiased approach to isolate and identify viral and cellular proteins that physically interact with Zta. This revealed 39 viral and cellular proteins. We found that one protein, termed NFATc2, was already known to be important for a very early step in viral replication. We identify that once this step has occurred, Zta reduces the effectiveness of NFATc2, and we suggest that this is important to prevent cells from dying before viral replication is complete and the mature virus is released from the cells.

A Framework for Aiding the Translation of Scientific Evidence into Policy: The Experience of a Hospital-Based Technology Assessment Unit.

OBJECTIVES: Very few practical frameworks exist to guide the formulation of recommendations at hospital-based health technology assessment (HTA) units. The objectives of our study were: (i) to identify decision criteria specific to the context of hospital-based health technologies and interventions, (ii) to estimate the extent to which the expert community agrees on the importance of the identified criteria, (iii) to incorporate the identified criteria into a decision-aid tool, and (iv) to illustrate the application of a prototype decision-aid tool. METHODS: Relevant decision criteria were identified using existing frameworks for HTA recommendations, our past experience, a literature search, and feedback from a survey of diverse stakeholders. RESULTS: Based on the survey results, twenty-three decision criteria were incorporated into the final framework. We defined an approach that eschewed a scoring system, but instead relied on a visual means for arriving at a final recommendation, by juxtaposing the importance rating for each criterion against the results of the health technology assessment. For a technology to be approved, a majority of criteria considered important should also have received favorable findings. CONCLUSIONS: We created a simple and practical decision-aid tool that incorporates all decision criteria relevant to a hospital-based HTA unit. With its ease of use and accessibility, our tool renders the subjective decision-making process more structured and transparent.

Mechanism of activation of the BNLF2a immune evasion gene of Epstein-Barr virus by Zta.

The human gamma herpes virus Epstein-Barr virus (EBV) exploits multiple routes to evade the cellular immune response. During the EBV lytic replication cycle, viral proteins are expressed that provide excellent targets for recognition by cytotoxic T cells. This is countered by the viral BNLF2a gene. In B cells during latency, where BNLF2a is not expressed, we show that its regulatory region is embedded in repressive chromatin. The expression of BNLF2a mirrors the expression of a viral lytic cycle transcriptional regulator, Zta (BZLF1, EB1, ZEBRA), in B cells and we propose that Zta plays a role in up-regulating BNLF2a. In cells undergoing EBV lytic replication, we identified two distinct regions of interaction of Zta with the chromatin-associated BNLF2a promoter. We identify five potential Zta-response elements (ZREs) in the promoter that are highly conserved between virus isolates. Zta binds to these elements in vitro and activates the expression of the BNLF2a promoter in both epithelial and B cells. We also found redundancy amongst the ZREs. The EBV genome undergoes a biphasic DNA methylation cycle during its infection cycle. One of the ZREs contains an integral CpG motif. We show that this can be DNA methylated during EBV latency and that both Zta binding and promoter activation are enhanced by its methylation. In summary, we find that the BNLF2a promoter is directly targeted by Zta and that DNA methylation within the proximal ZRE aids activation. The implications for regulation of this key viral gene during the reactivation of EBV from latency are discussed.

Evaluating the accuracy and economic value of a new test in the absence of a perfect reference test.

BACKGROUND: Streptococcus pneumoniae (SP) pneumonia is often treated empirically as diagnosis is challenging because of the lack of a perfect test. Using BinaxNOW-SP, a urinary antigen test, as an add-on to standard cultures may not only increase diagnostic yield but also increase costs. OBJECTIVE: To estimate the sensitivity and specificity of BinaxNOW-SP and subsequently estimate the cost-effectiveness of adding BinaxNOW-SP to the diagnostic work-up. DESIGN: We fit a Bayesian latent-class meta-analysis model to obtain estimates of BinaxNOW-SP accuracy that adjust for the imperfect accuracy of culture. Meta-analysis results were combined with information on prevalence of SP pneumonia to estimate the number of patients who are correctly classified under competing diagnostic strategies. Taking into consideration the cost of antibiotics, we determined the incremental cost of adding BinaxNOW-SP to the work-up per case correctly diagnosed. RESULTS: The BinaxNOW-SP test had a pooled sensitivity of 0.74 (95% credible interval [CrI], 0.67-0.83) and a pooled specificity of 0.96 (95% CrI, 0.92-0.99). An overall increase in diagnostic accuracy of 6.2% due to the addition of BinaxNOW-SP corresponded to an incremental cost per case correctly classified of $582 Canadian dollars. CONCLUSIONS: The methods we have described allow us to evaluate the accuracy and economic value of a new test in the absence of a perfect reference test using an evidence-based approach.

The Use of Chromatin Precipitation Coupled to DNA Sequencing (ChIP-Seq) for the Analysis of Zta Binding to the Human and EBV Genome.

Determining which components of the transcription machinery associate with the viral and cellular genome, and how this changes at specific stages of the viral life cycle is paramount to understanding how the distinct transcriptional programs associated with primary infection, latency, and disease are established and how they are reprogrammed during initiation and execution of the viral lytic replication cycle. Chromatin precipitations linked to next generation DNA sequencing (ChIP-Seq) allow for the interactions of proteins with DNA to be mapped across both viral and cellular genomes. This can be applied to viral and cellular transcription factors, coactivators and corepressors, modified histones, and modulators of chromatin.

Lactobacillus probiotics in the prevention of diarrhea associated with Clostridium difficile: a systematic review and Bayesian hierarchical meta-analysis.

BACKGROUND: Recent meta-analyses of the efficacy of probiotics for preventing diarrhea associated with Clostridium difficile have concluded there is a large effect favouring probiotics. We reexamined this evidence, which contradicts the results of a more recent large randomized controlled trial that found no benefit of Lactobacillus probiotics for preventing C. difficile-associated diarrhea. METHODS: We performed a systematic review of the efficacy of treatment with Lactobacillus probiotics for preventing nosocomial C. difficile-associated diarrhea in adults and carried out a meta-analysis using a Bayesian hierarchical model. We used credibility analysis and meta-regression to characterize the heterogeneity between studies. RESULTS: Ten studies met our inclusion criteria. The pooled risk ratio was highly statistically significant, at 0.25 (95% credible interval 0.08-0.47). However, the 95% prediction interval for the risk ratio in a future study, 0.02-1.34, was wider than the credible interval, owing to heterogeneity between studies. Furthermore, a credibility analysis showed that the strength of the evidence was weaker than the observed number of cases of C. difficile-associated diarrhea across studies would suggest. Meta-regression suggested that the beneficial effect of probiotics was more likely to be reported in studies with an increased risk of C. difficile-associated diarrhea in the control group, although this association was not statistically significant. INTERPRETATION: Accounting for between-study heterogeneity showed that there is considerable uncertainty regarding the apparently large efficacy estimate associated with Lactobacillus probiotic treatment in preventing C. difficile-associated diarrhea. Most studies to date have been carried out in populations with a low risk of C. difficile-associated diarrhea, such that the evidence is inconclusive and inadequate to support a policy concerning routine use of probiotics in to prevent this condition.

Repression of CIITA by the Epstein-Barr virus transcription factor Zta is independent of its dimerization and DNA binding.

Repression of the cellular CIITA gene is part of the immune evasion strategy of the γherpes virus Epstein-Barr virus (EBV) during its lytic replication cycle in B-cells. In part, this is mediated through downregulation of MHC class II gene expression via the targeted repression of CIITA, the cellular master regulator of MHC class II gene expression. This repression is achieved through a reduction in CIITA promoter activity, initiated by the EBV transcription and replication factor, Zta (BZLF1, EB1, ZEBRA). Zta is the earliest gene expressed during the lytic replication cycle. Zta interacts with sequence-specific elements in promoters, enhancers and the replication origin (ZREs), and also modulates gene expression through interaction with cellular transcription factors and co-activators. Here, we explore the requirements for Zta-mediated repression of the CIITA promoter. We find that repression by Zta is specific for the CIITA promoter and can be achieved in the absence of other EBV genes. Surprisingly, we find that the dimerization region of Zta is not required to mediate repression. This contrasts with an obligate requirement of this region to correctly orientate the DNA contact regions of Zta to mediate activation of gene expression through ZREs. Additional support for the model that Zta represses the CIITA promoter without direct DNA binding comes from promoter mapping that shows that repression does not require the presence of a ZRE in the CIITA promoter.

Identification of Epstein-Barr Virus Replication Proteins in Burkitt's Lymphoma Cells.

The working model to describe the mechanisms used to replicate the cancer-associated virus Epstein-Barr virus (EBV) is partly derived from comparisons with other members of the Herpes virus family. Many genes within the EBV genome are homologous across the herpes virus family. Published transcriptome data for the EBV genome during its lytic replication cycle show extensive transcription, but the identification of the proteins is limited. We have taken a global proteomics approach to identify viral proteins that are expressed during the EBV lytic replication cycle. We combined an enrichment method to isolate cells undergoing EBV lytic replication with SILAC-labeling coupled to mass-spectrometry and identified viral and host proteins expressed during the OPEN ACCESS Pathogens 2015, 4 740 EBV lytic replication cycle. Amongst the most frequently identified viral proteins are two components of the DNA replication machinery, the single strand DNA binding protein BALF2, DNA polymerase accessory protein BMRF1 and both subunits of the viral ribonucleoside-diphosphate reductase enzyme (BORF2 and BaRF1). An additional 42 EBV lytic cycle proteins were also detected. This provides proteomic identification for many EBV lytic replication cycle proteins and also identifies post-translational modifications.

Epstein-Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression.

Lytic replication of the human gamma herpes virus Epstein-Barr virus (EBV) is an essential prerequisite for the spread of the virus. Differential regulation of a limited number of cellular genes has been reported in B-cells during the viral lytic replication cycle. We asked whether a viral bZIP transcription factor, Zta (BZLF1, ZEBRA, EB1), drives some of these changes. Using genome-wide chromatin immunoprecipitation coupled to next-generation DNA sequencing (ChIP-seq) we established a map of Zta interactions across the human genome. Using sensitive transcriptome analyses we identified 2263 cellular genes whose expression is significantly changed during the EBV lytic replication cycle. Zta binds 278 of the regulated genes and the distribution of binding sites shows that Zta binds mostly to sites that are distal to transcription start sites. This differs from the prevailing view that Zta activates viral genes by binding exclusively at promoter elements. We show that a synthetic Zta binding element confers Zta regulation at a distance and that distal Zta binding sites from cellular genes can confer Zta-mediated regulation on a heterologous promoter. This leads us to propose that Zta directly reprograms the expression of cellular genes through distal elements.

Epigenetic control of Epstein-Barr virus transcription - relevance to viral life cycle?

DNA methylation normally leads to silencing of gene expression but Epstein-Barr virus (EBV) provides an exception to the epigenetic paradigm. DNA methylation is absolutely required for the expression of many viral genes. Although the viral genome is initially un-methylated in newly infected cells, it becomes extensively methylated during the establishment of viral latency. One of the major regulators of EBV gene expression is a viral transcription factor called Zta (BZLF1, ZEBRA, Z) that resembles the cellular AP1 transcription factor. Zta recognizes at least 32 variants of a 7-nucleotide DNA sequence element, the Zta-response element (ZRE), some of which contain a CpG motif. Zta only binds to the latter class of ZREs in their DNA-methylated form, whether they occur in viral or cellular promoters and is functionally relevant for the activity of these promoters. The ability of Zta to interpret the differential DNA methylation of the viral genome is paramount for both the establishment of viral latency and the release from latency to initiate viral replication.

Systematic review and meta-analysis of a urine-based pneumococcal antigen test for diagnosis of community-acquired pneumonia caused by Streptococcus pneumoniae.

Standard culture methods for diagnosis of Streptococcus pneumoniae pneumonia take at least 24 h. The BinaxNOW urine-based test for S. pneumoniae (BinaxNOW-SP) takes only 15 min to conduct, potentially enabling earlier diagnosis and targeted treatment. This study was conducted to assess whether the use of BinaxNOW-SP at the time of hospital admission would provide adequate sensitivity and specificity for diagnosis of community-acquired pneumonia (CAP) in adult patients. We searched PubMed, EMBASE/OVID, Cochrane Collaboration, Centre for Reviews and Dissemination, INAHTA, and CADTH for diagnostic or etiologic studies of hospitalized predominately adult patients with clinically defined CAP that reported the diagnostic performance of BinaxNOW-SP versus cultures. Two authors independently extracted study details and diagnostic two-by-two tables. We found that 27 studies met our inclusion criteria, and three different reference standards were used between them. A bivariate meta-analysis of 12 studies using a composite of culture tests as the reference standard estimated the sensitivity of BinaxNOW-SP as 68.5% (95% credibility interval [CrI], 62.6% to 74.2%) and specificity as 84.2% (95% CrI, 77.5% to 89.3%). A meta-analysis of all 27 studies, adjusting for the imperfect and variable nature of the reference standard, gave a higher sensitivity of 74.0% (CrI, 66.6% to 82·3%) and specificity of 97.2% (CrI, 92.7% to 99.8%). The analysis showed substantial heterogeneity across studies, which did not decrease with adjustment for covariates. We concluded that the higher pooled sensitivity (compared to culture) and high specificity of BinaxNOW-SP suggest it would be a useful addition to the diagnostic workup for community-acquired pneumonia. More research is needed regarding the impact of BinaxNOW-SP on clinical practice.

Induction of p16(INK4a) is the major barrier to proliferation when Epstein-Barr virus (EBV) transforms primary B cells into lymphoblastoid cell lines.

To explore the role of p16(INK4a) as an intrinsic barrier to B cell transformation by EBV, we transformed primary B cells from an individual homozygous for a deletion in the CDKN2A locus encoding p16(INK4a) and p14(ARF). Using recombinant EBV-BAC viruses expressing conditional EBNA3C (3CHT), we developed a system that allows inactivation of EBNA3C in lymphoblastoid cell lines (LCLs) lacking active p16(INK4a) protein but expressing a functional 14(ARF)-fusion protein (p14/p16). The INK4a locus is epigenetically repressed by EBNA3C--in cooperation with EBNA3A--despite the absence of functional p16(INK4a). Although inactivation of EBNA3C in LCLs from normal B cells leads to an increase in p16(INK4a) and growth arrest, EBNA3C inactivation in the p16(INK4a)-null LCLs has no impact on the rate of proliferation, establishing that the repression of INK4a is a major function of EBNA3C in EBV-driven LCL proliferation. This conditional LCL system allowed us to use microarray analysis to identify and confirm genes regulated specifically by EBNA3C, independently of proliferation changes modulated by the p16(INK4a)-Rb-E2F axis. Infections of normal primary B cells with recombinant EBV-BAC virus from which EBNA3C is deleted or with 3CHT EBV in the absence of activating ligand 4-hydroxytamoxifen, revealed that EBNA3C is necessary to overcome an EBV-driven increase in p16(INK4a) expression and concomitant block to proliferation 2-4 weeks post-infection. If cells are p16(INK4a)-null, functional EBNA3C is dispensable for the outgrowth of LCLs.

Preoperative axillary ultrasound and fine-needle aspiration biopsy in the diagnosis of axillary metastases in patients with breast cancer: predictors of accuracy and future implications.

BACKGROUND: The utility of axillary lymph node dissection after sentinel lymph node biopsy has been called into question. We sought to determine the sensitivity, specificity, and accuracy of axillary ultrasound and fine-needle aspiration biopsy (FNAB) in the identification of axillary nodal metastasis in early breast cancer patients. METHODS: Data of patients with stage I and II breast cancer who underwent surgery and staging were reviewed. Axillary ultrasound findings were assessed and lymph node status recorded after axillary dissection. The data were cross-tabulated, and test characteristics were calculated. RESULTS: Of 235 patients, none demonstrated more than 2 positive sentinel lymph nodes. Ductal carcinoma was present in 68%, estrogen and progesterone receptors were positive in 81 and 64%, respectively, Her-2/neu was positive in 10%, and 36% were axillary node positive. The sensitivity and specificity of ultrasound alone were 55 and 88%, respectively. Predictors of abnormal ultrasound included size of metastasis, estrogen receptor and Her-2 status, tumor grade, and presence of lymphovascular invasion. Addition of FNAB increased the sensitivity and specificity to 69 and 100%. In conjunction with FNAB, the positive and negative predictive values were 100 and 54%, respectively. Ten percent of patients with nodal metastases demonstrated a positive FNAB. Patients with a positive FNAB did not harbor more nodal metastases or a greater proportion of gross extranodal disease compared to patients not subjected to FNAB. CONCLUSIONS: Axillary ultrasound with FNAB has an accuracy of >70% in this series. It is easily performed and may avoid unnecessary sentinel lymph node biopsy in a significant number of patients.

A network meta-analysis of antibiotics for treatment of hospitalised patients with suspected or proven meticillin-resistant Staphylococcus aureus infection.

Infections due to meticillin-resistant Staphylococcus aureus (MRSA) pose a serious health risk. Novel methods for assessing comparative effectiveness and safety may provide valuable insights into therapeutic choices. We did a systematic review searching electronic databases including the archives of FDA/CDER and performed a Bayesian network meta-analysis to compare parenteral antibiotics used for treating hospitalised adults with complicated skin and soft-tissue infections (cSSTIs) or hospital-acquired or ventilator-associated pneumonia (HAP/VAP). Models were adjusted for clinical heterogeneity due to between-arm differences in the proportion of patients with diabetes (for cSSTI) and in those requiring mechanical ventilation (for pneumonia). Treatments were ranked on efficacy, defined as clinical success in the modified intention-to-treat population (MITT) and in the MITT population with MRSA at baseline (MRSA m-MITT), on all-cause mortality (in pneumonia only), and on serious adverse events and withdrawals due to adverse events. We identified 24 randomised controlled trials (17 for cSSTI and 10 for HAP/VAP) comparing one of six antibiotics with vancomycin. The network meta-analysis indicated that vancomycin ranked third (of six antibiotics) in cSSTI and second (of four) in pneumonia on both efficacy and safety. However, direct pairwise meta-analyses remained inconclusive as evidenced by the adjusted median odds ratios (ORs) and their 95% credible intervals. In cSSTI, linezolid and ceftaroline were non-significantly more effective than vancomycin. Linezolid ORs were 1.15 (0.74-1.71) and 1.01 (0.42-2.14) and ceftaroline ORs were 1.12 (0.78-1.64) and 1.59 (0.68-3.74) in the MITT and MRSA m-MITT populations, respectively. For HAP/VAP, linezolid was non-significantly better than vancomycin, with ORs of 1.05 (0.72-1.57) and 1.32 (0.71-2.48) in the MITT and MRSA m-MITT populations, respectively. We suspect performance and detection bias in cSSTI trials involving linezolid, but regression methods could not adjust for this potential bias. In these clinical trials, the preferred agents for treating serious MRSA infections were ceftaroline (for cSSTI, not studied in HAP/VAP) and linezolid. However, translation of these findings into practice should consider the small size of the evidence networks and the consequent uncertainty associated with the parameter estimates, the lack of evidence for ceftaroline in patients with severe renal impairment, and the lower internal validity of some of the linezolid trials.

Genome-wide analyses of Zta binding to the Epstein-Barr virus genome reveals interactions in both early and late lytic cycles and an epigenetic switch leading to an altered binding profile.

The Epstein-Barr virus (EBV) genome sustains substantial epigenetic modification involving chromatin remodelling and DNA methylation during lytic replication. Zta (ZEBRA, BZLF1), a key regulator of the EBV lytic cycle, is a transcription and replication factor, binding to Zta response elements (ZREs) in target promoters and EBV lytic origins of replication. In vitro, Zta binding is modulated by DNA methylation; a subset of CpG-containing Zta binding sites (CpG ZREs) is bound only in a DNA methylation-dependent manner. The question of how the dynamic epigenetic environment impacts Zta interaction during the EBV lytic cycle is unknown. To address this, we used chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-Seq) to identify Zta binding sites across the EBV genome before and after viral DNA replication. Replication did not alter the association of Zta across many regions of the EBV genome, but a striking reduction in Zta binding occurred at some loci that contain CpG ZREs. Separating Zta-bound DNA into methylated and nonmethylated fractions, we found that promoters that contain CpG ZREs were enriched in the methylated fraction but that Zta binding to promoters lacking CpG ZREs was not reduced. We hypothesize that the loss of DNA methylation on the EBV genome during the lytic cycle causes the reduced binding to CpG ZREs; this may act as a lytic cycle epigenetic switch. However, the epigenetic changes associated with the replicated EBV genome do not affect the interaction of Zta with many loci that are rich in non-CpG ZREs; this leads to sustained binding at these regions.