Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts

Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and RNA cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts that meet stringent criteria for expression. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORFs), six novel ORF-containing transcripts, and 15 transcripts encoding for messages that could alter protein functions through truncation or fusion of canonical ORFs. In addition, we detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking distinct gene transcription units. Among these chimeric proteins we detected an evolutionarily conserved protein containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies combined with mass spectrometry can reveal further complexity within viral transcriptomes and resulting proteomes.

A-03 Physical Therapy Compared to a Home Exercise Program for Protracted Pediatric Sport-Related Concussion Rehabilitation

Purpose: The purpose of this study was to compare the recovery time in days between protracted recovery (greater than or equal to 28 days since injury) patients who were prescribed physical therapy and those who were prescribed a home exercise program. We hypothesized that physical therapy would be associated with shorter recovery times relative to the home exercise program. Methods: The 159 participants (aged 8–18) were drawn from an ongoing study. This study was a retrospective cohort design of sports-related concussion patients with a protracted recovery who presented to an outpatient specialty concussion clinic between 2018 and 2021, with data collected from electronic medical records. Both prescribed physical therapy (PPT) and home exercise program (HEP) patients were provided vestibular/ocular motor rehabilitation exercises to be completed at home three times per day. PPT participants must have completed at least three PPT sessions, or they were excluded from the study. Multi-variable zero-truncated negative binomial regressions were used to evaluate associations between groups. Results: Among the 48 (30.2%) PPT and 111 (69.8%) HEP participants, the majority were female (57.9%), age was 15.3 ± 1.4 (PPT) and 14.2 ± 2.8 (HEP), and days to clinic was a median 6.0 (IQR = 3.0–27.0; PPT) and 7.0 (IQR = 3.0–23.0; HEP). After adjusting for demographic (age, sex) and clinical measures (concussion history, convergence, VOMS score, and days to clinic), PPT was associated with an additional 1.21 days (95% CI: 1.06, 1.39) than HEP. Conclusions: We unexpectedly found that PPT was not associated with a shorter recovery time relative to HEP. Future research should explore this hypothesis while aiming to evaluate the effect of PPT versus HEP using a randomized design.

A-05 Retrospective Comparison of Concussion Recovery Between School and All Star Cheerleaders

Purpose: Though often categorized together, All Star and school cheerleading are vastly different in concussion risk due to competitiveness and skill difficulty. The purpose of the current study was to compare concussion rate and recovery in school and All Star cheerleaders diagnosed with sports-related concussions (SRC). Methods: This study was a retrospective comparison of cheerleaders (aged 8–18 years) who were evaluated in a specialty concussion clinic and diagnosed with SRC from 2020–2022. A total of 64 female cheerleaders were included (33 school and 31 All Star). We compared days to clinic, prior history of concussion, Post-Concussion Symptom Scale (PCSS) total score, symptom provocation on the Vestibular Ocular Motor Screen, and recovery time in days for each group. Results: Reports of at least one prior concussion were higher in All Star cheerleaders (61%) compared to school cheerleaders (39%). Initial evaluation occurred an average of 4.0 ± 5.8 days post injury for All Star cheerleaders, with recovery occurring in 23.6 ± 17.4 days compared to school cheerleaders who were evaluated for initial evaluation an average of 4.2 ± 4.3 days post injury and recovered in 27.6 ± 19.7 days (P > 0.05). All Star cheerleaders experienced greater symptom provocation (P = 0.05) on horizontal vestibular-ocular reflex compared to school cheerleaders. There was no difference in symptom reporting on the PCSS (P = 0.23). Conclusions: Higher rates of prior concussion were reported in All Star cheerleaders. This may be a function of the more difficult skills being performed. Future research should investigate the impact of skill level and mechanism of injury on SRCs in All Star Cheerleading.

A-32 Association Between Adolescent Patient Emotional Factors and Adherence to a Sport-Related Concussion Treatment

Purpose: To determine the association between Anxiety Sensitivity Index (ASI) and Positive and Negative Affect Schedule (PANAS) and adherence to an exercise treatment for sport-related concussion (SRC). We hypothesized Positive Affect (PA) score would be positively associated, while ASI and Negative Affect (NA) score would be negatively associated with odds of treatment adherence. Methods: This was a prospective (2020–2021) analysis of adolescents (aged 14–17) diagnosed with SRC by a pediatric specialty concussion clinic and subsequently prescribed daily exercise. Adherence to the exercise protocol was defined as consistently increasing physical activity volume (measured by accelerometer) during recovery. Multivariable logistic regressions evaluated the independent associations between treatment adherence and ASI; PA score; NA score. Results: The mean (standard deviation [SD]) recovery time was 16.1 (9.0) days. Among the 32 (56.1%) adherent and 25 (43.9%) not adherent participants, the majority were aged 15 years (29.8%), male (50.9%), non-Hispanic White (70.2%), and had no concussion history (61.4%). After adjusting for age and sex, the odds of treatment adherence for each additional unit increase in ASI, PA score, and NA score was 1.03 (95% CI: 0.96–1.10), 1.14 (95% CI: 0.97–1.35), and 1.18 (95% CI: 0.95–1.47), respectively. Conclusions: Despite lack of statistical significance, it appears that PA score and NA score may contribute to exercise treatment adherence for SRC. As this study may be underpowered, future studies should aim to have a larger sample and investigate the discriminate utility of PANAS to identify those who may or may not adhere to SRC exercise treatments.

A-36 Tracking Compliance To A Home Exercise Program For Concussion Using Ecological Momentary Assessment: A Pilot Study

Purpose: The management of pediatric concussions creates a clinical challenge due to unknown patient compliance with prescribed therapies and interventions. The purpose of this pilot study was to describe the logistical use of ecological momentary assessment (EMA) to track compliance to a physical therapy facilitated vestibular/ocular motor home exercise program (HEP) in patients diagnosed with concussion. Methods: A convenience sample of 20 concussed patients (aged 13–18 years [mdn = 14.5, IQR = 14.0–16.8]) was included in this initial pilot study. All participants were evaluated within seven days of injury. Participants were instructed to complete one daily HEP compliance log until medical clearance on their parent or guardians’ mobile device using an EMA application. Results: Participants were evaluated a median 3.5 (IQR = 1.3–6.5) days post injury, recovered in a median 15.5 (IQR = 11.0–25.0) days, and completed a mean 5.85 (SD = 3.9) total EMA logs representing a 47% completion rate. Participants reported completing a mean 1.21 (SD = 0.77) HEPs per day with a range of 0.0 to 3.0. Self-reported HEP compliance did not significantly correlate with recovery time in days (P = 0.26). Conclusions: The overall response rate for EMA logs was 47% and participants reported completing 1.2 HEPs per day. Analysis of this preliminary data did not reveal a correlation between HEP compliance and recovery time in days. Participants reported the primary barrier to completing daily questionnaires was access to their parent or guardians’ mobile device at the time of the prompt. Overall, the data derived from EMA appears useful for tracking the progression of this heterogenous injury.

DRUMMER—Rapid detection of RNA modifications through comparative nanopore sequencing

Motivation

The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides.

Results

DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity.

Availability and implementation

DRUMMER is written in Python 3 and is available as open source in the GitHub repository: https://github.com/DepledgeLab/DRUMMER.

Supplementary information

Supplementary data are available at Bioinformatics online.

Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA

Eukaryotic cells recognize intracellular pathogens through pattern recognition receptors, including sensors of aberrant nucleic acid structures. Sensors of double-stranded RNA (dsRNA) are known to detect replication intermediates of RNA viruses. It has long been suggested that annealing of mRNA from symmetrical transcription of both top and bottom strands of DNA virus genomes can produce dsRNA during infection. Supporting this hypothesis, nearly all DNA viruses encode inhibitors of dsRNA-recognition pathways. However, direct evidence that DNA viruses produce dsRNA is lacking. Contrary to dogma, we show that the nuclear-replicating DNA virus adenovirus (AdV) does not produce detectable levels of dsRNA during infection. In contrast, abundant dsRNA is detected within the nucleus of cells infected with AdV mutants defective for viral RNA processing. In the presence of nuclear dsRNA, the cytoplasmic dsRNA sensor PKR is relocalized and activated within the nucleus. Accumulation of viral dsRNA occurs in the late phase of infection, when unspliced viral transcripts form intron/exon base pairs between top and bottom strand transcripts. We propose that DNA viruses actively limit dsRNA formation by promoting efficient splicing and mRNA processing, thus avoiding detection and restriction by host innate immune sensors of pathogenic nucleic acids.

Adenovirus Remodeling of the Host Proteome and Host Factors Associated with Viral Genomes

Viral infections are associated with extensive remodeling of the cellular proteome. Viruses encode gene products that manipulate host proteins to redirect cellular processes or subvert antiviral immune responses. Adenovirus (AdV) encodes proteins from the early E4 region which are necessary for productive infection. Some cellular antiviral proteins are known to be targeted by AdV E4 gene products, resulting in their degradation or mislocalization. However, the full repertoire of host proteome changes induced by viral E4 proteins has not been defined. To identify cellular proteins and processes manipulated by viral products, we developed a global, unbiased proteomics approach to analyze changes to the host proteome during infection with adenovirus serotype 5 (Ad5) virus. We used whole-cell proteomics to measure total protein abundances in the proteome during Ad5 infection. Since host antiviral proteins can antagonize viral infection by associating with viral genomes and inhibiting essential viral processes, we used Isolation of Proteins on Nascent DNA (iPOND) proteomics to identify proteins associated with viral genomes during infection with wild-type Ad5 or an E4 mutant virus. By integrating these proteomics data sets, we identified cellular factors that are degraded in an E4-dependent manner or are associated with the viral genome in the absence of E4 proteins. We further show that some identified proteins exert inhibitory effects on Ad5 infection. Our systems-level analysis reveals cellular processes that are manipulated during Ad5 infection and points to host factors counteracted by early viral proteins as they remodel the host proteome to promote efficient infection. IMPORTANCE Viral infections induce myriad changes to the host cell proteome. As viruses harness cellular processes and counteract host defenses, they impact abundance, post-translational modifications, interactions, or localization of cellular proteins. Elucidating the dynamic changes to the cellular proteome during viral replication is integral to understanding how virus-host interactions influence the outcome of infection. Adenovirus encodes early gene products from the E4 genomic region that are known to alter host response pathways and promote replication, but the full extent of proteome modifications they mediate is not known. We used an integrated proteomics approach to quantitate protein abundance and protein associations with viral DNA during virus infection. Systems-level analysis identifies cellular proteins and processes impacted in an E4-dependent manner, suggesting ways that adenovirus counteracts potentially inhibitory host defenses. This study provides a global view of adenovirus-mediated proteome remodeling, which can serve as a model to investigate virus-host interactions of DNA viruses.

Anaemia and coronary microvascular dysfunction in end-stage renal disease

Funding Acknowledgements

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): (1) University Hospitals Birmingham Charity (2) Metchley Park Medical Society

Introduction

 

Coronary microvascular dysfunction (CMD) is common among patients with end-stage renal disease (ESRD) and confers poor prognosis. Coronary flow velocity reserve (CFVR) is a marker of coronary microvascular function and can be reliably measured using Doppler echocardiography. Reduced CFVR in ESRD has been attributed to factors such as hypertension and left ventricular hypertrophy (LVH). Anaemia is prevalent in ESRD but the association between haemoglobin and CFVR in ESRD has not been studied. 

Purpose

 

To assess if CFVR is related to haemoglobin among patients with ESRD. 

Methods

 

22 subjects with ESRD and awaiting kidney transplant (8 pre-dialysis and 14 on peritoneal dialysis) were studied with adenosine myocardial contrast echocardiography, Doppler CFVR assessment and serum multiplex immunoassay analysis. Individuals with diabetes, uncontrolled hypertension or ischaemic heart disease were excluded.

Results 

7/22 (32%) of subjects had CMD (defined as CFVR <2). Age (47 years ± 15 vs 55 ± 10, p = 0.177), estimated glomerular filtration rate [7ml/min/1.73m² (5-11) vs 9 (7-10), p = 0.837], systolic blood pressure (129mmHg ± 25 vs 137 ± 20, p = 0.398) and left ventricular mass index (98g/m² ± 31 vs 98 ± 28, p = 0.936) did not significantly differ between subjects with or without CMD. There were no significant differences in other demographic, haemodynamic, laboratory or echocardiographic variables between the two groups.  A panel of biomarkers of inflammation, myocardial stretch, cardiac fibrosis and LVH studied by multiplex immunoassay also did not show any significant differences between the two groups. No subjects had wall motion abnormalities or perfusion defects on myocardial contrast echocardiography.

CFVR was significantly lower in subjects with CMD (1.6 ± 0.2 vs 3.2 ± 0.9, p < 0.001). Subjects with CMD had significantly lower haemoglobin than subjects without CMD (102g/L ± 12 vs 117g/L ± 11, p = 0.008). There was a moderate positive correlation between haemoglobin and CFVR (r = 0.65, p = 0.001) – figure 1. In a stepwise multiple regression model with CFVR as the dependent variable and age, haemoglobin, systolic blood pressure, left ventricular mass index and estimated glomerular filtration rate as independent variables, only haemoglobin was an independent predictor of CFVR (β=0.051 95%CI 0.023-0.079, p = 0.001). 

Conclusions 

Among our cohort of ESRD patients awaiting kidney transplant, there was a high prevalence of CMD despite well controlled blood pressure and no significant LVH. Subjects with CMD had significantly lower haemoglobin than subjects without CMD. Reduced haemoglobin causes impaired oxygen carrying capacity to the myocardium, which may lead to microvascular ischaemia and adverse microvascular remodelling, causing CMD. Thus, anaemia may be a potentially correctible driver of CMD in ESRD.  This association needs to be confirmed in larger studies.

Abstract Figure 1

Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription

Intrinsic antiviral host factors confer cellular defence by limiting virus replication and are often counteracted by viral countermeasures. We reasoned that host factors that inhibit viral gene expression could be identified by determining proteins bound to viral DNA (vDNA) in the absence of key viral antagonists. Herpes simplex virus 1 (HSV-1) expresses E3 ubiquitin-protein ligase ICP0 (ICP0), which functions as an E3 ubiquitin ligase required to promote infection. Cellular substrates of ICP0 have been discovered as host barriers to infection but the mechanisms for inhibition of viral gene expression are not fully understood. To identify restriction factors antagonized by ICP0, we compared proteomes associated with vDNA during HSV-1 infection with wild-type virus and a mutant lacking functional ICP0 (ΔICP0). We identified the cellular protein Schlafen family member 5 (SLFN5) as an ICP0 target that binds vDNA during HSV-1 ΔICP0 infection. We demonstrated that ICP0 mediates ubiquitination of SLFN5, which leads to its proteasomal degradation. In the absence of ICP0, SLFN5 binds vDNA to repress HSV-1 transcription by limiting accessibility of RNA polymerase II to viral promoters. These results highlight how comparative proteomics of proteins associated with viral genomes can identify host restriction factors and reveal that viral countermeasures can overcome SLFN antiviral activity.

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we profile m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.

Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing

Viruses promote infection by hijacking the ubiquitin machinery of the host to counteract or redirect cellular processes. Adenovirus encodes two early proteins, E1B55K and E4orf6, that together co-opt a cellular ubiquitin ligase complex to overcome host defences and promote virus production. Adenovirus mutants lacking E1B55K or E4orf6 display defects in viral RNA processing and protein production, but previously identified substrates of the redirected ligase do not explain these phenotypes. Here, we used a quantitative proteomics approach to identify substrates of E1B55K/E4orf6-mediated ubiquitination that facilitate RNA processing. While all currently known cellular substrates of E1B55K and E4orf6 are degraded by the proteasome, we uncovered RNA-binding proteins as high-confidence substrates that are not decreased in overall abundance. We focused on two RNA-binding proteins, RALY and hnRNP-C, which we confirm are ubiquitinated without degradation. Knockdown of RALY and hnRNP-C increased levels of viral RNA splicing, protein abundance and progeny production during infection with E1B55K-deleted virus. Furthermore, infection with E1B55K-deleted virus resulted in an increased interaction of hnRNP-C with viral RNA and attenuation of viral RNA processing. These data suggest that viral-mediated ubiquitination of RALY and hnRNP-C relieves a restriction on viral RNA processing and reveal an unexpected role for non-degradative ubiquitination in the manipulation of cellular processes during virus infection.

A-33 VOMS Scores Relationship to C3 Logix Trail Scores in Females

Objective

Burkhart and colleagues (2020) showed that positive screening on the Vestibular Ocular Motor Screening (VOMS) and slower C3 Logix Trails (C3LT) were predictive of protracted recovery in female adolescents. The purpose of this study was to see if there was a relationship between positive screening on the VOMS and slower C3LT times in a similar population.

Method

220 females aged 10–18 were administered the VOMS and C3LT between 2017–2019. We hypothesized that positive screening on the VOMS (i.e. symptom provocation of +2, convergence of > 6 mm) would be related to slower speeds on C3LT A and B. Odds ratios were calculated to estimate the likelihood of screening positive on the VOMS based on C3LT times.

Results

Slower times on C3LT A and B, one to two standard deviations (SD) above the mean, was not related to a positive screening on the VOMS. However, performing a faster C3LT A time, one SD below the mean, was 68% less likely to screen positively on the VOMS (OR = 0.32, 95%CI = 0.16–0.62, p = 0.001) compared to those not 1 SD below the mean.

Conclusions

Though C3LT has a visual scanning component, positive screening on the VOMS was not related to slower processing speeds on the C3LT in females age 10–18.

A-08 VOMS Scores Relationship to King-Devick Scores in Males

Objective

Burkhart and colleagues (2020) showed that positive screening on the Vestibular Ocular Motor Screening (VOMS) and slower King Devick scores were predictive of protracted recovery in male adolescents. The purpose of this study was to examine the relationship between positive VOMS screening and King-Devick Trial 1 scores in a similar population.

Method

300 male participants age 10–18 were administered VOMS and King-Devick Trial 1 within 7-days of their injury at a specialty concussion clinic between 2017–2019. We hypothesized that slower speeds on King-Devick Trial 1 would be related to a positive screening on the VOMS (i.e. symptom provocation of +2, convergence of > 6 mm). Odds ratios were calculated to estimate the likelihood of screening positive on the VOMS among those with a King-Devick Trial 1 score above the median compared to those with a score below the median.

Results

Those scoring above the median on King-Devick Trial 1 (i.e. slower times) were 74% more likely to have a positive screening on the VOMS, OR = 1.74, 95% CI [1.10–2.78], p = 0.02, relative to those with a King-Devick Trial 1 above the median.

Conclusions

The VOMS was created to be a symptom provocation tool sensitive to concussion. However, this study demonstrated that the VOMS is also related to performance on objective visual scanning task. Specifically, adolescent males with slower scores on the King-Devick Trial 1 were more likely to have a positive screening on the VOMS.

Identification of Host Biomarkers of Epstein-Barr Virus Latency IIb and Latency III

Deciphering the molecular pathogenesis of virally induced cancers is challenging due, in part, to the heterogeneity of both viral gene expression and host gene expression. Epstein-Barr virus (EBV) is a ubiquitous herpesvirus prevalent in B-cell lymphomas of immune-suppressed individuals. EBV infection of primary human B cells leads to their immortalization into lymphoblastoid cell lines (LCLs), serving as a model of these lymphomas. In previous studies, reports from our laboratory have described a temporal model for immortalization with an initial phase characterized by expression of Epstein-Barr nuclear antigens (EBNAs), high levels of c-Myc activity, and hyperproliferation in the absence of the latent membrane proteins (LMPs), called latency IIb. This is followed by the long-term outgrowth of LCLs expressing the EBNAs along with the LMPs, particularly NFκB-activating LMP1, defining latency III. However, LCLs express a broad distribution of LMP1 such that a subset of these cells express LMP1 at levels similar to those seen in latency IIb, making it difficult to distinguish these two latency states. In this study, we performed mRNA sequencing (mRNA-Seq) on early EBV-infected latency IIb cells and latency III LCLs sorted by NFκB activity. We found that latency IIb transcriptomes clustered independently from latency III independently of NFκB. We identified and validated mRNAs defining these latency states. Indeed, we were able to distinguish latency IIb cells from LCLs expressing low levels of LMP1 using multiplex RNA-fluorescence in situ hybridization (RNA-FISH) targeting EBV EBNA2 or LMP1 and human CCR7 or MGST1 This report defines latency IIb as a bona fide latency state independent from latency III and identifies biomarkers for understanding EBV-associated tumor heterogeneity.IMPORTANCE EBV is a ubiquitous pathogen, with >95% of adults harboring a life-long latent infection in memory B cells. In immunocompromised individuals, latent EBV infection can result in lymphoma. The established expression profile of these lymphomas is latency III, which includes expression of all latency genes. However, single-cell analysis of EBV latent gene expression in these lymphomas suggests heterogeneity where most cells express the transcription factor, EBNA2, and only a fraction of the cells express membrane protein LMP1. Our work describes an early phase after infection where the EBNAs are expressed without LMP1, called latency IIb. However, LMP1 levels within latency III vary widely, making these states hard to discriminate. This may have important implications for therapeutic responses. It is crucial to distinguish these states to understand the molecular pathogenesis of these lymphomas. Ultimately, better tools to understand the heterogeneity of these cancers will support more-efficacious therapies in the future.

Premature coronary artery disease and early stage chronic kidney disease

A 30 year old asymptomatic male with stage 3 chronic kidney disease (CKD) secondary to Focal Segmental Glomerulosclerosis was found to have features of CKD associated cardiomyopathy including left ventricular hypertrophy (LVH) and focal sub-endocardial scarring on cardiac magnetic resonance imaging. There was also a significantly raised CT coronary calcium score and evidence of non-flow limiting coronary artery disease (CAD) on a CT coronary angiogram. Early stage CKD is a major risk factor for cardiovascular risk causing myocardial hypertrophy and fibrosis and coronary artery atheroma. Cardiovascular risk begins to increase from an eGFR of around 75ml/min/1.73m2. The pathophysiology of cardiovascular disease in CKD is under investigation but to date, treatment options are limited. Blood pressure control and statins have the strongest supportive evidence.

Take your PIKK: tumour viruses and DNA damage response pathways

Viruses regulate cellular processes to facilitate viral replication. Manipulation of nuclear proteins and pathways by nuclear replicating viruses often causes cellular genome instability that contributes to transformation. The cellular DNA damage response (DDR) safeguards the host to maintain genome integrity, but DNA tumour viruses can manipulate the DDR to promote viral propagation. In this review, we describe the interactions of DNA tumour viruses with the phosphatidylinositol 3-kinase-like protein kinase (PIKK) pathways, which are central regulatory arms of the DDR. We review how signalling through the ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3 related (ATR), and DNA-dependent protein kinases (DNA-PK) influences viral life cycles, and how their manipulation by viral proteins may contribute to tumour formation.This article is part of the themed issue 'Human oncogenic viruses'.

The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis

The Epstein-Barr virus (EBV) miR-BHRF1 microRNA (miRNA) cluster has been shown to facilitate B-cell transformation and promote the rapid growth of the resultant lymphoblastoid cell lines (LCLs). However, we find that expression of physiological levels of the miR-BHRF1 miRNAs in LCLs transformed with a miR-BHRF1 null mutant (∆123) fails to increase their growth rate. We demonstrate that the pri-miR-BHRF1-2 and 1-3 stem-loops are present in the 3'UTR of transcripts encoding EBNA-LP and that excision of pre-miR-BHRF1-2 and 1-3 by Drosha destabilizes these mRNAs and reduces expression of the encoded protein. Therefore, mutational inactivation of pri-miR-BHRF1-2 and 1-3 in the ∆123 mutant upregulates the expression of not only EBNA-LP but also EBNA-LP-regulated mRNAs and proteins, including LMP1. We hypothesize that this overexpression causes the reduced transformation capacity of the ∆123 EBV mutant. Thus, in addition to regulating cellular mRNAs in trans, miR-BHRF1-2 and 1-3 also regulate EBNA-LP mRNA expression in cis.

Epstein-Barr virus ensures B cell survival by uniquely modulating apoptosis at early and late times after infection

Latent Epstein-Barr virus (EBV) infection is causally linked to several human cancers. EBV expresses viral oncogenes that promote cell growth and inhibit the apoptotic response to uncontrolled proliferation. The EBV oncoprotein LMP1 constitutively activates NFκB and is critical for survival of EBV-immortalized B cells. However, during early infection EBV induces rapid B cell proliferation with low levels of LMP1 and little apoptosis. Therefore, we sought to define the mechanism of survival in the absence of LMP1/NFκB early after infection. We used BH3 profiling to query mitochondrial regulation of apoptosis and defined a transition from uninfected B cells (BCL-2) to early-infected (MCL-1/BCL-2) and immortalized cells (BFL-1). This dynamic change in B cell survival mechanisms is unique to virus-infected cells and relies on regulation of MCL-1 mitochondrial localization and BFL-1 transcription by the viral EBNA3A protein. This study defines a new role for EBNA3A in the suppression of apoptosis with implications for EBV lymphomagenesis.

DOI:http://dx.doi.org/10.7554/eLife.22509.001

Over 90% of adults around the world are infected with the Epstein-Barr virus. Like other closely related viruses, such as those that cause chicken pox and cold sores, an infection lasts for the rest of the person’s life, although the virus generally remains in a latent or dormant state. However, under certain conditions the latent viruses can cause cancers to develop; in fact, it is estimated that such infections are responsible for nearly 2% of all cancer deaths worldwide.

One way that healthy human cells prevent cancer is by triggering their own death in a process called apoptosis. The Epstein-Barr virus can block apoptosis, therefore making the cells more likely to become cancerous. Previous research identified one protein in the Epstein-Barr virus that promotes cancer by preventing infected cells from dying as normal. However, even in the absence of this protein, Epstein-Barr virus-infected cells remain resistant to apoptosis. This suggests that the virus has another way of blocking cell death.

Price et al. have now used a technique that stresses living cells in a way that reveals which proteins prevent apoptosis to study human cells infected with the Epstein-Barr virus. This revealed that soon after infection, the virus could force the human cell to produce MCL-1, a protein that prevents cell death. Later, the Epstein-Barr virus enlisted a second human protein called BFL-1, which makes the infected cell further resistant to apoptosis.

Price et al. discovered that a protein in the Epstein-Barr virus called EBNA3A controls the production of the MCL-1 and BFL-1 proteins. In the future, developing therapies that target these proteins may lead to new treatments for cancers caused by the Epstein-Barr virus. Such treatments would be likely to have fewer side effects for patients than traditional chemotherapies.

DOI:http://dx.doi.org/10.7554/eLife.22509.002

Dynamic Epstein-Barr virus gene expression on the path to B-cell transformation

Epstein-Barr virus (EBV) is an oncogenic human herpesvirus in the γ-herpesvirinae subfamily that contains a 170-180kb double-stranded DNA genome. In vivo, EBV commonly infects B and epithelial cells and persists for the life of the host in a latent state in the memory B-cell compartment of the peripheral blood. EBV can be reactivated from its latent state, leading to increased expression of lytic genes that primarily encode for enzymes necessary to replicate the viral genome and structural components of the virion. Lytic cycle proteins also aid in immune evasion, inhibition of apoptosis, and the modulation of other host responses to infection. In vitro, EBV has the potential to infect primary human B cells and induce cellular proliferation to yield effectively immortalized lymphoblastoid cell lines, or LCLs. EBV immortalization of B cells in vitro serves as a model system for studying EBV-mediated lymphomagenesis. While much is known about the steady-state viral gene expression within EBV-immortalized LCLs and other EBV-positive cell lines, relatively little is known about the early events after primary B-cell infection. It was previously thought that upon latent infection, EBV only expressed the well-characterized latency-associated transcripts found in LCLs. However, recent work has characterized the early, but transient, expression of lytic genes necessary for efficient transformation and delayed responses in the known latency genes. This chapter summarizes these recent findings that show how dynamic and controlled expression of multiple EBV genes can control the activation of B cells, entry into the cell cycle, the inhibition of apoptosis, and innate and adaptive immune responses.

Nurse-led weaning from mechanical ventilation: where's the evidence?

BACKGROUND

Several authors have suggested clinical protocols as a means of shortening ventilation time and the important role of the nurse in reducing ventilation time has also been highlighted. Despite the many references in the literature to reducing weaning times using clinical protocols, it is not clear whether nurse-led weaning strategies hasten weaning from mechanical ventilation compared with physician-led care.

OBJECTIVE

to systematically review the published literature to answer the question: Does nurse-led weaning from mechanical ventilation reduce duration of ventilation compared with doctor-led care?

DATA SOURCES

MEDLINE, CINHAL, EMBASE, Cochrane Library, Best Evidence, hand search, expert opinion, controlled trials register.

STUDY SELECTION

randomized controlled trials (RCTs) and cohort studies where nurses or respiratory therapists lead the weaning from mechanical ventilation; duration of ventilation must be stated.

DATA EXTRACTION

performed by the author, who extracted data on statistical significance of the difference in duration of ventilation between control and trial groups, complication rates (such as reintubation) and mortality.

DATA SYNTHESIS

statistical synthesis was not attempted but narrative synthesis was performed.

RESULTS

only 1 randomized controlled trial and 2 cohort studies were found where nurses or respiratory therapists led weaning using a protocol. Two studies showed reduction in ventilation time without additional complications; the third study had the weakest evidence, because it was retrospective, and showed no difference between control and treatment groups.

CONCLUSIONS

There is limited evidence suggesting that nurse-led weaning may reduce ventilation time; however, it is not clear whether it was the nurse-led aspect or the clinical protocol that produced the effect.

Distribution of 8-oxygenated leaf-surface flavones in the genus Ocimum

Nine species of Ocimum (Lamiaceae) were surveyed for leaf-surface flavonoids by means of HPLC with diode array detection and atmospheric pressure chemical ionisation (APCI) mass spectrometry. The analysis revealed the presence of 23 different flavones, most of which were identified by comparing their UV and mass spectra with those of standards. Almost all taxa investigated contained flavones methoxylated in the 6- and 8-positions, such as nevadensin, xanthomicrol and gardenin B. The same taxa also produced flavones methoxylated in the 6-position but hydroxylated in the 8-position, including isothymusin (5,8,4'-trihydroxy-6,7-dimethoxyflavone), pedunculin (5,8-dihydroxy-6,7,4'-trimethoxyflavone) and a new flavone, 5,7,8-trihydroxy-6,4'-dimethoxyflavone, which was given the trivial name pilosin. This compound was isolated from O. americanum var. pilosum and also detected as a minor constituent in O. x citriodorum leaf extracts. Its molecular structure was elucidated by means of NMR spectroscopy. 8-Oxygenated flavones were absent only from O. lamiifolium. APCI mass spectrometry of the flavonoids revealed that the product ions formed by collision induced dissociation of the protonated molecule provided structural information about the substitution pattern of the A-ring. The chemotaxonomic and biogenetic implications of the results are discussed.

Our journey with clinical supervision in an intensive care unit

In 1991, the nursing profession began to pursue the idea of reflective practice with vigour, despite little evidence that reflective practice improved nursing care (Burnard 1991; Hunt 1993). A small qualitative study on the experiences of nurses writing reflective journals was undertaken in the intensive care unit at Newham General Hospital. (A Price 1995). This highlighted the need for clear initial guidance and support when introducing reflective practice. It also demonstrated a lack of knowledge about reflection within the unit. During this time, a group of nurses who were interested in developing clinical supervision as a method of support for staff was formed. Kohner's (1994) definition of clinical supervision, adopted by the group after review of literature, makes it clear that this involves reflection on practice. Johns' (1993) Model of Structured Reflection was amended and used to promote in-depth analysis of situations, and journal writing was encouraged within the group. A continuing process of group clinical supervision was started, initially with the help of a facilitator experienced in it. On the basis of this experience, a strategy for implementation of clinical supervision in the intensive care unit was developed and put into action by the group members. Consideration of the progress and problems experienced leads to the conclusion that continuing staff motivation and commitment, and adequate time are essential for implementation of clinical supervision.

Osmolality affects ion and water fluxes and secretion in the ferret trachea

Nonisosmolar solutions were placed in the lumen of the ferret trachea in vitro in an organ bath. Hyposmolar (150 mmol/kg) solutions progressively increased in osmolarity over 1 h. Increases in luminal concentration of impermeant blue dextran occurred only after 5 min, suggesting that the initial changes were due to ion rather than water fluxes. With hyperosmolar solutions the osmolarity decreased over 1 h with no change in blue dextran concentration, indicating that ion but not water fluxes were taking place. Cooling the preparation to 4 degrees C greatly reduced the osmolaity changes with hyperosmolar solutions and halved those with hyposmolar solutions, suggesting that active ion transport was involved. Hyposmolar (75-150 mmol/kg) and hyperosmolar (450-900 mmol/kg) solutions both increased albumin output into the lumen, but the response was prevented by cooling the trachea to 4 degrees C. Hyposmolar and hyperosmolar solutions both increased the output of lysozyme from glandular serous cells into the lumen. The response to hyposmolar solutions was stronger. Cooling the trachea abolished the lysozyme response to hyperosmolar solutions. Thus hypo- and hyperosmolar solutions promote ion transport in directions to restore isosmolarity. Both nonisosmolar solutions promote albumin movement by active transport across the mucosa and lysozyme secretion from submucosal glands, responses inhibited by tracheal cooling and therefore dependent on metabolically active processes.

Transport of albumin by the rabbit trachea in vitro

The rabbit whole trachea was mounted in vitro in an organ bath containing Krebs-Henseleit (KH) solution. When the trachea was air filled there was no resting secretion and none was induced by methacholine (0.02 mM). Histology showed that the trachea has very few submucosal glands. When the trachea was filled with KH, with fluorescent bovine serum albumin in the surrounding KH solution, the rate of transport of albumin into the lumen was measured. Methacholine (0.02 mM) and phenylephrine (0.1 mM) more than doubled the output of albumin, and albuterol (0.1 mM) increased it more than fourfold. Cooling the preparation to 4 degrees C decreased the spontaneous output of albumin to less than one-half control and abolished the increase in output due to albuterol. Addition of sodium cyanide (1 mM) to the preparation abolished the increase in albumin transport due to albuterol. Serosal-to-mucosal transport of fluorescent dextran (mol wt 70,000) was less than one-third that of albumin and was not enhanced by methacholine, phenylephrine, or albuterol. Lysozyme output, an index of serous cell secretion, was barely detectable in controls and was not enhanced by any of the drugs. We conclude that the rabbit trachea has no measurable submucosal gland secretion and that it can actively transport albumin into the lumen via the epithelium. The transport rate is enhanced by methacholine, phenylephrine, and especially by albuterol.