Publications by authors named "James R Brown"

78 Publications

Expanding the drug discovery space with predicted metabolite-target interactions.

Commun Biol 2021 Mar 5;4(1):288. Epub 2021 Mar 5.

GlaxoSmithKline Pharma R&D, 1250 S. Collegeville Rd, Collegeville, PA, 19426-0989, USA.

Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite-host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potential metabolite-target interactions using the Inflammatory Bowel Disease (IBD) cohort dataset of the Human Microbiome Project 2 (HMP2). Using a consensus of multiple machine learning methods, we ranked metabolites based on importance to IBD, followed by virtual ligand-based screening to identify possible human targets and adding evidence from compound assay, differential gene expression, pathway enrichment, and genome-wide association studies. We confirmed known metabolite-target pairs such as nicotinic acid-GPR109a or linoleoyl ethanolamide-GPR119 and inferred interactions of interest including oleanolic acid-GABRG2 and alpha-CEHC-THRB. Eleven metabolites were tested for bioactivity in vitro using human primary cell-types. By expanding the universe of possible microbial metabolite-host protein interactions, we provide multiple drug targets for potential immune-therapies.
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http://dx.doi.org/10.1038/s42003-021-01822-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7935942PMC
March 2021

Inflammatory Endotype Associated Airway Microbiome in COPD Clinical Stability and Exacerbations - A Multi-Cohort Longitudinal Analysis.

Am J Respir Crit Care Med 2020 Dec 17. Epub 2020 Dec 17.

University of Leicester, 4488, Institute for Lung Health, Leicester NIHR Biomedical Research Centre, Department of Respiratory Sciences, Leicester, United Kingdom of Great Britain and Northern Ireland.

Rationale: Understanding the role of airway microbiome in chronic obstructive pulmonary disease (COPD) inflammatory endotypes may help to develop microbiome-based diagnostic and therapeutic approaches.

Objectives: To understand the association of airway microbiome with neutrophilic and eosinophilic COPD at stability and exacerbations.

Methods: An integrative analysis was performed on 1,706 sputum samples collected longitudinally from 510 COPD patients recruited at four UK sites in BEAT-COPD, COPDMAP and AERIS cohorts. The microbiome was analyzed using COPDMAP and AERIS as discovery dataset and BEAT-COPD as validation dataset.

Results: The airway microbiome in neutrophilic COPD was heterogeneous with two primary community types differentiated by the predominance of Haemophilus. The Haemophilus-predominant subgroup had elevated sputum IL-1b and TNFa and was relatively stable over time. The other neutrophilic subgroup with a balanced microbiome profile had elevated sputum and serum IL-17A and was temporally dynamic. Patients in this state at stability were susceptible to greatest microbiome shifts during exacerbations. This subgroup can temporally switch to both neutrophilic-Haemophilus-predominant and eosinophilic states which were otherwise mutually exclusive. Time-series analysis on the microbiome showed the temporal trajectories of Campylobacter and Granulicatella were indicative of intra-patient switches from neutrophilic to eosinophilic inflammation, and in track with patient sputum eosinophilia over time. Network analysis revealed distinct host-microbiome interaction patterns between neutrophilic-Haemophilus-predominant, neutrophilic-balanced-microbiome and eosinophilic subgroups.

Conclusions: The airway microbiome can stratify neutrophilic COPD into subgroups that justify different therapies. Neutrophilic and eosinophilic COPD are inter-changeable in some patients. Monitoring temporal variability of the airway microbiome may track patient inflammatory status over time.
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http://dx.doi.org/10.1164/rccm.202009-3448OCDOI Listing
December 2020

Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease.

ISME J 2020 11 27;14(11):2748-2765. Epub 2020 Jul 27.

Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China.

The interaction between airway microbiome and host in chronic obstructive pulmonary disease (COPD) is poorly understood. Here we used a multi-omic meta-analysis approach to characterize the functional signature of airway microbiome in COPD. We retrieved all public COPD sputum microbiome datasets, totaling 1640 samples from 16S rRNA gene datasets and 26 samples from metagenomic datasets from across the world. We identified microbial taxonomic shifts using random effect meta-analysis and established a global classifier for COPD using 12 microbial genera. We inferred the metabolic potentials for the airway microbiome, established their molecular links to host targets, and explored their effects in a separate meta-analysis on 1340 public human airway transcriptome samples for COPD. 29.6% of differentially expressed human pathways were predicted to be targeted by microbiome metabolism. For inferred metabolite-host interactions, the flux of disease-modifying metabolites as predicted from host transcriptome was generally concordant with their predicted metabolic turnover in microbiome, suggesting a synergistic response between microbiome and host in COPD. The meta-analysis results were further validated by a pilot multi-omic study on 18 COPD patients and 10 controls, in which airway metagenome, metabolome, and host transcriptome were simultaneously characterized. 69.9% of the proposed "microbiome-metabolite-host" interaction links were validated in the independent multi-omic data. Butyrate, homocysteine, and palmitate were the microbial metabolites showing strongest interactions with COPD-associated host genes. Our meta-analysis uncovered functional properties of airway microbiome that interacted with COPD host gene signatures, and demonstrated the possibility of leveraging public multi-omic data to interrogate disease biology.
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http://dx.doi.org/10.1038/s41396-020-0727-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7784873PMC
November 2020

The sputum microbiome is distinct between COPD and health, independent of smoking history.

Respir Res 2020 Jul 14;21(1):183. Epub 2020 Jul 14.

Institute for Lung Health, NIHR, BRC, Department of Respiratory Sciences, College of Life Sciences, University of Leicester, Leicester, LE1 7RH, UK.

Background: Airway bacterial dysbiosis is a feature of chronic obstructive pulmonary disease (COPD). However, there is limited comparative data of the lung microbiome between healthy smokers, non-smokers and COPD.

Methods: We compared the 16S rRNA gene-based sputum microbiome generated from pair-ended Illumina sequencing of 124 healthy subjects (28 smokers and 96 non-smokers with normal lung function), with single stable samples from 218 COPD subjects collected from three UK clinical centres as part of the COPDMAP consortium.

Results: In healthy subjects Firmicutes, Bacteroidetes and Actinobacteria were the major phyla constituting 88% of the total reads, and Streptococcus, Veillonella, Prevotella, Actinomyces and Rothia were the dominant genera. Haemophilus formed only 3% of the healthy microbiome. In contrast, Proteobacteria was the most dominant phylum accounting for 50% of the microbiome in COPD subjects, with Haemophilus and Moraxella at genus level contributing 25 and 3% respectively. There were no differences in the microbiome profile within healthy and COPD subgroups when stratified based on smoking history. Principal coordinate analysis on operational taxonomic units showed two distinct clusters, representative of healthy and COPD subjects (PERMANOVA, p = 0·001).

Conclusion: The healthy and COPD sputum microbiomes are distinct and independent of smoking history. Our results underline the important role for Gammaproteobacteria in COPD.
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http://dx.doi.org/10.1186/s12931-020-01448-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362436PMC
July 2020

Microbiome Metabolite Mimics Accelerate Drug Discovery.

Trends Mol Med 2020 05 3;26(5):435-437. Epub 2020 Apr 3.

Computational Biology, Human Genetics, GlaxoSmithKline R&D, Collegeville, PA, USA. Electronic address:

A recent study by Dvořák et al. supports metabolite mimicry as a drug development strategy. A potent agonist of the human pregnane X receptor (hPXR) was designed from two ligands that are products of the microbial catabolism of tryptophan. Its validity was demonstrated in cellular assays and a murine colitis model expressing hPXR by a significant reduction in inflammation biomarkers.
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http://dx.doi.org/10.1016/j.molmed.2020.03.006DOI Listing
May 2020

Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients.

Nat Commun 2019 12 13;10(1):5711. Epub 2019 Dec 13.

Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.

In order to improve targeted therapeutic approaches for asthma patients, insights into the molecular mechanisms that differentially contribute to disease phenotypes, such as obese asthmatics or severe asthmatics, are required. Here we report immunological and microbiome alterations in obese asthmatics (n = 50, mean age = 45), non-obese asthmatics (n = 53, mean age = 40), obese non-asthmatics (n = 51, mean age = 44) and their healthy counterparts (n = 48, mean age = 39). Obesity is associated with elevated proinflammatory signatures, which are enhanced in the presence of asthma. Similarly, obesity or asthma induced changes in the composition of the microbiota, while an additive effect is observed in obese asthma patients. Asthma disease severity is negatively correlated with fecal Akkermansia muciniphila levels. Administration of A. muciniphila to murine models significantly reduces airway hyper-reactivity and airway inflammation. Changes in immunological processes and microbiota composition are accentuated in obese asthma patients due to the additive effects of both disease states, while A. muciniphila may play a non-redundant role in patients with a severe asthma phenotype.
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http://dx.doi.org/10.1038/s41467-019-13751-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911092PMC
December 2019

Activity and Microbiological Efficacy of Gepotidacin from a Phase 2, Randomized, Multicenter, Dose-Ranging Study in Patients with Acute Bacterial Skin and Skin Structure Infections.

Antimicrob Agents Chemother 2020 02 21;64(3). Epub 2020 Feb 21.

Medicine Opportunities Research Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA.

A phase 2 study of gepotidacin demonstrated the safety and efficacy of 3 gepotidacin doses (750 mg every 12 h [q12h], 1,000 mg q12h, and 1,000 mg every 8 h [q8h]) in hospitalized patients with suspected/confirmed Gram-positive acute bacterial skin and skin structure infections (ABSSSIs). Evaluating microbiology outcomes and responses were secondary endpoints. Pretreatment isolates recovered from infected lesions underwent susceptibility testing per Clinical and Laboratory Standards Institute guidelines. accounted for 78/102 (76%) of Gram-positive isolates; 54/78 (69%) were methicillin-resistant (MRSA), and 24/78 (31%) were methicillin-susceptible (MSSA). Posttherapy microbiological success (culture-confirmed eradication of the pretreatment pathogen or presumed eradication based on a clinical outcome of success) for was 90% for the gepotidacin 750-mg q12h group, 89% for the 1,000-mg q12h, and 73% in the 1000-mg q8h group. For 78 isolates obtained from pretreatment lesions, gepotidacin MIC/MIC values were 0.25/0.5 μg/ml against both MRSA and MSSA. Isolates recovered from the few patients with posttreatment cultures showed no significant reduction in gepotidacin susceptibility (≥4-fold MIC increase) between pretreatment and posttreatment isolates. Two of the 78 isolates from pretreatment lesions had elevated gepotidacin MICs and had mutations known to occur in quinolone-resistant (GyrA S84L, ParC S80Y, and ParE D422E) or to confer elevated MICs to novel bacterial topoisomerase inhibitors (GyrA D83N, both isolates; ParC V67A, one isolate). This first report of microbiological outcomes and responses of gepotidacin in patients with ABSSSIs supports further evaluation of gepotidacin as a novel first-in-class antibacterial agent. (This study has been registered at ClinicalTrials.gov under identifier NCT02045797.).
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http://dx.doi.org/10.1128/AAC.01302-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038298PMC
February 2020

The Microbiome Factor in Drug Discovery and Development.

Chem Res Toxicol 2020 01 23;33(1):119-124. Epub 2019 Dec 23.

Computational Biology, Human Genetics, R&D , GlaxoSmithKline , Mail Stop UP12-200 1250 South Collegeville Road , Collegeville , Pennsylvania 19426-0989 , United States.

Here we review recent studies that illustrate three areas where the microbiome directly impacts drug development: (1) microbial effects on drug safety and efficacy, (2) the effects of drugs on causing collateral restructuring of microbiome communities, and (3) the potential side-effects of novel therapies targeting the microbiome. On the basis of the findings of these and other studies, we advocate the systematic incorporation of microbiome analyses in early to late stage clinical trials as a strategy to increase the overall success rate of the drug discovery and development process.
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http://dx.doi.org/10.1021/acs.chemrestox.9b00333DOI Listing
January 2020

Shared Molecular Signatures Across Neurodegenerative Diseases and Herpes Virus Infections Highlights Potential Mechanisms for Maladaptive Innate Immune Responses.

Sci Rep 2019 06 19;9(1):8795. Epub 2019 Jun 19.

Computational Biology, Human Genetics, Research and Development (R&D), GlaxoSmithKline (GSK), Collegeville, PA, 19426, USA.

Growing evidence suggests that peripheral factors to the brain driving neuro-inflammation could affect Alzheimer's Disease (AD) and Parkinson's Disease (PD) severity. Herpes simplex virus type 1 (HSV1) infection has been associated with AD while other related viruses, including cytomegalovirus (CMV), Epstein-Bar virus and human herpesvirus 6 (HHV6), are known to infect neurons. Here we compare gene expression profiles between AD or PD patients to those afflicted with herpes viral infections as to discover novel potential neuro-inflammation pathways. We found multiple significant differentially expressed genes (DEGs) shared between AD/PD and viral infections including SESN3 which has a genetic association for increased AD risk. Pathway enrichment analysis revealed viruses shared Oxidative Stress Defense System and LRRK2 pathways with AD and PD, respectively. We further processed our data to identify novel target and drug-repurposing opportunities including anti-inflammatory therapy, immune-modulators and cholinesterase inhibitors which could lead to new therapeutics paradigms for these neurodegenerative diseases.
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http://dx.doi.org/10.1038/s41598-019-45129-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584587PMC
June 2019

Airway host-microbiome interactions in chronic obstructive pulmonary disease.

Respir Res 2019 Jun 6;20(1):113. Epub 2019 Jun 6.

University of Manchester and University Hospital of South Manchester, Manchester, M23 9QZ, UK.

Background: Little is known about the interactions between the lung microbiome and host response in chronic obstructive pulmonary disease (COPD).

Methods: We performed a longitudinal 16S ribosomal RNA gene-based microbiome survey on 101 sputum samples from 16 healthy subjects and 43 COPD patients, along with characterization of host sputum transcriptome and proteome in COPD patients.

Results: Dysbiosis of sputum microbiome was observed with significantly increased relative abundance of Moraxella in COPD versus healthy subjects and during COPD exacerbations, and Haemophilus in COPD ex-smokers versus current smokers. Multivariate modeling on sputum microbiome, host transcriptome and proteome profiles revealed that significant associations between Moraxella and Haemophilus, host interferon and pro-inflammatory signaling pathways and neutrophilic inflammation predominated among airway host-microbiome interactions in COPD. While neutrophilia was positively correlated with Haemophilus, interferon signaling was more strongly linked to Moraxella. Moreover, while Haemophilus was significantly associated with host factors both in stable state and during exacerbations, Moraxella-associated host responses were primarily related to exacerbations.

Conclusions: Our study highlights a significant airway host-microbiome interplay associated with COPD inflammation and exacerbations. These findings indicate that Haemophilus and Moraxella influence different components of host immune response in COPD, and that novel therapeutic strategies should consider targeting these bacteria and their associated host pathways in COPD.
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http://dx.doi.org/10.1186/s12931-019-1085-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6555748PMC
June 2019

Left Off the Route: A Qualitative Examination of Urban Bus Drivers Wanting to be Players in the Bully Prevention Solution.

J Interpers Violence 2021 Apr 10;36(7-8):NP4271-NP4295. Epub 2018 Jul 10.

University of Wisconsin-Green Bay, USA.

Every school day millions of children board the bus from home and school oftentimes with 90 others including a bus driver. Perhaps not found in a bus drivers' job description are the details to monitor and respond to all suspected bullying behaviors. Being bullied can have long-term negative consequences for both bullies and victims. The school bus has been identified as a potential hot spot for student bullying, wherein bus drivers may see, hear, and respond to several types of bullying on a daily basis that often require support from school officials. However, a bus driver's ability to intercede effectively in cases of school bus bullying may be limited. This qualitative study used a nonprobability, purposeful sample to examine 18 urban African American school bus drivers' and bus attendants'experiences in addressing school bus bullying within the context of their riders and school officials. Using focus groups, a definition of school bullying was read aloud to provide context to six questions from a semistructured interview guide that related bus drivers' experiences in responding to acts of bullying. An interpretive phenomenology method was used throughout the data analysis process. Several key themes and practices emerged. Results suggest bus drivers' reports were mostly passified and not taken seriously. Furthermore, these bus drivers' experiences overwhelmingly reflected a lack of both being taken seriously and being included in decision making. This led to a key stakeholder: bus drivers, being left out of the process. From these drivers' interviews, a model was developed to illustrate their lived experiences from behind the wheel to working with the school in responding to bullying.
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http://dx.doi.org/10.1177/0886260518787204DOI Listing
April 2021

Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations.

Thorax 2018 05 31;73(5):422-430. Epub 2018 Jan 31.

Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.

Background: Alterations in the composition of the lung microbiome associated with adverse clinical outcomes, known as dysbiosis, have been implicated with disease severity and exacerbations in COPD.

Objective: To characterise longitudinal changes in the lung microbiome in the AERIS study (Acute Exacerbation and Respiratory InfectionS in COPD) and their relationship with associated COPD outcomes.

Methods: We surveyed 584 sputum samples from 101 patients with COPD to analyse the lung microbiome at both stable and exacerbation time points over 1 year using high-throughput sequencing of the 16S ribosomal RNA gene. We incorporated additional lung microbiology, blood markers and in-depth clinical assessments to classify COPD phenotypes.

Results: The stability of the lung microbiome over time was more likely to be decreased in exacerbations and within individuals with higher exacerbation frequencies. Analysis of exacerbation phenotypes using a Markov chain model revealed that bacterial and eosinophilic exacerbations were more likely to be repeated in subsequent exacerbations within a subject, whereas viral exacerbations were not more likely to be repeated. We also confirmed the association of bacterial genera, including and , with disease severity, exacerbation events and bronchiectasis.

Conclusions: Subtypes of COPD have distinct bacterial compositions and stabilities over time. Some exacerbation subtypes have non-random probabilities of repeating those subtypes in the future. This study provides insights pertaining to the identification of bacterial targets in the lung and biomarkers to classify COPD subtypes and to determine appropriate treatments for the patient.

Trial Registration Number: Results, NCT01360398.
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http://dx.doi.org/10.1136/thoraxjnl-2017-210408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909767PMC
May 2018

Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets.

BMC Syst Biol 2018 01 10;12(1). Epub 2018 Jan 10.

Computational Biology, Target Sciences, GlaxoSmithKline (GSK) R & D, Collegeville, PA, 19426, USA.

Background: With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors.

Results: Here we performed a statistical meta-analysis of human gene expression in response to both latent and active pulmonary tuberculosis infections from nine published datasets. We found 1655 genes that were significantly differentially expressed during active tuberculosis infection. In contrast, no gene was significant for latent tuberculosis. Pathway enrichment analysis identified 90 significant canonical human pathways, including several pathways more commonly related to non-infectious diseases such as the LRRK2 pathway in Parkinson's disease, and PD-1/PD-L1 signaling pathway important for new immuno-oncology therapies. The analysis of human genome-wide association studies datasets revealed tuberculosis-associated genetic variants proximal to several genes in major histocompatibility complex for antigen presentation. We propose several new targets and drug-repurposing opportunities including intravenous immunoglobulin, ion-channel blockers and cancer immuno-therapeutics for development as combination therapeutics with anti-mycobacterial agents.

Conclusions: Our meta-analysis provides novel insights into host genes and pathways important for tuberculosis and brings forth potential drug repurposing opportunities for host-directed therapies.
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http://dx.doi.org/10.1186/s12918-017-0524-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763539PMC
January 2018

Gut microbiome differences between metformin- and liraglutide-treated T2DM subjects.

Endocrinol Diabetes Metab 2018 Jan 28;1(1):e00009. Epub 2017 Dec 28.

Computational Biology Target Sciences GlaxoSmithKline Research and Development (R&D) Collegeville PA USA.

Introduction: Metformin and glucagon-like peptide-1 (GLP-1) agonists are widely used for treating type two diabetes mellitus (T2DM). While recent studies suggest these drugs might modify the gastrointestinal tract (GIT) microbiome, further confirmation is required from human clinical trials.

Materials And Methods: Here, we compare, in patients with T2DM, the effects of metformin (n=18 subjects) and liraglutide (n=19), a GLP-1 agonist, on their GIT microbiomes over a 42 day period (n=74 samples) using 16S ribosomal RNA (rRNA) sequencing.

Results: We found that these drugs had markedly different effects on the microbiome composition. At both baseline and Day 42, subjects taking metformin had a significant increase (Baseline adj. =.038, Day 42 adj. =.041) in the relative abundance of the bacterial genus , whereas liraglutide dosing is associated with a significant increase (Baseline adj. =.048, Day 42 adj. =.003) in the genus , a GIT bacteria positively associated with gut barrier homoeostasis. and relative abundances were also significantly associated with duration of subject diabetes (adj <.05). Specifically, there was a significantly higher abundance of in subjects with short and medium durations than those with long duration of diabetes.

Discussion: To our knowledge, this is the first report of GLP-1 agonist-associated changes in the human microbiome and its differentiating effects to metformin. Our study suggests that modulation of the GIT microbiome is a potentially important component in the mechanism of action of these drugs.
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http://dx.doi.org/10.1002/edm2.9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360918PMC
January 2018

Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study.

Thorax 2018 04 21;73(4):331-338. Epub 2017 Dec 21.

Computational Biology, Target Sciences, Research and Development (R&D), GlaxoSmithKline, Collegeville, Pennsylvania, USA.

Background: Recent studies suggest that lung microbiome dysbiosis, the disease associated disruption of the lung microbial community, might play a key role in chronic obstructive pulmonary disease (COPD) exacerbations. However, characterising temporal variability of the microbiome from large longitudinal COPD cohorts is needed to better understand this phenomenon.

Methods: We performed a 16S ribosomal RNA survey of microbiome on 716 sputum samples collected longitudinally at baseline and exacerbations from 281 subjects with COPD at three UK clinical centres as part of the COPDMAP consortium.

Results: The microbiome composition was similar among centres and between stable and exacerbations except for a small significant decrease of at exacerbations. The abundance of was negatively associated with bacterial alpha diversity. Microbiomes were distinct between exacerbations associated with bacteria versus eosinophilic airway inflammation. Dysbiosis at exacerbations, measured as significant within subject deviation of microbial composition relative to baseline, was present in 41% of exacerbations. Dysbiosis was associated with increased exacerbation severity indicated by a greater fall in forced expiratory volume in one second, forced vital capacity and a greater increase in CAT score, particularly in exacerbations with concurrent eosinophilic inflammation. There was a significant difference of temporal variability of microbial alpha and beta diversity among centres. The variation of beta diversity significantly decreased in those subjects with frequent historical exacerbations.

Conclusions: Microbial dysbiosis is a feature of some exacerbations and its presence, especially in concert with eosinophilic inflammation, is associated with more severe exacerbations indicated by a greater fall in lung function.

Trial Registration Number: Results, NCT01620645.
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http://dx.doi.org/10.1136/thoraxjnl-2017-210741DOI Listing
April 2018

Preparing Nursing and Social Work Students to Care for Patients in Acute Alcohol Withdrawal.

J Addict Nurs 2017 Jul/Sep;28(3):143-147

Sharon A. Gates, EdD, RN, CNS, School of Nursing, Indiana University. James R. Brown, PhD, MSW, LCSW, School of Social Work, Indiana University.

Alcohol and other drug abuse has become a national crisis with approximately 26% of general medical patients having alcohol-related problems. New nurses and social workers are often not prepared to care for patients with severe alcohol withdrawal symptoms because they lack experience in actual crisis situations. The purpose of this study was to prepare nursing and social work students to care for a patient undergoing an acute alcohol withdrawal process. Nine groups of 8-10 students participated in a 2.5-hour simulation event that included an alcohol withdrawal seizure, team meeting, and discharge of the patient. Students recognized the importance of all the professional roles and how each professional benefits patient care. Before the simulation, students thought they were prepared to care for patients experiencing alcohol withdrawal; however, the crisis of an alcohol seizure decreased the student's ability to perform skills and communicate effectively. These findings suggest that new nurses and social workers may not be prepared to care for the acute alcohol withdrawal patient.
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http://dx.doi.org/10.1097/JAN.0000000000000178DOI Listing
May 2018

SUMO Ligase Protein Inhibitor of Activated STAT1 (PIAS1) Is a Constituent Promyelocytic Leukemia Nuclear Body Protein That Contributes to the Intrinsic Antiviral Immune Response to Herpes Simplex Virus 1.

J Virol 2016 07 10;90(13):5939-5952. Epub 2016 Jun 10.

MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom

Unlabelled: Aspects of intrinsic antiviral immunity are mediated by promyelocytic leukemia nuclear body (PML-NB) constituent proteins. During herpesvirus infection, these antiviral proteins are independently recruited to nuclear domains that contain infecting viral genomes to cooperatively promote viral genome silencing. Central to the execution of this particular antiviral response is the small ubiquitin-like modifier (SUMO) signaling pathway. However, the participating SUMOylation enzymes are not fully characterized. We identify the SUMO ligase protein inhibitor of activated STAT1 (PIAS1) as a constituent PML-NB protein. We show that PIAS1 localizes at PML-NBs in a SUMO interaction motif (SIM)-dependent manner that requires SUMOylated or SUMOylation-competent PML. Following infection with herpes simplex virus 1 (HSV-1), PIAS1 is recruited to nuclear sites associated with viral genome entry in a SIM-dependent manner, consistent with the SIM-dependent recruitment mechanisms of other well-characterized PML-NB proteins. In contrast to that of Daxx and Sp100, however, the recruitment of PIAS1 is enhanced by PML. PIAS1 promotes the stable accumulation of SUMO1 at nuclear sites associated with HSV-1 genome entry, whereas the accumulation of other evaluated PML-NB proteins occurs independently of PIAS1. We show that PIAS1 cooperatively contributes to HSV-1 restriction through mechanisms that are additive to those of PML and cooperative with those of PIAS4. The antiviral mechanisms of PIAS1 are counteracted by ICP0, the HSV-1 SUMO-targeted ubiquitin ligase, which disrupts the recruitment of PIAS1 to nuclear domains that contain infecting HSV-1 genomes through mechanisms that do not directly result in PIAS1 degradation.

Importance: Adaptive, innate, and intrinsic immunity cooperatively and efficiently restrict the propagation of viral pathogens. Intrinsic immunity mediated by constitutively expressed cellular proteins represents the first line of intracellular defense against infection. PML-NB constituent proteins mediate aspects of intrinsic immunity to restrict herpes simplex virus 1 (HSV-1) as well as other viruses. These proteins repress viral replication through mechanisms that rely on SUMO signaling. However, the participating SUMOylation enzymes are not known. We identify the SUMO ligase PIAS1 as a constituent PML-NB antiviral protein. This finding distinguishes a SUMO ligase that may mediate signaling events important in PML-NB-mediated intrinsic immunity. Moreover, this research complements the recent identification of PIAS4 as an intrinsic antiviral factor, supporting a role for PIAS proteins as both positive and negative regulators of host immunity to virus infection.
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http://dx.doi.org/10.1128/JVI.00426-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907222PMC
July 2016

Novel Role for Protein Inhibitor of Activated STAT 4 (PIAS4) in the Restriction of Herpes Simplex Virus 1 by the Cellular Intrinsic Antiviral Immune Response.

J Virol 2016 May 14;90(9):4807-4826. Epub 2016 Apr 14.

MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland, United Kingdom

Unlabelled: Small ubiquitin-like modifier (SUMO) is used by the intrinsic antiviral immune response to restrict viral pathogens, such as herpes simplex virus 1 (HSV-1). Despite characterization of the host factors that rely on SUMOylation to exert their antiviral effects, the enzymes that mediate these SUMOylation events remain to be defined. We show that unconjugated SUMO levels are largely maintained throughout infection regardless of the presence of ICP0, the HSV-1 SUMO-targeted ubiquitin ligase. Moreover, in the absence of ICP0, high-molecular-weight SUMO-conjugated proteins do not accumulate if HSV-1 DNA does not replicate. These data highlight the continued importance for SUMO signaling throughout infection. We show that the SUMO ligase protein inhibitor of activated STAT 4 (PIAS4) is upregulated during HSV-1 infection and localizes to nuclear domains that contain viral DNA. PIAS4 is recruited to sites associated with HSV-1 genome entry through SUMO interaction motif (SIM)-dependent mechanisms that are destabilized by ICP0. In contrast, PIAS4 accumulates in replication compartments through SIM-independent mechanisms irrespective of ICP0 expression. Depletion of PIAS4 enhances the replication of ICP0-null mutant HSV-1, which is susceptible to restriction by the intrinsic antiviral immune response. The mechanisms of PIAS4-mediated restriction are synergistic with the restriction mechanisms of a characterized intrinsic antiviral factor, promyelocytic leukemia protein, and are antagonized by ICP0. We provide the first evidence that PIAS4 is an intrinsic antiviral factor. This novel role for PIAS4 in intrinsic antiviral immunity contrasts with the known roles of PIAS proteins as suppressors of innate immunity.

Importance: Posttranslational modifications with small ubiquitin-like modifier (SUMO) proteins regulate multiple aspects of host immunity and viral replication. The protein inhibitor of activated STAT (PIAS) family of SUMO ligases is predominantly associated with the suppression of innate immune signaling. We now identify a unique and contrasting role for PIAS proteins as positive regulators of the intrinsic antiviral immune response to herpes simplex virus 1 (HSV-1) infection. We show that PIAS4 relocalizes to nuclear domains that contain viral DNA throughout infection. Depletion of PIAS4, either alone or in combination with the intrinsic antiviral factor promyelocytic leukemia protein, significantly impairs the intrinsic antiviral immune response to HSV-1 infection. Our data reveal a novel and dynamic role for PIAS4 in the cellular-mediated restriction of herpesviruses and establish a new functional role for the PIAS family of SUMO ligases in the intrinsic antiviral immune response to DNA virus infection.
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http://dx.doi.org/10.1128/JVI.03055-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836348PMC
May 2016

Lung microbiome dynamics in COPD exacerbations.

Eur Respir J 2016 Apr 25;47(4):1082-92. Epub 2016 Feb 25.

Computational Biology, Target Sciences, GSK R&D, Collegeville, PA, USA Both authors contributed equally.

Increasing evidence suggests that the lung microbiome plays an important role in chronic obstructive pulmonary disease (COPD) severity. However, the dynamics of the lung microbiome during COPD exacerbations and its potential role in disease aetiology remain poorly understood.We completed a longitudinal 16S ribosomal RNA survey of the lung microbiome on 476 sputum samples collected from 87 subjects with COPD at four visits defined as stable state, exacerbation, 2 weeks post-therapy and 6 weeks recovery.Our analysis revealed a dynamic lung microbiota where changes appeared to be associated with exacerbation events and indicative of specific exacerbation phenotypes. Antibiotic and steroid treatments appear to have differential effects on the lung microbiome. We depict a microbial interaction network for the lung microbiome and suggest that perturbation of a few bacterial operational taxonomic units, in particular Haemophilus spp., could greatly impact the overall microbial community structure. Furthermore, several serum and sputum biomarkers, in particular sputum interleukin-8, appear to be highly correlated with the structure and diversity of the microbiome.Our study furthers the understanding of lung microbiome dynamics in COPD patients and highlights its potential as a biomarker, and possibly a target, for future respiratory therapeutics.
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http://dx.doi.org/10.1183/13993003.01406-2015DOI Listing
April 2016

Human microbial metabolites as a source of new drugs.

Drug Discov Today 2016 Apr 22;21(4):692-8. Epub 2016 Feb 22.

Computational Biology, Target Sciences, R&D, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA 19426-0989, USA. Electronic address:

Crosstalk between the microbiome and the human host is mediated by specific ligand-receptor interactions involving microbially generated metabolites that can be either agonists or antagonists of human proteins. The evolved co-compatibility of gut microbiota with human systems points to a potentially rich area for discovering new drug-like molecules that are both highly specific modulators of human pathways and derisked for adverse effects. In this review, we discuss the rapidly growing research into the role of microbial metabolites in human health and suggest potential strategies for developing these molecules into therapeutic agents.
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http://dx.doi.org/10.1016/j.drudis.2016.02.009DOI Listing
April 2016

Orthogonal intercellular signaling for programmed spatial behavior.

Mol Syst Biol 2016 Jan 25;12(1):849. Epub 2016 Jan 25.

Department of Plant Sciences, University of Cambridge, Cambridge, UK

Bidirectional intercellular signaling is an essential feature of multicellular organisms, and the engineering of complex biological systems will require multiple pathways for intercellular signaling with minimal crosstalk. Natural quorum-sensing systems provide components for cell communication, but their use is often constrained by signal crosstalk. We have established new orthogonal systems for cell-cell communication using acyl homoserine lactone signaling systems. Quantitative measurements in contexts of differing receiver protein expression allowed us to separate different types of crosstalk between 3-oxo-C6- and 3-oxo-C12-homoserine lactones, cognate receiver proteins, and DNA promoters. Mutating promoter sequences minimized interactions with heterologous receiver proteins. We used experimental data to parameterize a computational model for signal crosstalk and to estimate the effect of receiver protein levels on signal crosstalk. We used this model to predict optimal expression levels for receiver proteins, to create an effective two-channel cell communication device. Establishment of a novel spatial assay allowed measurement of interactions between geometrically constrained cell populations via these diffusible signals. We built relay devices capable of long-range signal propagation mediated by cycles of signal induction, communication and response by discrete cell populations. This work demonstrates the ability to systematically reduce crosstalk within intercellular signaling systems and to use these systems to engineer complex spatiotemporal patterning in cell populations.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731010PMC
http://dx.doi.org/10.15252/msb.20156590DOI Listing
January 2016

Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models.

PLoS One 2015 28;10(12):e0145499. Epub 2015 Dec 28.

Computational Biology, Target Sciences, Research and Development, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America.

The gastrointestinal tract microbiome has been suggested as a potential therapeutic target for metabolic diseases such as obesity and Type 2 diabetes mellitus (T2DM). However, the relationship between changes in microbial communities and metabolic disease-phenotypes are still poorly understood. In this study, we used antibiotics with markedly different antibacterial spectra to modulate the gut microbiome in a diet-induced obesity mouse model and then measured relevant biochemical, hormonal and phenotypic biomarkers of obesity and T2DM. Mice fed a high-fat diet were treated with either ceftazidime (a primarily anti-Gram negative bacteria antibiotic) or vancomycin (mainly anti-Gram positive bacteria activity) in an escalating three-dose regimen. We also dosed animals with a well-known prebiotic weight-loss supplement, 10% oligofructose saccharide (10% OFS). Vancomycin treated mice showed little weight change and no improvement in glycemic control while ceftazidime and 10% OFS treatments induced significant weight loss. However, only ceftazidime showed significant, dose dependent improvement in key metabolic variables including glucose, insulin, protein tyrosine tyrosine (PYY) and glucagon-like peptide-1 (GLP-1). Subsequently, we confirmed the positive hyperglycemic control effects of ceftazidime in the Zucker diabetic fatty (ZDF) rat model. Metagenomic DNA sequencing of bacterial 16S rRNA gene regions V1-V3 showed that the microbiomes of ceftazidime dosed mice and rats were enriched for the phylum Firmicutes while 10% OFS treated mice had a greater abundance of Bacteroidetes. We show that specific changes in microbial community composition are associated with obesity and glycemic control phenotypes. More broadly, our study suggests that in vivo modulation of the microbiome warrants further investigation as a potential therapeutic strategy for metabolic diseases.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145499PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692534PMC
July 2016

Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery.

PLoS One 2015 7;10(12):e0142293. Epub 2015 Dec 7.

Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain.

As a follow up to the antimycobacterial screening exercise and the release of GSK´s first Tres Cantos Antimycobacterial Set (TCAMS-TB), this paper presents the results of a second antitubercular screening effort of two hundred and fifty thousand compounds recently added to the GSK collection. The compounds were further prioritized based on not only antitubercular potency but also on physicochemical characteristics. The 50 most attractive compounds were then progressed for evaluation in three different predictive computational biology algorithms based on structural similarity or GSK historical biological assay data in order to determine their possible mechanisms of action. This effort has resulted in the identification of novel compounds and their hypothesized targets that will hopefully fuel future TB drug discovery and target validation programs alike.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142293PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671658PMC
June 2016

Characterization of Intrinsic Properties of Promoters.

ACS Synth Biol 2016 Jan 7;5(1):89-98. Epub 2016 Jan 7.

Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge CB2 3EA, United Kingdom.

Accurate characterization of promoter behavior is essential for the rational design of functional synthetic transcription networks such as logic gates and oscillators. However, transcription rates observed from promoters can vary significantly depending on the growth rate of host cells and the experimental and genetic contexts of the measurement. Furthermore, in vivo measurement methods must accommodate variation in translation, protein folding, and maturation rates of reporter proteins, as well as metabolic load. The external factors affecting transcription activity may be considered to be extrinsic, and the goal of characterization should be to obtain quantitative measures of the intrinsic characteristics of promoters. We have developed a promoter characterization method that is based on a mathematical model for cell growth and reporter gene expression and exploits multiple in vivo measurements to compensate for variation due to extrinsic factors. First, we used optical density and fluorescent reporter gene measurements to account for the effect of differing cell growth rates. Second, we compared the output of reporter genes to that of a control promoter using concurrent dual-channel fluorescence measurements. This allowed us to derive a quantitative promoter characteristic (ρ) that provides a robust measure of the intrinsic properties of a promoter, relative to the control. We imposed different extrinsic factors on growing cells, altering carbon source and adding bacteriostatic agents, and demonstrated that the use of ρ values reduced the fraction of variance due to extrinsic factors from 78% to less than 4%. This is a simple and reliable method to quantitatively describe promoter properties.
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http://dx.doi.org/10.1021/acssynbio.5b00116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5023225PMC
January 2016

New compound sets identified from high throughput phenotypic screening against three kinetoplastid parasites: an open resource.

Sci Rep 2015 Mar 5;5:8771. Epub 2015 Mar 5.

Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain.

Using whole-cell phenotypic assays, the GlaxoSmithKline high-throughput screening (HTS) diversity set of 1.8 million compounds was screened against the three kinetoplastids most relevant to human disease, i.e. Leishmania donovani, Trypanosoma cruzi and Trypanosoma brucei. Secondary confirmatory and orthogonal intracellular anti-parasiticidal assays were conducted, and the potential for non-specific cytotoxicity determined. Hit compounds were chemically clustered and triaged for desirable physicochemical properties. The hypothetical biological target space covered by these diversity sets was investigated through bioinformatics methodologies. Consequently, three anti-kinetoplastid chemical boxes of ~200 compounds each were assembled. Functional analyses of these compounds suggest a wide array of potential modes of action against kinetoplastid kinases, proteases and cytochromes as well as potential host-pathogen targets. This is the first published parallel high throughput screening of a pharma compound collection against kinetoplastids. The compound sets are provided as an open resource for future lead discovery programs, and to address important research questions.
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http://dx.doi.org/10.1038/srep08771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350103PMC
March 2015

Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase.

Antimicrob Agents Chemother 2015 Feb 8;59(2):1182-92. Epub 2014 Dec 8.

Computational Biology, GSK R&D, Collegeville, Pennsylvania, USA

GSK1322322 is a novel antibacterial agent under development, and it has known antibacterial activities against multidrug-resistant respiratory and skin pathogens through its inhibition of the bacterial peptide deformylase. Here, we used next-generation sequencing (NGS) of the bacterial 16S rRNA genes from stool samples collected from 61 healthy volunteers at the predosing and end-of-study time points to determine the effects of GSK1322322 on the gastrointestinal (GI) microbiota in a phase I, randomized, double-blind, and placebo-controlled study. GSK1322322 was administered either intravenously (i.v.) only or in an oral-i.v. combination in single- and repeat-dose-escalation infusions. Analysis of the 16S rRNA sequence data found no significant changes in the relative abundances of GI operational taxonomic units (OTUs) between the prestudy and end-of-study samples for either the placebo- or i.v.-only-treated subjects. However, oral-i.v. treatment resulted in significant decreases in some bacterial taxa, the Firmicutes and Bacteroidales, and increases in others, the Betaproteobacteria, Gammaproteobacteria, and Bifidobacteriaceae. Microbiome diversity plots clearly differentiated the end-of-study oral-i.v.-dosed samples from all others collected. The changes in genome function as inferred from species composition suggest an increase in bacterial transporter and xenobiotic metabolism pathways in these samples. A phylogenetic analysis of the peptide deformylase protein sequences collected from the published genomes of clinical isolates previously tested for GSK1322322 in vitro susceptibility and GI bacterial reference genomes suggests that antibiotic target homology is one of several factors that influences the response of GI microbiota to this antibiotic. Our study shows that dosing regimen and target class are important factors when considering the impact of antibiotic usage on GI microbiota. (This clinical trial was registered at the GlaxoSmithKline Clinical Study Register under study identifier PDF 113376.).
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http://dx.doi.org/10.1128/AAC.04506-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335841PMC
February 2015

Bacterial resistance to leucyl-tRNA synthetase inhibitor GSK2251052 develops during treatment of complicated urinary tract infections.

Antimicrob Agents Chemother 2015 Jan 27;59(1):289-98. Epub 2014 Oct 27.

Computational Biology, Quantitative Sciences, GlaxoSmithKline R&D, Collegeville, Pennsylvania, USA

GSK2251052, a novel leucyl-tRNA synthetase (LeuRS) inhibitor, was in development for the treatment of infections caused by multidrug-resistant Gram-negative pathogens. In a phase II study (study LRS114688) evaluating the efficacy of GSK2251052 in complicated urinary tract infections, resistance developed very rapidly in 3 of 14 subjects enrolled, with ≥32-fold increases in the GSK2251052 MIC of the infecting pathogen being detected. A fourth subject did not exhibit the development of resistance in the baseline pathogen but posttherapy did present with a different pathogen resistant to GSK2251052. Whole-genome DNA sequencing of Escherichia coli isolates collected longitudinally from two study LRS114688 subjects confirmed that GSK2251052 resistance was due to specific mutations, selected on the first day of therapy, in the LeuRS editing domain. Phylogenetic analysis strongly suggested that resistant Escherichia coli isolates resulted from clonal expansion of baseline susceptible strains. This resistance development likely resulted from the confluence of multiple factors, of which only some can be assessed preclinically. Our study shows the challenges of developing antibiotics and the importance of clinical studies to evaluate their effect on disease pathogenesis. (These studies have been registered at ClinicalTrials.gov under registration no. NCT01381549 for the study of complicated urinary tract infections and registration no. NCT01381562 for the study of complicated intra-abdominal infections.).
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http://dx.doi.org/10.1128/AAC.03774-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291364PMC
January 2015

Use of a 3D printed hollow aortic model to assist EVAR planning in a case with complex neck anatomy: potential of 3D printing to improve patient outcome.

J Endovasc Ther 2014 Oct;21(5):760-2

Departments of 1Radiology and 3Surgery, Southend University Hospital NHS Foundation Trust, Westcliff on Sea, UK 2Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford, UK,

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http://dx.doi.org/10.1583/14-4810L.1DOI Listing
October 2014

No association found between the detection of either xenotropic murine leukemia virus-related virus or polytropic murine leukemia virus and chronic fatigue syndrome in a blinded, multi-site, prospective study by the establishment and use of the SolveCFS BioBank.

BMC Res Notes 2014 Aug 4;7:461. Epub 2014 Aug 4.

Division of Infectious Diseases, GlaxoSmithKline, Research Triangle Park, NC, USA.

Background: In 2009, a retrospective study reported the detection of xenotropic murine leukemia virus-related virus (XMRV) in clinical isolates derived from individuals with chronic fatigue syndrome or myalgic encephalomyelitis (CFS). While many efforts to confirm this observation failed, one report detected polytropic murine leukemia virus (pMLV), instead of XMRV. In both studies, Polymerase Chain Reaction (PCR)-based methods were employed which could provide the basis for the development of a practical diagnostic tool. To confirm these studies, we hypothesized that the ability to detect these viruses will not only depend upon the technical details of the methods employed but also on the criteria used to diagnose CFS and the availability of well characterized clinical isolates.

Methods: A repository of clinical isolates from geographically distinct sites was generated by the collection of fresh blood samples from well characterized CFS and healthy subjects. Molecular techniques were used to generate assay positive controls and to determine the lower limit of detection (LLOD) for murine retroviral and Intracisternal A particle (Cell 12(4):963-72, 1977) detection methods.

Results: We report the establishment of a repository of well-defined, clinical isolates from five, geographically distinct regions of the US, the comparative determination of the LLODs and validation efforts for the previously reported detection methods and the results of an effort to confirm the association of these retroviral signatures in isolates from individuals with CFS in a blinded, multi-site, prospective study. We detected various, murine retroviral DNA signatures but were unable to resolve a difference in the incidence of their detection between isolates from CFS (5/72; 6.7%) and healthy (2/37; 5.4%) subjects (Fisher's Exact Test, p-value = 1). The observed sequences appeared to reflect the detection of endogenous murine retroviral DNA, which was not identical to either XMRV or pMLV.

Conclusions: We were unable to confirm a previously reported association between the detection of XMRV or pMLV sequences and CFS in a prospective, multi-site study. Murine retroviral sequences were detected at a low frequency that did not differ between CFS and control subjects. The nature of these sequences appeared to reflect the detection of pre-existing, endogenous, murine retroviral DNA in the PCR reagents employed.
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http://dx.doi.org/10.1186/1756-0500-7-461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236736PMC
August 2014