Peter Ghazal

The University of Edinburgh, Edinburgh, Scotland, United Kingdom

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Publications (203)1063.32 Total impact

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    ABSTRACT: Interferons (IFNs) play a central role in immunity and emerging evidence suggests that IFN-signalling coordinately regulates sterol biosynthesis in macrophages, via Sterol Regulatory Element-Binding Protein (SREBP) dependent and independent pathways. However, the precise mechanisms and kinetic steps by which IFN controls sterol biosynthesis are as yet not fully understood. Here, we elucidate the molecular circuitry governing how IFN controls the first regulated step in the mevalonate-sterol pathway, 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), through the synthesis of 25-Hydroxycholesterol (25-HC) from cholesterol by the IFN-inducible Cholesterol-25-Hydroxylase (CH25H). We show for the first 30-minutes of IFN stimulation the rate of de novo synthesis of the Ch25h transcript is markedly increased but by 120-minutes becomes transcriptionally curtailed, coincident with induction of the Activating Transcription Factor 3 (ATF3) repressor. We demonstrate ATF3 induction by Toll-like receptors is strictly dependent on IFN-signalling. While the SREBP-pathway dependent rates of de novo transcription of Hmgcr are relatively unchanged in the first 90-minutes of IFN treatment, HMGCR enzyme levels undergo a rapid proteasomal-mediated degradation, defining a previously unappreciated SREBP-independent mechanism for IFN-action. These events precede a sustained marked reduction in Hmgcr RNA levels involving SREBP-dependent mechanisms. We demonstrate that HMGCR proteasomal-degradation by IFN strictly requires the synthesis of endogenous 25-HC and functionally couples HMGCR to CH25H to coordinately suppress sterol biosynthesis. In conclusion, we quantitatively delineate proteomic and transcriptional levels of IFN-mediated control of HMGCR, the primary enzymatic step of the mevalonate-sterol biosynthesis pathway, providing a foundational framework for mathematically modelling the therapeutic outcome of immune-metabolic pathways. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Steroids 03/2015; 21. DOI:10.1016/j.steroids.2015.02.022 · 2.72 Impact Factor
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    ABSTRACT: Neonatal sepsis Whole blood Gene expression profiling Microarray Neonatal infection remains a primary cause of infant morbidity and mortality worldwide and yet our understand-ing of how human neonates respond to infection remains incomplete. Changes in host gene expression in response to infection may occur in any part of the body, with the continuous interaction between blood and tissues allowing blood cells to act as biosensors for the changes. In this study we have used whole blood tran-scriptome profiling to systematically identify signatures and the pathway biology underlying the pathogenesis of neonatal infection. Blood samples were collected from neonates at the first clinical signs of suspected sepsis alongside age matched healthy control subjects. Here we report a detailed description of the study design, includ-ing clinical data collected, experimental methods used and data analysis workflows and which correspond with data in Gene Expression Omnibus (GEO) data sets (GSE25504). Our data set has allowed identification of a patient invariant 52-gene classifier that predicts bacterial infection with high accuracy and lays the foundation for advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis. Specifications Organism/cell line/tissue Homo sapiens/whole blood Sex Male and female (continued) Specifications Sequencer or array type Illumina HT-12V3.0 Whole Human Genome microarray, CodeLink 55K Whole Human Genome microarray, Affymetrix U219 Whole Human Genome microarray and Affymetrix HG U133 Plus 2.0 Whole Human Genome microarray Data format Raw data (Tab delimited text files of background subtracted signals and .CEL files) Experimental factors Blood culture or cerebrospinal fluid positive bacterial sepsis vs. healthy control whole blood samples and culture negative suspected infected samples Experimental features A case–control gene expression profiling study of whole blood taken from neonates at the first clinical sign of sepsis and control healthy neonates. Study includes training and replication sets for blood culture positive samples and clinical evaluation set of blood culture negative sepsis cases. Results compared blood culture or cerebrospinal fluid positive septic neonates, blood culture negative septic neonates and healthy control neonates. Prior power calculations were based on Healthy Edinburgh neonates using the CodeLink platform and Gambian infants (9 months of age) were used for further refinement of power calculations using Illumina HT-12 platform. article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).
    03/2015; 3:41-48. DOI:10.1016/j.gdata.2014.11.003
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    ABSTRACT: CD200 receptor (CD200R) negatively regulates peripheral and mucosal innate immune responses. Viruses, including herpesviruses, have acquired functional CD200 orthologs, implying that viral exploitation of this pathway is evolutionary advantageous. However, the role that CD200R signaling plays during herpesvirus infection in vivo requires clarification. Utilizing the murine cytomegalovirus (MCMV) model, we demonstrate that CD200R facilitates virus persistence within mucosal tissue. Specifically, MCMV infection of CD200R-deficient mice (CD200R-/-) elicited heightened mucosal virus-specific CD4 T cell responses that restricted virus persistence in the salivary glands. CD200R did not directly inhibit lymphocyte effector function. Instead, CD200R-/- mice exhibited enhanced APC accumulation that in the mucosa was a consequence of elevated cellular proliferation. Although MCMV does not encode an obvious CD200 homolog, productive replication in macrophages induced expression of cellular CD200. CD200 from hematopoietic and non-hematopoietic cells contributed independently to suppression of antiviral control in vivo. These results highlight the CD200-CD200R pathway as an important regulator of antiviral immunity during cytomegalovirus infection that is exploited by MCMV to establish chronicity within mucosal tissue.
    PLoS Pathogens 02/2015; 11(2):e1004641. DOI:10.1371/journal.ppat.1004641 · 8.06 Impact Factor
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    ABSTRACT: The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing “Big Data” – the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of “divide and conquer” for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using “virtual partitioning”. HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples.
    Journal of Biomedical Informatics 01/2015; DOI:10.1016/j.jbi.2015.01.008 · 2.48 Impact Factor
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    ABSTRACT: Herein, we report the draft genome sequence for isolate ED-NGS-1015 of Serratia marcescens, cultivated from a blood sample obtained from a neonatal sepsis patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.
    Genome Announcements 09/2014; 2(5). DOI:10.1128/genomeA.00908-14
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    ABSTRACT: Herein, we report the draft genome sequence of Staphylococcus warneri ED-NGS-1001, cultivated from a blood sample taken from a preterm neonate blood sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
    Genome Announcements 09/2014; 2(5). DOI:10.1128/genomeA.00877-14
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    ABSTRACT: Herein, we report the draft genome sequence of Staphylococcus aureus ED-NGS-1006, cultivated from a blood sample taken from a neonatal sepsis patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.
    Genome Announcements 09/2014; 2(5). DOI:10.1128/genomeA.00906-14
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    ABSTRACT: Herein, we report the draft genome sequence of Enterococcus faecalis ED-NGS-1009, cultivated from a blood sample taken from a neonatal sepsis patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.
    Genome Announcements 09/2014; 2(5). DOI:10.1128/genomeA.00907-14
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    ABSTRACT: Herein, we report the draft genome sequence of Streptococcus agalactiae ED-NGS-1000, cultivated from a blood sample taken from a preterm neonate blood sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
    Genome Announcements 09/2014; 2(5). DOI:10.1128/genomeA.00875-14
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    ABSTRACT: Herein, we report the draft genome sequence of Pantoea sp. ED-NGS-1003, cultivated from a blood sample taken from a neonatal sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
    Genome Announcements 09/2014; 2(5). DOI:10.1128/genomeA.00904-14
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    ABSTRACT: Understanding how human neonates respond to infection remains incomplete. Here, a system-level investigation of neonatal systemic responses to infection shows a surprisingly strong but unbalanced homeostatic immune response; developing an elevated set-point of myeloid regulatory signalling and sugar-lipid metabolism with concomitant inhibition of lymphoid responses. Innate immune-negative feedback opposes innate immune activation while suppression of T-cell co-stimulation is coincident with selective upregulation of CD85 co-inhibitory pathways. By deriving modules of co-expressed RNAs, we identify a limited set of networks associated with bacterial infection that exhibit high levels of inter-patient variability. Whereas, by integrating immune and metabolic pathways, we infer a patient-invariant 52-gene-classifier that predicts bacterial infection with high accuracy using a new independent patient population. This is further shown to have predictive value in identifying infection in suspected cases with blood culture-negative tests. Our results lay the foundation for future translation of host pathways in advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis.
    Nature Communications 08/2014; 5:4649. DOI:10.1038/ncomms5649 · 10.74 Impact Factor
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    ABSTRACT: Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics.
    PLoS ONE 06/2014; 9(6):e98431. DOI:10.1371/journal.pone.0098431 · 3.53 Impact Factor
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    ABSTRACT: The statistical language R is favoured by many biostatisticians for processing microarray data. In recent times, the quantity of data that can be obtained in experiments has risen significantly, making previously fast analyses time consuming or even not possible at all with the existing software infrastructure. High performance computing (HPC) systems offer a solution to these problems but at the expense of increased complexity for the end user. The Simple Parallel R Interface is a library for R that aims to reduce the complexity of using HPC systems by providing biostatisticians with drop-in parallelised replacements of existing R functions. In this paper we describe parallel implementations of two popular techniques: exploratory clustering analyses using the random forest classifier and feature selection through identification of differentially expressed genes using the rank product method.
    Concurrency and Computation Practice and Experience 03/2014; 26(4). DOI:10.1002/cpe.2928 · 0.85 Impact Factor
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    Kai A Kropp, Ana Angulo, Peter Ghazal
    PLoS Pathogens 02/2014; 10(2):e1003804. DOI:10.1371/journal.ppat.1003804 · 8.06 Impact Factor
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    ABSTRACT: Bootstrapping is a popular and computationally demanding resampling method used for measuring the accuracy of sample estimates and assisting with statistical inference. R is a freely available language and environment for statistical computing popular with biostatisticians for genomic data analyses. A survey of such R users highlighted its implementation of bootstrapping as a prime candidate for parallelization to overcome computational bottlenecks. The Simple Parallel R Interface (SPRINT) is a package that allows R users to exploit high performance computing in multi-core desktops and supercomputers without expert knowledge of such systems. This paper describes the parallelization of bootstrapping for inclusion in the SPRINT R package. Depending on the complexity of the bootstrap statistic and the number of resamples, this implementation has close to optimal speed up on up to 16 nodes of a supercomputer and close to 100 on 512 nodes. This performance in a multi-node setting compares favourably with an existing parallelization option in the native R implementation of bootstrapping.
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    ABSTRACT: An MRSA assay requiring neither labeling nor amplification of target DNA has been developed. Sequence specific binding of fragments of bacterial genomic DNA is detected at femtomolar concentrations using electrochemical impedance spectroscopy (EIS). This has been achieved using systematic optimisation of probe chemistry (PNA self-assembled monolayer film on gold electrode), electrode film structure (the size and nature of the chemical spacer) and DNA fragmentation, as these are found to play an important role in assay performance. These sensitivity improvements allow the elimination of the PCR step and DNA labeling and facilitate the development of a simple and rapid point of care test for MRSA. Assay performance is then evaluated and specific direct detection of the MRSA diagnostic mecA gene from genomic DNA, extracted directly from bacteria without further treatment is demonstrated for bacteria spiked into saline (10(6) cells per mL) on gold macrodisc electrodes and into human wound fluid (10(4) cells per mL) on screen printed gold electrodes. The latter detection level is particularly relevant to clinical requirements and point of care testing where the general threshold for considering a wound to be infected is 10(5) cells per mL. By eliminating the PCR step typically employed in nucleic acid assays, using screen printed electrodes and achieving sequence specific discrimination under ambient conditions, the test is extremely simple to design and engineer. In combination with a time to result of a few minutes this means the assay is well placed for use in point of care testing.
    The Analyst 10/2013; DOI:10.1039/c3an01319g · 3.91 Impact Factor
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    ABSTRACT: Uterine NK cells (uNK) play a role in the regulation of placentation, but their functions in nonpregnant endometrium are not understood. We have previously reported suppression of endometrial bleeding and alteration of spiral artery morphology in women exposed to asoprisnil, a progesterone receptor modulator. We now compare global endometrial gene expression in asoprisnil-treated versus control women, and we demonstrate a statistically significant reduction of genes in the IL-15 pathway, known to play a key role in uNK development and function. Suppression of IL-15 by asoprisnil was also observed at mRNA level (p < 0.05), and immunostaining for NK cell marker CD56 revealed a striking reduction of uNK in asoprisnil-treated endometrium (p < 0.001). IL-15 levels in normal endometrium are progesterone-responsive. Progesterone receptor (PR) positive stromal cells transcribe both IL-15 and IL-15RA. Thus, the response of stromal cells to progesterone will be to increase IL-15 trans-presentation to uNK, supporting their expansion and differentiation. In asoprisnil-treated endometrium, there is a marked downregulation of stromal PR expression and virtual absence of uNK. These novel findings indicate that the IL-15 pathway provides a missing link in the complex interplay among endometrial stromal cells, uNK, and spiral arteries affecting physiologic and pathologic endometrial bleeding.
    The Journal of Immunology 08/2013; 191(5). DOI:10.4049/jimmunol.1300958 · 5.36 Impact Factor
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    ABSTRACT: Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome.
    PLoS Pathogens 08/2013; 9(8):e1003514. DOI:10.1371/journal.ppat.1003514 · 8.06 Impact Factor
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    ABSTRACT: Interferons (IFN) play a pivotal role in innate immunity, orchestrating a cell-intrinsic anti-pathogenic state and stimulating adaptive immune responses. The complex interplay between the primary response to IFNs and its modulation by positive and negative feedback loops is incompletely understood. Here, we implement the combination of high-resolution gene-expression profiling of nascent RNA with translational inhibition of secondary feedback by cycloheximide. Unexpectedly, this approach revealed a prominent role of negative feedback mechanisms during the immediate (≤60 min) IFNα response. In contrast, a more complex picture involving both negative and positive feedback loops was observed on IFNγ treatment. IFNγ-induced repression of genes associated with regulation of gene expression, cellular development, apoptosis and cell growth resulted from cycloheximide-resistant primary IFNγ signalling. In silico promoter analysis revealed significant overrepresentation of SP1/SP3-binding sites and/or GC-rich stretches. Although signal transducer and activator of transcription 1 (STAT1)-binding sites were not overrepresented, repression was lost in absence of STAT1. Interestingly, basal expression of the majority of these IFNγ-repressed genes was dependent on STAT1 in IFN-naïve fibroblasts. Finally, IFNγ-mediated repression was also found to be evident in primary murine macrophages. IFN-repressed genes include negative regulators of innate and stress response, and their decrease may thus aid the establishment of a signalling perceptive milieu.
    Nucleic Acids Research 07/2013; DOI:10.1093/nar/gkt589 · 8.81 Impact Factor

Publication Stats

6k Citations
1,063.32 Total Impact Points

Institutions

  • 2001–2015
    • The University of Edinburgh
      • • Centre for Synthetic and Systems Biology (SynthSys)
      • • Division of Pathway Medicine
      Edinburgh, Scotland, United Kingdom
  • 2012
    • University of Exeter
      Exeter, England, United Kingdom
  • 2011
    • University of Barcelona
      • Department of Cell Biology, Immunology and Neurosciences
      Barcino, Catalonia, Spain
    • University of Rijeka
      • Department of Histology and Embryology
      Vitipolis, Primorsko-Goranska, Croatia
  • 2006–2011
    • IDIBAPS August Pi i Sunyer Biomedical Research Institute
      Barcino, Catalonia, Spain
  • 2010
    • King's College London
      • Department of Biostatistics
      London, ENG, United Kingdom
  • 2008–2009
    • University of Strathclyde
      • Department of Electronic and Electrical Engineering (EEE)
      Glasgow, SCT, United Kingdom
    • Royal Veterinary College
      Londinium, England, United Kingdom
  • 2003–2007
    • Biomathematics and Statistics Scotland
      Edinburgh, Scotland, United Kingdom
  • 2002–2006
    • University of California, Irvine
      • Department of Molecular Biology and Biochemistry
      Irvine, CA, United States
  • 2005
    • Plymouth Marine Laboratory
      Plymouth, England, United Kingdom
    • University of Glasgow
      Glasgow, Scotland, United Kingdom
  • 1992–2005
    • The Scripps Research Institute
      • Department of Immunology and Microbial Science
      La Jolla, California, United States
  • 2004
    • La Jolla Institute for Allergy & Immunology
      La Jolla, California, United States
  • 1998–2003
    • Ludwig-Maximilian-University of Munich
      • Max-von-Pettenkofer Institute for Hygiene and Medical Microbiology
      München, Bavaria, Germany
  • 2000
    • Max von Pettenkofer-Institut
      München, Bavaria, Germany
  • 1993–1996
    • Oregon Health and Science University
      • • Department of Medicine
      • • Department of Molecular Microbiology & Immunology
      Portland, OR, United States
  • 1990
    • Eastern Virginia Medical School
      Norfolk, Virginia, United States
  • 1988
    • The National Institute of Diabetes and Digestive and Kidney Diseases
      Maryland, United States