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Parmar R, Pickering H, Ahn R, Rossetti M, Gjertson DW, Ruffin F, Chan LC, Fowler VG, Yeaman MR, Reed EF. Integrated transcriptomic analysis reveals immune signatures distinguishing persistent versus resolving outcomes in MRSA bacteremia. Front Immunol 2024; 15:1373553. [PMID: 38846955 PMCID: PMC11153731 DOI: 10.3389/fimmu.2024.1373553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/02/2024] [Indexed: 06/09/2024] Open
Abstract
Introduction Staphylococcus aureus bacteremia (SAB) is a life-threatening infection particularly involving methicillin-resistant S. aureus (MRSA). In contrast to resolving MRSA bacteremia (RB), persistent MRSA bacteremia (PB) blood cultures remain positive despite appropriate antibiotic treatment. Host immune responses distinguishing PB vs. RB outcomes are poorly understood. Here, integrated transcriptomic, IL-10 cytokine levels, and genomic analyses sought to identify signatures differentiating PB vs. RB outcomes. Methods Whole-blood transcriptomes of propensity-matched PB (n=28) versus RB (n=30) patients treated with vancomycin were compared in one independent training patient cohort. Gene expression (GE) modules were analyzed and prioritized relative to host IL-10 cytokine levels and DNA methyltransferase-3A (DNMT3A) genotype. Results Differential expression of T and B lymphocyte gene expression early in MRSA bacteremia discriminated RB from PB outcomes. Significant increases in effector T and B cell signaling pathways correlated with RB, lower IL-10 cytokine levels and DNMT3A heterozygous A/C genotype. Importantly, a second PB and RB patient cohort analyzed in a masked manner demonstrated high predictive accuracy of differential signatures. Discussion Collectively, the present findings indicate that human PB involves dysregulated immunity characterized by impaired T and B cell responses associated with excessive IL-10 expression in context of the DNMT3A A/A genotype. These findings reveal distinct immunologic programs in PB vs. RB outcomes, enable future studies to define mechanisms by which host and/or pathogen drive differential signatures and may accelerate prediction of PB outcomes. Such prognostic assessment of host risk could significantly enhance early anti-infective interventions to avert PB and improve patient outcomes.
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Affiliation(s)
- Rajesh Parmar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Harry Pickering
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Richard Ahn
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
| | - Maura Rossetti
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - David W. Gjertson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Felicia Ruffin
- Division of Infectious Diseases, Duke University, Durham, NC, United States
| | - Liana C. Chan
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
- Divisions of Molecular Medicine and Infectious Diseases, Los Angeles County Harbor-UCLA Medical Center, Torrance, CA, United States
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Vance G. Fowler
- Division of Infectious Diseases, Duke University, Durham, NC, United States
| | - Michael R. Yeaman
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
- Divisions of Molecular Medicine and Infectious Diseases, Los Angeles County Harbor-UCLA Medical Center, Torrance, CA, United States
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Elaine F. Reed
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
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Corrêa RDS, Leal-Calvo T, Mafort TT, Santos AP, Leung J, Pinheiro RO, Rufino R, Moraes MO, Rodrigues LS. Reanalysis and validation of the transcriptional pleural fluid signature in pleural tuberculosis. Front Immunol 2024; 14:1256558. [PMID: 38288122 PMCID: PMC10822927 DOI: 10.3389/fimmu.2023.1256558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Pleural tuberculosis (PlTB), the most common site of extrapulmonary TB, is characterized by a paucibacillary nature and a compartmentalized inflammatory response in the pleural cavity, both of which make diagnosis and management extremely challenging. Although transcriptional signatures for pulmonary TB have already been described, data obtained by using this approach for extrapulmonary tuberculosis and, specifically, for pleural tuberculosis are scarce and heterogeneous. In the present study, a set of candidate genes previously described in pulmonary TB was evaluated to identify and validate a transcriptional signature in clinical samples from a Brazilian cohort of PlTB patients and those with other exudative causes of pleural effusion. Methods As a first step, target genes were selected by a random forest algorithm with recursive feature elimination (RFE) from public microarray datasets. Then, peripheral blood (PB) and pleural fluid (PF) samples from recruited patients presenting exudative pleural effusion were collected during the thoracentesis procedure. Transcriptional analysis of the selected top 10 genes was performed by quantitative RT-PCR (RT-qPCR). Results Reanalysis of the public datasets identified a set of candidate genes (CARD17, BHLHE40, FCGR1A, BATF2, STAT1, BTN3A1, ANKRD22, C1QB, GBP2, and SEPTIN4) that demonstrated a global accuracy of 89.5% in discriminating pulmonary TB cases from other respiratory diseases. Our validation cohort consisted of PlTB (n = 35) patients and non-TB (n = 34) ones. The gene expressions of CARD17, GBP2, and C1QB in PF at diagnosis were significantly different between the two (PlTB and non-TB) groups (p < 0.0001). It was observed that the gene expressions of CARD17 and GBP2 were higher in PlTB PF than in non-TB patients. C1QB showed the opposite behavior, being higher in the non-TB PF. After anti-TB therapy, however, GBP2 gene expression was significantly reduced in PlTB patients (p < 0.001). Finally, the accuracy of the three above-cited highlighted genes in the PF was analyzed, showing AUCs of 91%, 90%, and 85%, respectively. GBP2 was above 80% (sensitivity = 0.89/specificity = 0.81), and CARD17 showed significant specificity (Se = 0.69/Sp = 0.95) in its capacity to discriminate the groups. Conclusion CARD17, GBP2, and C1QB showed promise in discriminating PlTB from other causes of exudative pleural effusion by providing accurate diagnoses, thus accelerating the initiation of anti-TB therapy.
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Affiliation(s)
- Raquel da Silva Corrêa
- Laboratory of Immunopathology, Medical Sciences Faculty, Rio de Janeiro State University (FCM/UERJ), Rio de Janeiro, Brazil
| | - Thyago Leal-Calvo
- Laboratory of Leprosy, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Thiago Thomaz Mafort
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Ana Paula Santos
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Janaína Leung
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Roberta Olmo Pinheiro
- Laboratory of Leprosy, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Rogério Rufino
- Department of Pulmonary Care, Pedro Ernesto University Hospital, Rio de Janeiro State University (HUPE/UERJ), Rio de Janeiro, Brazil
| | - Milton Ozório Moraes
- Laboratory of Leprosy, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Luciana Silva Rodrigues
- Laboratory of Immunopathology, Medical Sciences Faculty, Rio de Janeiro State University (FCM/UERJ), Rio de Janeiro, Brazil
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Banerji R, Joshi R, Saroj SD. Acyl Homoserine Lactone Sensitised Streptococcus Pyogenes Differentially Regulates the Transcriptional Expression of Early Growth Response 1 (EGR1) in Epithelial and Macrophage Cells. Curr Microbiol 2023; 80:268. [PMID: 37402084 DOI: 10.1007/s00284-023-03375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/14/2023] [Indexed: 07/05/2023]
Abstract
The host transcriptional activator Early growth response 1 (EGR1) plays a vital role in cell cycle and differentiation, cell proliferation, and regulation of cytokines and several growth factors. It is an immediate-early gene that is expressed as an initial response to various environmental stimuli. Bacterial infection is one such factor that can trigger the expression of EGR1 in host. Therefore, it is imperative to understand expression of EGR1 during early stages of host-pathogen interaction. Streptococcus pyogenes is an opportunistic bacteria causing skin and respiratory tract infections in humans. The quorum-sensing molecule, N-(3-oxododecanoyl)-l-homoserine lactone (Oxo-C12), not synthesised by S. pyogenes, can be sensed by S. pyogenes leading to molecular changes in the pathogen. In this study, we investigated the role of Oxo-C12 on EGR1 regulation in lung epithelial and murine macrophage cell line upon S. pyogenes infection. We report that Oxo-C12 sensitised S. pyogenes upregulates the transcriptional expression of EGR1 through ERK1/2 pathway. It was observed that EGR1 was not involved in the intial attachment of S. pyogenes to A549 cells. However, inhibition of EGR1 in macrophage cell line, J774A.1, through the ERK1/2 pathway resulted in decreased adhesion of S. pyogenes. The EGR1 upregulation by Oxo-C12 sensitised S. pyogenes plays a vital role in enhancing the survival of S. pyogenes in murine macrophages, leading to persistent infection. Thus, understanding the molecular modulation in the host during bacterial infection will further help develop therapeutics to target specific sites.
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Affiliation(s)
- Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Maharashtra, 412115, Pune, India
| | - Riya Joshi
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Maharashtra, 412115, Pune, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Maharashtra, 412115, Pune, India.
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4
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Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. NATURE COMPUTATIONAL SCIENCE 2023; 3:644-657. [PMID: 37974651 PMCID: PMC10653299 DOI: 10.1038/s43588-023-00476-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/06/2023] [Indexed: 11/19/2023]
Abstract
Resolving chromatin-remodeling-linked gene expression changes at cell-type resolution is important for understanding disease states. Here we describe MAGICAL (Multiome Accessibility Gene Integration Calling and Looping), a hierarchical Bayesian approach that leverages paired single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single-cell data that we generated from subjects with bloodstream infection and uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be activated by bacterial sepsis. We addressed the challenging problem of distinguishing host regulatory circuit responses to methicillin-resistant and methicillin-susceptible S. aureus infections. Although differential expression analysis failed to show predictive value, MAGICAL identified epigenetic circuit biomarkers that distinguished methicillin-resistant from methicillin-susceptible S. aureus infections.
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Affiliation(s)
- Xi Chen
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yuan Wang
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wan-Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aliza B. Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alicja Tadych
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Chandra L. Theesfeld
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexandria Vornholt
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Felicia Ruffin
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Michael Dagher
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Daniel G. Chawla
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | | | | | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven H. Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Christopher W. Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
| | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
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5
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Oruganti S, Rodrigues PRS, White D, Watkins WJ, Shapey S, Barrow A, Al Samsam R, Ali S, Gajraj M, Skone R, Jardine M, Evans J, Struik S, Song JE, Abood L, Paquete B, Foulkes S, Saunders B, Strang A, Kotecha SJ, Phillips B, Evans A, Buchanan I, Bowes S, Ali B, Gore M, Thomas-Turner R, Andrews R, Zaher S, Sharma S, Chakraborty M, Parkinson E, Liberatore F, Woolley T, Edkins S, Davies LC, Moet L, McLaren JE, Watson GL, O'Donnell V, Hood K, Ghazal P. Immune and metabolic markers for identifying and investigating severe Coronavirus disease and Sepsis in children and young people (pSeP/COVID ChYP study): protocol for a prospective cohort study. BMJ Open 2023; 13:e067002. [PMID: 36972964 PMCID: PMC10069273 DOI: 10.1136/bmjopen-2022-067002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
INTRODUCTION Early recognition and appropriate management of paediatric sepsis are known to improve outcomes. A previous system's biology investigation of the systemic immune response in neonates to sepsis identified immune and metabolic markers that showed high accuracy for detecting bacterial infection. Further gene expression markers have also been reported previously in the paediatric age group for discriminating sepsis from control cases. More recently, specific gene signatures were identified to discriminate between COVID-19 and its associated inflammatory sequelae. Through the current prospective cohort study, we aim to evaluate immune and metabolic blood markers which discriminate between sepses (including COVID-19) from other acute illnesses in critically unwell children and young persons, up to 18 years of age. METHODS AND ANALYSIS We describe a prospective cohort study for comparing the immune and metabolic whole-blood markers in patients with sepsis, COVID-19 and other illnesses. Clinical phenotyping and blood culture test results will provide a reference standard to evaluate the performance of blood markers from the research sample analysis. Serial sampling of whole blood (50 μL each) will be collected from children admitted to intensive care and with an acute illness to follow time dependent changes in biomarkers. An integrated lipidomics and RNASeq transcriptomics analyses will be conducted to evaluate immune-metabolic networks that discriminate sepsis and COVID-19 from other acute illnesses. This study received approval for deferred consent. ETHICS AND DISSEMINATION The study has received research ethics committee approval from the Yorkshire and Humber Leeds West Research Ethics Committee 2 (reference 20/YH/0214; IRAS reference 250612). Submission of study results for publication will involve making available all anonymised primary and processed data on public repository sites. TRIAL REGISTRATION NUMBER NCT04904523.
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Affiliation(s)
- Sivakumar Oruganti
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | - Daniel White
- School of Medicine, Cardiff University, Cardiff, UK
| | - William John Watkins
- Cochrane Institute of Primary Care and Public Health, Cardiff University, Cardiff, UK
| | - Selyf Shapey
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Anna Barrow
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Rim Al Samsam
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Sara Ali
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Malcolm Gajraj
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Richard Skone
- Department of Paediatric Intensive Care, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Michelle Jardine
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Jennifer Evans
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Siske Struik
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Jong Eun Song
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | - Barbara Paquete
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Sian Foulkes
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Benjamin Saunders
- Infectious Diseases services for Wales, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | | | - Bethan Phillips
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Awen Evans
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Iona Buchanan
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Susan Bowes
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Begum Ali
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Maya Gore
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Rhian Thomas-Turner
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | | | - Summia Zaher
- Department of Obstetrics and Gynaecology, University Hospital of Wales, Cardiff, UK
| | - Simran Sharma
- Infection and Immunity, Cardiff University, Cardiff, UK
- Women's Unit, Cardiff and Vale NHS Trust, Cardiff, UK
| | | | | | | | | | - Sarah Edkins
- School of Medicine, Cardiff University, Cardiff, UK
| | | | - Linda Moet
- School of Medicine, Cardiff University, Cardiff, UK
| | | | | | - Valerie O'Donnell
- Centre for Trials Research, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Kerry Hood
- Centre for Trials Research, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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6
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Rao AM, Popper SJ, Gupta S, Davong V, Vaidya K, Chanthongthip A, Dittrich S, Robinson MT, Vongsouvath M, Mayxay M, Nawtaisong P, Karmacharya B, Thair SA, Bogoch I, Sweeney TE, Newton PN, Andrews JR, Relman DA, Khatri P. A robust host-response-based signature distinguishes bacterial and viral infections across diverse global populations. Cell Rep Med 2022; 3:100842. [PMID: 36543117 PMCID: PMC9797950 DOI: 10.1016/j.xcrm.2022.100842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
Limited sensitivity and specificity of current diagnostics lead to the erroneous prescription of antibiotics. Host-response-based diagnostics could address these challenges. However, using 4,200 samples across 69 blood transcriptome datasets from 20 countries from patients with bacterial or viral infections representing a broad spectrum of biological, clinical, and technical heterogeneity, we show current host-response-based gene signatures have lower accuracy to distinguish intracellular bacterial infections from viral infections than extracellular bacterial infections. Using these 69 datasets, we identify an 8-gene signature to distinguish intracellular or extracellular bacterial infections from viral infections with an area under the receiver operating characteristic curve (AUROC) > 0.91 (85.9% specificity and 90.2% sensitivity). In prospective cohorts from Nepal and Laos, the 8-gene classifier distinguished bacterial infections from viral infections with an AUROC of 0.94 (87.9% specificity and 91% sensitivity). The 8-gene signature meets the target product profile proposed by the World Health Organization and others for distinguishing bacterial and viral infections.
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Affiliation(s)
- Aditya M. Rao
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Immunology Graduate Program, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen J. Popper
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Sanjana Gupta
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Krista Vaidya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Anisone Chanthongthip
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew T. Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Pruksa Nawtaisong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Biraj Karmacharya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Simone A. Thair
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Isaac Bogoch
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David A. Relman
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA,Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA,Corresponding author
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7
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Beesetty P, Si Y, Li Z, Yang C, Zhao F, Chong AS, Montgomery CP. Tissue specificity drives protective immunity against Staphylococcus aureus infection. Front Immunol 2022; 13:795792. [PMID: 35983063 PMCID: PMC9380724 DOI: 10.3389/fimmu.2022.795792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Infections caused by Staphylococcus aureus range from mild to severe and frequently recur. Emerging evidence suggests that the site and severity of infection drive the potency of elicited immune responses and susceptibility to recurrent infection. In this study, we used tractable mouse models of S. aureus skin infection (SSTI) and pneumonia to determine the relative magnitude of elicited protective immunity. Surprisingly, despite both SSTI and pneumonia eliciting antibody and local effector T cell responses, only SSTI elicited protective antibody and memory T cell responses and subsequent protection against secondary SSTI and pneumonia. The failure of pneumonia to elicit protective immunity was attributed to an inability of S. aureus pneumonia to elicit toxin-specific antibodies that confer protection during secondary infection and was associated with a failure to expand antigen-specific memory T cells. Taken together, these findings emphasize the importance of understanding protective immunity in the context of the tissue-specificity.
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Affiliation(s)
- Pavani Beesetty
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Youhui Si
- Department of Surgery, the University of Chicago, Chicago, IL, United States
| | - Zhaotao Li
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Ching Yang
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, United States
| | - Fan Zhao
- Department of Surgery, the University of Chicago, Chicago, IL, United States
| | - Anita S. Chong
- Department of Surgery, the University of Chicago, Chicago, IL, United States
| | - Christopher P. Montgomery
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States
- Division of Critical Care Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
- *Correspondence: Christopher P. Montgomery,
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8
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Shahzad M, Andrews SC, Ul-Haq Z. Exploring the role of Microbiome in Susceptibility, Treatment Response and Outcome among Tuberculosis Patients from Pakistan: study protocol for a prospective cohort study (Micro-STOP). BMJ Open 2022; 12:e058463. [PMID: 35672071 PMCID: PMC9174774 DOI: 10.1136/bmjopen-2021-058463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Tuberculosis (TB) caused by Mycobacterium tuberculosis is a common infectious disease associated with significant morbidity and mortality, especially in low-income and middle-income countries. Successful treatment of the disease requires prolonged intake (6-8 months) of multiple antibiotics with potentially detrimental consequences on the composition and functional potential of the human microbiome. The protocol described in the current study aims to identify microbiome (oral and gut) signatures associated with TB pathogenesis, treatment response and outcome in humans. METHODS AND ANALYSIS Four hundred and fifty, newly diagnosed patients with TB from three district levels (Peshawar, Mardan and Swat) TB diagnosis and treatment centres, will be recruited in this non-interventional, prospective cohort study and will be followed and monitored until treatment completion. Demographic and dietary intake data, anthropometric measurement and blood, stool and salivary rinse samples will be collected at baseline, day 15, month-2 and end of the treatment. Additionally, we will recruit age (±3 years) and sex-matched healthy controls (n=30). Blood sampling will allow monitoring of the immune response during the treatment, while salivary rinse and faecal samples will allow monitoring of dynamic changes in oral and gut microbiome diversity. Within this prospective cohort study, a nested case-control study design will be conducted to assess perturbations in oral and gut microbiome diversity (microbial dysbiosis) and immune response and compare between the patients groups (treatment success vs failure). ETHICS AND DISSEMINATION The study has received ethics approval from the Ethic Board of Khyber Medical University Peshawar, and administrative approval from Provincial TB Control Programme of Khyber Pakhtunkhwa, Pakistan. The study results will be presented in national and international conferences and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER NCT04985994.
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Affiliation(s)
- Muhammad Shahzad
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
- School of Biological Sciences, University of Reading, Reading, UK
| | - Simon C Andrews
- School of Biological Sciences, University of Reading, Reading, UK
| | - Zia Ul-Haq
- Institute of Public Health & Social Sciences, Khyber Medical University, Peshawar, Pakistan
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9
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Li Z, Beesetty P, Gerges G, Kleinhenz M, Moore-Clingenpeel M, Yang C, Ahmed LB, Hensley J, Steele L, Chong AS, Montgomery CP. Impaired T lymphocyte responses during childhood Staphylococcus aureus infection. J Infect Dis 2021; 225:177-185. [PMID: 34145461 DOI: 10.1093/infdis/jiab326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Staphylococcus aureus infections are common throughout the lifespan, with recurrent infections occuring in nearly half of infected children. There is no licensed vaccine, underscoring the need to better understand how S. aureus evades protective immunity. Despite much study, the relative contributions of antibodies and T cells to protection against S. aureus infections in humans are not fully understood. METHODS We prospectively quantified S. aureus-specific antibody levels by ELISA and T cell responses by ELISpot in S. aureus-infected and healthy children. RESULTS S. aureus-specific antibody levels and T cell responses increased with age in healthy children, suggesting a coordinated development of anti-staphylococcal immunity. Antibody levels against leukotoxin E (LukE) and Panton-Valentine leukocidin (LukS-PV), but not α-hemolysin (Hla), were higher in younger infected children, compared with healthy children; these differences disappeared in older children. We observed a striking impairment of global and S. aureus-specific T cell function in children with invasive and non-invasive infection, suggesting that S. aureus-specific immune responses are dysregulated during childhood infection regardless of the infection phenotype. CONCLUSIONS These findings identify a potential mechanism by which S. aureus infection actively evades adaptive immune responses, thereby preventing the development of protective immunty and maintaining susceptibility to recurrent infection.
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Affiliation(s)
- Zhaotao Li
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Pavani Beesetty
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - George Gerges
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Maureen Kleinhenz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Ching Yang
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Luul B Ahmed
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Josey Hensley
- Division of Critical Care Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Lisa Steele
- Division of Critical Care Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Anita S Chong
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Christopher P Montgomery
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Division of Critical Care Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, USA
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10
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Chen CW, Bennion KB, Swift DA, Morrow KN, Zhang W, Oami T, Coopersmith CM, Ford ML. Tumor-Specific T Cells Exacerbate Mortality and Immune Dysregulation during Sepsis. THE JOURNAL OF IMMUNOLOGY 2021; 206:2412-2419. [PMID: 33911005 DOI: 10.4049/jimmunol.2000865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/08/2021] [Indexed: 11/19/2022]
Abstract
Sepsis induces significant immune dysregulation characterized by lymphocyte apoptosis and alterations in the cytokine milieu. Because cancer patients exhibit a 10-fold greater risk of developing sepsis compared with the general population, we aimed to understand how pre-existing malignancy alters sepsis-induced immune dysregulation. To address this question, we assessed the impact of tumor-specific CD8+ T cells on the immune response in a mouse model of cecal ligation and puncture (CLP)-induced sepsis. Tumor-bearing animals containing Thy1.1+ tumor-specific CD8+ T cells were subjected to CLP, and groups of animals received anti-Thy1.1 mAb to deplete tumor-specific CD8+ T cells or isotype control. Results indicated that depleting tumor-specific T cells significantly improved mortality from sepsis. The presence of tumor-specific CD8+ T cells resulted in increased expression of the 2B4 coinhibitory receptor and increased apoptosis of endogenous CD8+ T cells. Moreover, tumor-specific T cells were not reduced in number in the tumors during sepsis but did exhibit impaired IFN-γ production in the tumor, tumor draining lymph node, and spleen 24 h after CLP. Our research provides novel insight into the mechanisms by which pre-existing malignancy contributes to increased mortality during sepsis.
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Affiliation(s)
- Ching-Wen Chen
- Immunology and Molecular Pathogenesis Graduate Program, Laney Graduate School, Emory University, Atlanta, GA.,Department of Surgery, Emory University School of Medicine, Atlanta, GA
| | - Kelsey B Bennion
- Department of Surgery, Emory University School of Medicine, Atlanta, GA.,Cancer Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA
| | - David A Swift
- Department of Surgery, Emory University School of Medicine, Atlanta, GA
| | - Kristen N Morrow
- Immunology and Molecular Pathogenesis Graduate Program, Laney Graduate School, Emory University, Atlanta, GA.,Department of Surgery, Emory University School of Medicine, Atlanta, GA
| | - Wenxiao Zhang
- Department of Surgery, Emory University School of Medicine, Atlanta, GA.,Department of Critical Care Medicine, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Takehiko Oami
- Department of Surgery, Emory University School of Medicine, Atlanta, GA.,Department of Emergency and Critical Care Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Craig M Coopersmith
- Department of Surgery, Emory University School of Medicine, Atlanta, GA .,Emory Critical Care Center, Emory University School of Medicine, Atlanta, GA
| | - Mandy L Ford
- Department of Surgery, Emory University School of Medicine, Atlanta, GA .,Emory Transplant Center, Emory University School of Medicine, Atlanta, GA
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11
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Banerji R, Saroj SD. Early growth response 1 (EGR1) activation in initial stages of host-pathogen interactions. Mol Biol Rep 2021; 48:2935-2943. [PMID: 33783681 DOI: 10.1007/s11033-021-06305-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/19/2021] [Indexed: 12/11/2022]
Abstract
The factors that determine the outcomes of host-pathogen interactions, such as host specificity, tissue specificity, and transition from asymptomatic to symptomatic behavior of a pathogen, are yet to be deciphered. The initial interaction of a pathogen with host and host-associated factors play a crucial role in deciding such outcomes. One of the several host-factors that contribute to bacterial adhesion and the outcome of an infection is the activation of early growth response 1 (EGR1). EGR1 is an initial response transcriptional regulator that plays a vital role in regulating cell growth, differentiation, and survival. EGR1 expression is seen in most of the mammalian tissues. Multiple post-translational modifications occur, which modulate the EGR1 transcriptional activity. Upon activation, EGR1 can transactivate several genes with diverse cellular functions, including transcriptional regulatory proteins and cell proliferation. EGR1 has also been identified as a potential mediator of inflammatory gene expression. Recent studies have highlighted the role of EGR1 as a potent signaling molecule that facilitates bacterial adhesion to host epithelial cells, thus modulating colonization pathways. The pathways for the regulation of EGR1 during host-pathogen interaction remain yet unidentified. The review focuses on the role and regulation of EGR1 during host-pathogen interaction.
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Affiliation(s)
- Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Pune, Maharashtra, 412115, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Pune, Maharashtra, 412115, India.
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12
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Rinchai D, Roelands J, Toufiq M, Hendrickx W, Altman MC, Bedognetti D, Chaussabel D. BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R. Bioinformatics 2021; 37:2382-2389. [PMID: 33624743 PMCID: PMC8388021 DOI: 10.1093/bioinformatics/btab121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/14/2021] [Accepted: 02/23/2021] [Indexed: 11/28/2022] Open
Abstract
Motivation We previously described the construction and characterization of fixed reusable blood transcriptional module repertoires. More recently we released a third iteration (‘BloodGen3’ module repertoire) that comprises 382 functionally annotated modules and encompasses 14 168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here an R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability and implementation The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | | | - Matthew C Altman
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA.,Systems Immunology, Benaroya Research Institute, Seattle, Washington, USA
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13
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Wang Y, Lin Y, Cheng C, Chen P, Zhang P, Wu H, Li K, Deng Y, Qian J, Zhang X, Yu B. NF-κB/TWIST1 Mediates Migration and Phagocytosis of Macrophages in the Mice Model of Implant-Associated Staphylococcus aureus Osteomyelitis. Front Microbiol 2020; 11:1301. [PMID: 32595631 PMCID: PMC7304240 DOI: 10.3389/fmicb.2020.01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus (S. aureus) infection-induced osteomyelitis is a great challenge in clinic treatment. Identification of the essential genes and biological processes that are specifically changed in mononuclear cells at an early stage of S. aureus osteomyelitis is of great clinical significance. Based on transcriptional dataset GSE16129 available publicly, a bioinformatic analysis was performed to identify the differentially expressed genes of osteomyelitis caused by S. aureus infection. ERBB2, TWIST1, and NANOG were screened out as the most valuable osteomyelitis-related genes (OMRGs). A mice model of implant-associated S. aureus osteomyelitis was used to verify the above genes. We found significantly up-regulated expression of TWIST1 in macrophages and accumulation of macrophages around the infected implant. Meanwhile, S. aureus infection increased the expression of TWIST1, MMP9, and MMP13, and stimulated the migration and phagocytosis function of Raw 264.7 cells. Additionally, knock-down of the expression of TWIST1 by siRNA could significantly down-regulate MMP9 and MMP13 and suppress the migration and phagocytosis ability of macrophages in response to S. aureus infection. Furthermore, we found that NF-κB signaling was activated in Raw 264.7 cells by S. aureus and that inhibition of NF-κB signaling by Bay11-7082 blocked the expression of TWIST1, MMP9, and MMP13 as well as cell migration and phagocytosis evoked by S. aureus. Our findings demonstrate that NF-κB/TWIST1 is necessary for migration and phagocytosis of macrophages in response to S. aureus infection. Our study highlights the essential role of NF-κB/TWIST1 in early innate immune response to S. aureus infection in bone.
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Affiliation(s)
- Yutian Wang
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yihuang Lin
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Caiyu Cheng
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Pengyu Chen
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ping Zhang
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hangtian Wu
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kaiqun Li
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ye Deng
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jikun Qian
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xianrong Zhang
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bin Yu
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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14
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Cooper AM, Shope AJ, Javid M, Parsa A, Chinoy MA, Parvizi J. Musculoskeletal Infection in Pediatrics: Assessment of the 2018 International Consensus Meeting on Musculoskeletal Infection. J Bone Joint Surg Am 2019; 101:e133. [PMID: 31567692 DOI: 10.2106/jbjs.19.00572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Second International Consensus Meeting (ICM) on Musculoskeletal Infection was held in July 2018 in Philadelphia, Pennsylvania. This meeting involved contributions from an international multidisciplinary consortium of experts from orthopaedic surgery, infectious disease, pharmacology, rheumatology, microbiology, and others. Through strict delegate engagement in a comprehensive 13-step consensus process based on the Delphi technique, evidence-based consensus guidelines on musculoskeletal infection were developed. The 2018 ICM produced updates to recommendations from the inaugural ICM that was held in 2013, which primarily focused on periprosthetic infection of the hip and the knee, and added new guidelines with the expansion to encompass all subspecialties of orthopaedic surgery. The following proceedings from the pediatrics section are an overview of the ICM consensus recommendations on the prevention, diagnosis, and treatment of pediatric musculoskeletal infection.
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Affiliation(s)
- Alexus M Cooper
- Rothman Orthopaedic Institute at Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Alexander J Shope
- Rothman Orthopaedic Institute at Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Mahzad Javid
- Department of Orthopedic Surgery, Bone and Joint Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Parsa
- Hip Preservation Surgery Division, Department of Orthopedic Surgery, Massachusetts General Hospital at Harvard Medical School, Boston, Massachusetts.,Orthopedic Research Center, Department of Orthopedic Surgery, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Javad Parvizi
- Rothman Orthopaedic Institute at Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
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15
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Roelands J, Garand M, Hinchcliff E, Ma Y, Shah P, Toufiq M, Alfaki M, Hendrickx W, Boughorbel S, Rinchai D, Jazaeri A, Bedognetti D, Chaussabel D. Long-Chain Acyl-CoA Synthetase 1 Role in Sepsis and Immunity: Perspectives From a Parallel Review of Public Transcriptome Datasets and of the Literature. Front Immunol 2019; 10:2410. [PMID: 31681299 PMCID: PMC6813721 DOI: 10.3389/fimmu.2019.02410] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 09/26/2019] [Indexed: 12/21/2022] Open
Abstract
A potential role for the long-chain acyl-CoA synthetase family member 1 (ACSL1) in the immunobiology of sepsis was explored during a hands-on training workshop. Participants first assessed the robustness of the potential gap in biomedical knowledge identified via an initial screen of public transcriptome data and of the literature associated with ACSL1. Increase in ACSL1 transcript abundance during sepsis was confirmed in several independent datasets. Querying the ACSL1 literature also confirmed the absence of reports associating ACSL1 with sepsis. Inferences drawn from both the literature (via indirect associations) and public transcriptome data (via correlation) point to the likely participation of ACSL1 and ACSL4, another family member, in inflammasome activation in neutrophils during sepsis. Furthermore, available clinical data indicate that levels of ACSL1 and ACSL4 induction was significantly higher in fatal cases of sepsis. This denotes potential translational relevance and is consistent with involvement in pathways driving potentially deleterious systemic inflammation. Finally, while ACSL1 expression was induced in blood in vitro by a wide range of pathogen-derived factors as well as TNF, induction of ACSL4 appeared restricted to flagellated bacteria and pathogen-derived TLR5 agonists and IFNG. Taken together, this joint review of public literature and omics data records points to two members of the acyl-CoA synthetase family potentially playing a role in inflammasome activation in neutrophils. Translational relevance of these observations in the context of sepsis and other inflammatory conditions remain to be investigated.
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Affiliation(s)
- Jessica Roelands
- Sidra Medicine, Doha, Qatar.,Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | | | - Emily Hinchcliff
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ying Ma
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Parin Shah
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | | | | | | | - Amir Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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16
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Transketolase and vitamin B1 influence on ROS-dependent neutrophil extracellular traps (NETs) formation. PLoS One 2019; 14:e0221016. [PMID: 31415630 PMCID: PMC6695114 DOI: 10.1371/journal.pone.0221016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Neutrophil extracellular traps (NETs) are a recently identified, web-like, extracellular structure composed of decondensed nuclear DNA and associated antimicrobial granules. NETs are extruded into the extracellular environment via the reactive oxygen species (ROS)-dependent cell death pathway participating in inflammation and autoimmune diseases. Transketolase (TKT) is a thiamine pyrophosphate (vitamin B1)-dependent enzyme that links the pentose phosphate pathway with the glycolytic pathway by feeding excess sugar phosphates into the main carbohydrate metabolic pathways to generate biosynthetic reducing capacity in the form of NADPH as a substrate for ROS generation. In this work, TKT was selected as a lead candidate from 24 NET-associated proteins obtained by literature screening and knowledge gap assessment. Consequently, we determined whether TKT influenced NET formation in vitro. We firstly established that the release of ROS-dependent NETs was significantly decreased after purified human PMNs were pretreated with oxythiamine, a TKT inhibitor, and in a concentration dependent manner. As a cofactor for TKT reaction, we evaluated the release of NET formation either in vitamin B1 treatment or in combined use of oxythiamine and vitamin B1, and found that those treatments also exerted a significant suppressive effect on the amount of NET-DNA and ROS production. The regulation of TKT by oxythiamine and/or vitamin B1 may therefore be associated with response to the modulation of NET formation by preventing generation of excessive NETs in inflammatory diseases.
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17
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Hong S, Banchereau R, Maslow BSL, Guerra MM, Cardenas J, Baisch J, Branch DW, Porter TF, Sawitzke A, Laskin CA, Buyon JP, Merrill J, Sammaritano LR, Petri M, Gatewood E, Cepika AM, Ohouo M, Obermoser G, Anguiano E, Kim TW, Nulsen J, Nehar-Belaid D, Blankenship D, Turner J, Banchereau J, Salmon JE, Pascual V. Longitudinal profiling of human blood transcriptome in healthy and lupus pregnancy. J Exp Med 2019; 216:1154-1169. [PMID: 30962246 PMCID: PMC6504211 DOI: 10.1084/jem.20190185] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Healthy and uncomplicated lupus pregnancies exhibit early and sustained transcriptional modulation of lupus-related pathways. This might contribute to fetal tolerance while predisposing pregnant women to certain infections. Failure to modulate these pathways is associated with lupus pregnancy complications. Systemic lupus erythematosus carries an increased risk of pregnancy complications, including preeclampsia and fetal adverse outcomes. To identify the underlying molecular mechanisms, we longitudinally profiled the blood transcriptome of 92 lupus patients and 43 healthy women during pregnancy and postpartum and performed multicolor flow cytometry in a subset of them. We also profiled 25 healthy women undergoing assisted reproductive technology to monitor transcriptional changes around embryo implantation. Sustained down-regulation of multiple immune signatures, including interferon and plasma cells, was observed during healthy pregnancy. These changes appeared early after embryo implantation and were mirrored in uncomplicated lupus pregnancies. Patients with preeclampsia displayed early up-regulation of neutrophil signatures that correlated with expansion of immature neutrophils. Lupus pregnancies with fetal complications carried the highest interferon and plasma cell signatures as well as activated CD4+ T cell counts. Thus, blood immunomonitoring reveals that both healthy and uncomplicated lupus pregnancies exhibit early and sustained transcriptional modulation of lupus-related signatures, and a lack thereof associates with adverse outcomes.
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Affiliation(s)
- Seunghee Hong
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | - Romain Banchereau
- Baylor Institute for Immunology Research, Dallas, TX.,Oncology Biomarker Development, Genentech, South San Francisco, CA
| | | | - Marta M Guerra
- Department of Medicine and Program in Inflammation and Autoimmunity, Hospital for Special Surgery, New York, NY
| | | | - Jeanine Baisch
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | - D Ware Branch
- University of Utah Health Sciences Center, Salt Lake City, UT.,Intermountain Healthcare, Salt Lake City, UT
| | - T Flint Porter
- University of Utah Health Sciences Center, Salt Lake City, UT.,Intermountain Healthcare, Salt Lake City, UT
| | - Allen Sawitzke
- University of Utah Health Sciences Center, Salt Lake City, UT
| | - Carl A Laskin
- Mount Sinai Hospital and the University of Toronto, Toronto, Ontario, Canada
| | - Jill P Buyon
- New York University School of Medicine, New York, NY
| | - Joan Merrill
- Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Lisa R Sammaritano
- Department of Medicine and Program in Inflammation and Autoimmunity, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Michelle Petri
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - Marina Ohouo
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | | | | | - Tae Whan Kim
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | - John Nulsen
- University of Connecticut School of Medicine, Farmington, CT
| | | | | | - Jacob Turner
- Baylor Institute for Immunology Research, Dallas, TX
| | | | - Jane E Salmon
- Department of Medicine and Program in Inflammation and Autoimmunity, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Virginia Pascual
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
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18
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Kopp BT, Thompson R, Kim J, Konstan R, Diaz A, Smith B, Shrestha C, Rogers LK, Hayes D, Tumin D, Woodley FW, Ramilo O, Sanders DB, Groner JA, Mejias A. Secondhand smoke alters arachidonic acid metabolism and inflammation in infants and children with cystic fibrosis. Thorax 2019; 74:237-246. [PMID: 30661024 DOI: 10.1136/thoraxjnl-2018-211845] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 11/09/2018] [Accepted: 12/24/2018] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mechanisms that facilitate early infection and inflammation in cystic fibrosis (CF) are unclear. We previously demonstrated that children with CF and parental-reported secondhand smoke exposure (SHSe) have increased susceptibility to bacterial infections. SHSe hinders arachidonic acid (AA) metabolites that mediate immune function in patients without CF, and may influence CF immune dysfunction. We aimed to define SHSe's impact on inflammation mediators and infection in children with CF. METHODS Seventy-seven children with CF <10 years of age (35 infants <1 year; 42 children 1-10 years) were enrolled and hair nicotine concentrations measured as an objective surrogate of SHSe. AA signalling by serum and macrophage lipidomics, inflammation using blood transcriptional profiles and in vitro macrophage responses to bacterial infection after SHSe were assessed. RESULTS Hair nicotine concentrations were elevated in 63% of patients. Of the AA metabolites measured by plasma lipidomics, prostaglandin D2 (PGD2) concentrations were decreased in children with CF exposed to SHSe, and associated with more frequent hospitalisations (p=0.007) and worsened weight z scores (p=0.008). Children with CF exposed to SHSe demonstrated decreased expression of the prostaglandin genes PTGES3 and PTGR2 and overexpression of inflammatory pathways. These findings were confirmed using an in vitro model, where SHSe was associated with a dose-dependent decrease in PGD2 and increased methicillin-resistant Staphylococcus aureus survival in human CF macrophages. CONCLUSIONS Infants and young children with CF and SHSe have altered AA metabolism and dysregulated inflammatory gene expression resulting in impaired bacterial clearance. Our findings identified potential therapeutic targets to halt early disease progression associated with SHSe in the young population with CF.
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Affiliation(s)
- Benjamin T Kopp
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Rohan Thompson
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jeeho Kim
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Robert Konstan
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Alejandro Diaz
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Bennett Smith
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Chandra Shrestha
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Lynette K Rogers
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Don Hayes
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Dmitry Tumin
- Department of Anesthesiology and Pain Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Frederick W Woodley
- Division of Gastroenterology, Hepatology and Nutrition, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Octavio Ramilo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Don B Sanders
- Riley Children's Hospital, Indianapolis, Indiana, USA
| | - Judith A Groner
- Section of Ambulatory Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
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19
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Brummaier T, Syed Ahamed Kabeer B, Lindow S, Konje JC, Pukrittayaamee S, Utzinger J, Toufiq M, Antoniou A, Marr AK, Suriyakan S, Kino T, Al Khodor S, Terranegra A, Nosten F, Paris DH, McGready R, Chaussabel D. A prospective cohort for the investigation of alteration in temporal transcriptional and microbiome trajectories preceding preterm birth: a study protocol. BMJ Open 2019; 9:e023417. [PMID: 30782707 PMCID: PMC6340419 DOI: 10.1136/bmjopen-2018-023417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Preterm birth (PTB) results from heterogeneous influences and is a major contributor to neonatal mortality and morbidity that continues to have adverse effects on infants beyond the neonatal period. This protocol describes the procedures to determine molecular signatures predictive of PTB through high-frequency sampling during pregnancy, at delivery and the postpartum period. METHODS AND ANALYSIS Four hundred first trimester pregnant women from either Myanmar or Thailand of either Karen or Burman ethnicity, with a viable, singleton pregnancy will be enrolled in this non-interventional, prospective pregnancy birth cohort study and will be followed through to the postpartum period. Fortnightly finger prick capillary blood sampling will allow the monitoring of genome-wide transcript abundance in whole blood. Collection of stool samples and vaginal swabs each trimester, at delivery and postpartum will allow monitoring of intestinal and vaginal microbial composition. In a nested case-control analysis, perturbations of transcript abundance in capillary blood as well as longitudinal changes of the gut, vaginal and oral microbiome will be compared between mothers giving birth to preterm and matched cases giving birth to term neonates. Placenta tissue of preterm and term neonates will be used to determine bacterial colonisation as well as for the establishment of coding and non-coding RNA profiles. In addition, RNA profiles of circulating, non-coding RNA in cord blood serum will be compared with those of maternal peripheral blood serum at time of delivery. ETHICS AND DISSEMINATION This research protocol that aims to detect perturbations in molecular trajectories preceding adverse pregnancy outcomes was approved by the ethics committee of the Faculty of Tropical Medicine, Mahidol University in Bangkok, Thailand (Ethics Reference: TMEC 15-062), the Oxford Tropical Research Ethics Committee (Ethics Reference: OxTREC: 33-15) and the local Tak Province Community Ethics Advisory Board. The results of this cooperative project will be disseminated in multiple publications staggered over time in international peer-reviewed scientific journals. TRIAL REGISTRATION NUMBER NCT02797327; Pre-results.
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Affiliation(s)
- Tobias Brummaier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | | | | | | | | | - Juerg Utzinger
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | | | | | | | - Sangrawee Suriyakan
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | | | | | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Daniel H Paris
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
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20
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Esposito S, Rinaldi VE, Argentiero A, Farinelli E, Cofini M, D'Alonzo R, Mencacci A, Principi N. Approach to Neonates and Young Infants with Fever without a Source Who Are at Risk for Severe Bacterial Infection. Mediators Inflamm 2018; 2018:4869329. [PMID: 30581369 PMCID: PMC6287153 DOI: 10.1155/2018/4869329] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/07/2018] [Accepted: 10/15/2018] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Among neonates and infants <3 months of age with fever without a source (FWS), 5% to 15% of cases are patients with fever caused by a serious bacterial infection (SBI). To favour the differentiation between low- and high-risk infants, several algorithms based on analytical and clinical parameters have been developed. The aim of this review is to describe the management of young infants with FWS and to discuss the impact of recent knowledge regarding FWS management on clinical practice. MATERIALS AND METHODS PubMed was used to search for all of the studies published over the last 35 years using the keywords: "fever without source" or "fever of unknown origin" or "meningitis" or "sepsis" or "urinary tract infection" and "neonate" or "newborn" or "infant <90 days of life" or "infant <3 months". RESULTS AND DISCUSSION The selection of neonates and young infants who are <3 months old with FWS who are at risk for SBI remains a problem without a definitive solution. The old Rochester criteria remain effective for identifying young infants between 29 and 60 days old who do not have severe bacterial infections (SBIs). However, the addition of laboratory tests such as C-reactive protein (CRP) and procalcitonin (PCT) can significantly improve the identification of children with SBI. The approach in evaluating neonates is significantly more complicated, as their risk of SBIs, including bacteremia and meningitis, remains relevant and none of the suggested approaches can reduce the risk of dramatic mistakes. In both groups, the best antibiotic must be carefully selected considering the clinical findings, the laboratory data, the changing epidemiology, and increasing antibiotic resistance of the most common infectious bacteria.
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Affiliation(s)
- Susanna Esposito
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Victoria Elisa Rinaldi
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Alberto Argentiero
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Edoardo Farinelli
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Marta Cofini
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Renato D'Alonzo
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Antonella Mencacci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
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21
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Jaggi P, Mejias A, Xu Z, Yin H, Moore-Clingenpeel M, Smith B, Burns JC, Tremoulet AH, Jordan-Villegas A, Chaussabel D, Texter K, Pascual V, Ramilo O. Whole blood transcriptional profiles as a prognostic tool in complete and incomplete Kawasaki Disease. PLoS One 2018; 13:e0197858. [PMID: 29813106 PMCID: PMC5973615 DOI: 10.1371/journal.pone.0197858] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Background Early identification of children with Kawasaki Disease (KD) is key for timely initiation of intravenous immunoglobulin (IVIG) therapy. However, the diagnosis of the disease remains challenging, especially in children with an incomplete presentation (inKD). Moreover, we currently lack objective tools for identification of non-response (NR) to IVIG. Methods Children with KD were enrolled and samples obtained before IVIG treatment and sequentially at 24 h and 4–6 weeks post-IVIG in a subset of patients. We also enrolled children with other febrile illnesses [adenovirus (AdV); group A streptococcus (GAS)] and healthy controls (HC) for comparative analyses. Blood transcriptional profiles were analyzed to define: a) the cKD and inKD biosignature, b) compare the KD signature with other febrile illnesses and, c) identify biomarkers predictive of clinical outcomes. Results We identified a cKD biosignature (n = 39; HC, n = 16) that was validated in two additional cohorts of children with cKD (n = 37; HC, n = 20) and inKD (n = 13; HC, n = 8) and was characterized by overexpression of inflammation, platelets, apoptosis and neutrophil genes, and underexpression of T and NK cell genes. Classifier genes discriminated KD from adenovirus with higher sensitivity and specificity (92% and 100%, respectively) than for GAS (75% and 87%, respectively). We identified a genomic score (MDTH) that was higher at baseline in IVIG-NR [median 12,290 vs. 5,572 in responders, p = 0.009] and independently predicted IVIG-NR. Conclusion A reproducible biosignature from KD patients was identified, and was similar in children with cKD and inKD. A genomic score allowed early identification of children at higher risk for non-response to IVIG.
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Affiliation(s)
- Preeti Jaggi
- Division of Pediatric Infectious Disease, Nationwide Children’s Hospital, Columbus, OH, United States of America
| | - Asuncion Mejias
- Division of Pediatric Infectious Disease, Nationwide Children’s Hospital, Columbus, OH, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Zhaohui Xu
- Baylor Institute for Immunology Research, Dallas, TX, United States of America
| | - Han Yin
- Center for Biostatistics, The Research Institute at Nationwide Children’s Hospital Columbus, OH, United States of America
| | - Melissa Moore-Clingenpeel
- Center for Biostatistics, The Research Institute at Nationwide Children’s Hospital Columbus, OH, United States of America
| | - Bennett Smith
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Jane C. Burns
- Department of Pediatrics, University of California San Diego and Rady Children’s Hospital, San Diego, CA, United States of America
| | - Adriana H. Tremoulet
- Department of Pediatrics, University of California San Diego and Rady Children’s Hospital, San Diego, CA, United States of America
| | - Alejandro Jordan-Villegas
- Division of Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | | | - Karen Texter
- Division of Pediatric Cardiology, Nationwide Children’s Hospital, Columbus, OH, United States of America
| | - Virginia Pascual
- Drukier Institute for Children’s Health, and Weill Cornell Medicine, New York City, NY, United States of America
| | - Octavio Ramilo
- Division of Pediatric Infectious Disease, Nationwide Children’s Hospital, Columbus, OH, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, United States of America
- * E-mail:
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22
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Chen P, Yao Z, Deng G, Hou Y, Chen S, Hu Y, Yu B. Differentially Expressed Genes in Osteomyelitis Induced by Staphylococcus aureus Infection. Front Microbiol 2018; 9:1093. [PMID: 29887852 PMCID: PMC5982613 DOI: 10.3389/fmicb.2018.01093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/07/2018] [Indexed: 12/21/2022] Open
Abstract
Osteomyelitis (OM) is a complicated and serious disease and its underlying molecular signatures of disease initiation and progression remain unclear. Staphylococcus aureus (S. aureus) is the most common causative agent of OM. Previous study of Banchereau et al. has established a link between whole blood transcription profiles and clinical manifestations in patients infected with S. aureus. However, the differentially expressed genes (DEGs) in OM induced by S. aureus infection have not been intensively investigated. In this study, we downloaded the gene expression profile dataset GSE30119 from Gene Expression Omnibus, and performed bioinformatic analysis to identify DEGs in S. aureus infection induced OM from the transcriptional level. The study consisted of 143 whole blood samples, including 44 healthy controls, 42 OM-free, and 57 OM infection patients. A total of 209 S. aureus infection-related genes (SARGs) and 377 OM-related genes (OMRGs) were identified. The SARGs were primarily involved in the immune response by GO functional and pathway enrichment analysis. Several proteins adhere to neutrophil extracellular traps may be critical for the immune response to the process of S. aureus infection. By contrast, the OMRGs differ from the SARGs. The OMRGs were enriched in transmembrane signaling receptor and calcium channel activity, cilium morphogenesis, chromatin silencing, even multicellular organism development. Several key proteins, including PHLPP2 and EGF, were hub nodes in protein–protein interaction network of the OMRGs. In addition, alcoholism, systemic lupus erythematosus and proteoglycans in cancer were the top pathways influenced by the OMRGs associated with OM. Thus, this study has further explored the DEGs and their biological functions associated with S. aureus infection and OM, comparing with the previous study, and may light the further insight into the underlying molecular mechanisms and the potential critical biomarkers in OM development.
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Affiliation(s)
- Peisheng Chen
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zilong Yao
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ganming Deng
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yilong Hou
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Siwei Chen
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanjun Hu
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bin Yu
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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23
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Herman P, Stein A, Gibbs K, Korsunsky I, Gregersen P, Bloom O. Persons with Chronic Spinal Cord Injury Have Decreased Natural Killer Cell and Increased Toll-Like Receptor/Inflammatory Gene Expression. J Neurotrauma 2018; 35:1819-1829. [PMID: 29310515 PMCID: PMC6033303 DOI: 10.1089/neu.2017.5519] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Infections are the leading cause of death for individuals with traumatic spinal cord injury (SCI). Along with increased infection rates, inflammation is often also observed in persons with chronic SCI. Together, immunological changes post-SCI are also poised to impede neurological recovery and mediate common medical consequences of SCI, including atherogenesis and neuropathic pain. The molecular mechanisms contributing to increased infection susceptibility and inflammation in persons living with SCI are poorly understood. Here, we used tools of functional genomics to perform a pilot study to compare whole-blood gene expression in individuals with chronic SCI (≥1 year from initial injury; N = 31) and uninjured individuals (N = 26). We identified 1815 differentially expressed genes in all SCI participants and 2226 differentially expressed genes in persons with SCI rostral to thoracic level 5, compared to uninjured participants. This included marked downregulation of natural killer cell genes and upregulation of the proinflammatory Toll-like receptor signaling pathway. These data provide novel mechanistic insights into the causes underlying the symptoms of immune dysfunction in individuals living with SCI.
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Affiliation(s)
- Paige Herman
- 1 The Feinstein Institute for Medical Research , Northwell Health
| | - Adam Stein
- 2 Department of Physical Medicine and Rehabilitation, Zucker School of Medicine at Hofstra Northwell
| | - Katie Gibbs
- 1 The Feinstein Institute for Medical Research , Northwell Health.,2 Department of Physical Medicine and Rehabilitation, Zucker School of Medicine at Hofstra Northwell
| | - Ilya Korsunsky
- 3 Robert S. Boas Center for Genomics & Human Genetics , The Feinstein Institute for Medical Research
| | - Peter Gregersen
- 3 Robert S. Boas Center for Genomics & Human Genetics , The Feinstein Institute for Medical Research.,4 Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra Northwell , Northwell Health, Hempstead, NewYork
| | - Ona Bloom
- 1 The Feinstein Institute for Medical Research , Northwell Health.,2 Department of Physical Medicine and Rehabilitation, Zucker School of Medicine at Hofstra Northwell .,4 Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra Northwell , Northwell Health, Hempstead, NewYork
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24
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Sweeney TE, Wong HR, Khatri P. Robust classification of bacterial and viral infections via integrated host gene expression diagnostics. Sci Transl Med 2017; 8:346ra91. [PMID: 27384347 DOI: 10.1126/scitranslmed.aaf7165] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/13/2016] [Indexed: 12/17/2022]
Abstract
Improved diagnostics for acute infections could decrease morbidity and mortality by increasing early antibiotics for patients with bacterial infections and reducing unnecessary antibiotics for patients without bacterial infections. Several groups have used gene expression microarrays to build classifiers for acute infections, but these have been hampered by the size of the gene sets, use of overfit models, or lack of independent validation. We used multicohort analysis to derive a set of seven genes for robust discrimination of bacterial and viral infections, which we then validated in 30 independent cohorts. We next used our previously published 11-gene Sepsis MetaScore together with the new bacterial/viral classifier to build an integrated antibiotics decision model. In a pooled analysis of 1057 samples from 20 cohorts (excluding infants), the integrated antibiotics decision model had a sensitivity and specificity for bacterial infections of 94.0 and 59.8%, respectively (negative likelihood ratio, 0.10). Prospective clinical validation will be needed before these findings are implemented for patient care.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA. Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, OH 45223, USA. Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA. Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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25
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Acuff NV, LaGatta M, Nagy T, Watford WT. Severe Dermatitis Associated with Spontaneous Staphylococcus xylosus Infection in Rag-/-Tpl2-/- Mice. Comp Med 2017; 67:344-349. [PMID: 28830581 PMCID: PMC5557206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/21/2016] [Accepted: 10/18/2016] [Indexed: 06/07/2023]
Abstract
Staphylococcus xylosus is a commensal bacterium found on the skin and mucosal surfaces of SPF mice. S. xylosus is rarely pathogenic, most often causing skin lesions and dermatitis in immunocompromised mice, particularly those with impaired NADPH oxidase function. Here we report spontaneous infection with S. xylosus in Rag1-/-Tpl2-/- mice. Infection was characterized by the presence of alopecia, crusts, and scaly skin. S. xylosus was detected in the feces, skin, lymph nodes, and lungs of Rag1-/-Tpl2-/- mice and led to mortality or euthanasia due to humane endpoints. C57BL/6 mice were culture-positive for S. xylosus on the skin, and Rag1-/- and Tpl2-/- mice were culture-positive on the skin and occasionally in the feces. However, S. xylosus did not cause clinical symptoms in C57BL/6, Rag1-/-, or Tpl2-/- mice. Compared with those in Rag1-/- mice, relative concentrations of circulating monocytes, but not neutrophils or lymphocytes, were increased in Rag1-/-Tpl2-/- mice, consistent with their increased incidence of clinical symptoms. Overall, this case study suggests a novel role for Tpl2 in T-cell-independent host resistance to the otherwise commensal organism S. xylosus.
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Affiliation(s)
- Nicole V Acuff
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Monica LaGatta
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Tamas Nagy
- Department of Pathology, University of Georgia, Athens, Georgia, USA
| | - Wendy T Watford
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA.
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26
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A Four-Biomarker Blood Signature Discriminates Systemic Inflammation Due to Viral Infection Versus Other Etiologies. Sci Rep 2017; 7:2914. [PMID: 28588308 PMCID: PMC5460227 DOI: 10.1038/s41598-017-02325-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023] Open
Abstract
The innate immune system of humans and other mammals responds to pathogen-associated molecular patterns (PAMPs) that are conserved across broad classes of infectious agents such as bacteria and viruses. We hypothesized that a blood-based transcriptional signature could be discovered indicating a host systemic response to viral infection. Previous work identified host transcriptional signatures to individual viruses including influenza, respiratory syncytial virus and dengue, but the generality of these signatures across all viral infection types has not been established. Based on 44 publicly available datasets and two clinical studies of our own design, we discovered and validated a four-gene expression signature in whole blood, indicative of a general host systemic response to many types of viral infection. The signature’s genes are: Interferon Stimulated Gene 15 (ISG15), Interleukin 16 (IL16), 2′,5′-Oligoadenylate Synthetase Like (OASL), and Adhesion G Protein Coupled Receptor E5 (ADGRE5). In each of 13 validation datasets encompassing human, macaque, chimpanzee, pig, mouse, rat and all seven Baltimore virus classification groups, the signature provides statistically significant (p < 0.05) discrimination between viral and non-viral conditions. The signature may have clinical utility for differentiating host systemic inflammation (SI) due to viral versus bacterial or non-infectious causes.
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27
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Pollara G, Murray MJ, Heather JM, Byng-Maddick R, Guppy N, Ellis M, Turner CT, Chain BM, Noursadeghi M. Validation of Immune Cell Modules in Multicellular Transcriptomic Data. PLoS One 2017; 12:e0169271. [PMID: 28045996 PMCID: PMC5207692 DOI: 10.1371/journal.pone.0169271] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/14/2016] [Indexed: 01/16/2023] Open
Abstract
Numerous gene signatures, or modules have been described to evaluate the immune cell composition in transcriptomes of multicellular tissue samples. However, significant diversity in module gene content for specific cell types is associated with heterogeneity in their performance. In order to rank modules that best reflect their purported association, we have generated the modular discrimination index (MDI) score that assesses expression of each module in the target cell type relative to other cells. We demonstrate that MDI scores predict modules that best reflect independently validated differences in cellular composition, and correlate with the covariance between cell numbers and module expression in human blood and tissue samples. Our analyses demonstrate that MDI scores provide an ordinal summary statistic that reliably ranks the accuracy of gene expression modules for deconvolution of cell type abundance in transcriptional data.
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Affiliation(s)
- Gabriele Pollara
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Matthew J. Murray
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - James M. Heather
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Rachel Byng-Maddick
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Naomi Guppy
- UCL Advanced Diagnostics, University College London, London, United Kingdom
| | - Matthew Ellis
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, United Kingdom
| | - Carolin T. Turner
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Benjamin M. Chain
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Mahdad Noursadeghi
- Division of Infection & Immunity, University College London, London, United Kingdom
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Napier BA, Brubaker SW, Sweeney TE, Monette P, Rothmeier GH, Gertsvolf NA, Puschnik A, Carette JE, Khatri P, Monack DM. Complement pathway amplifies caspase-11-dependent cell death and endotoxin-induced sepsis severity. J Exp Med 2016; 213:2365-2382. [PMID: 27697835 PMCID: PMC5068231 DOI: 10.1084/jem.20160027] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 08/25/2016] [Indexed: 01/18/2023] Open
Abstract
Cell death and release of proinflammatory mediators contribute to mortality during sepsis. Specifically, caspase-11-dependent cell death contributes to pathology and decreases in survival time in sepsis models. Priming of the host cell, through TLR4 and interferon receptors, induces caspase-11 expression, and cytosolic LPS directly stimulates caspase-11 activation, promoting the release of proinflammatory cytokines through pyroptosis and caspase-1 activation. Using a CRISPR-Cas9-mediated genome-wide screen, we identified novel mediators of caspase-11-dependent cell death. We found a complement-related peptidase, carboxypeptidase B1 (Cpb1), to be required for caspase-11 gene expression and subsequent caspase-11-dependent cell death. Cpb1 modifies a cleavage product of C3, which binds to and activates C3aR, and then modulates innate immune signaling. We find the Cpb1-C3-C3aR pathway induces caspase-11 expression through amplification of MAPK activity downstream of TLR4 and Ifnar activation, and mediates severity of LPS-induced sepsis (endotoxemia) and disease outcome in mice. We show C3aR is required for up-regulation of caspase-11 orthologues, caspase-4 and -5, in primary human macrophages during inflammation and that c3aR1 and caspase-5 transcripts are highly expressed in patients with severe sepsis; thus, suggesting that these pathways are important in human sepsis. Our results highlight a novel role for complement and the Cpb1-C3-C3aR pathway in proinflammatory signaling, caspase-11 cell death, and sepsis severity.
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Affiliation(s)
- Brooke A Napier
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Sky W Brubaker
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Timothy E Sweeney
- Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305
| | - Patrick Monette
- Department of Biology, Middlebury College, Middlebury, VT 05753
| | | | - Nina A Gertsvolf
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Andreas Puschnik
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Purvesh Khatri
- Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305
| | - Denise M Monack
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
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Mahajan P, Kuppermann N, Mejias A, Suarez N, Chaussabel D, Casper TC, Smith B, Alpern ER, Anders J, Atabaki SM, Bennett JE, Blumberg S, Bonsu B, Borgialli D, Brayer A, Browne L, Cohen DM, Crain EF, Cruz AT, Dayan PS, Gattu R, Greenberg R, Hoyle JD, Jaffe DM, Levine DA, Lillis K, Linakis JG, Muenzer J, Nigrovic LE, Powell EC, Rogers AJ, Roosevelt G, Ruddy RM, Saunders M, Tunik MG, Tzimenatos L, Vitale M, Dean JM, Ramilo O. Association of RNA Biosignatures With Bacterial Infections in Febrile Infants Aged 60 Days or Younger. JAMA 2016; 316:846-57. [PMID: 27552618 PMCID: PMC5122927 DOI: 10.1001/jama.2016.9207] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
IMPORTANCE Young febrile infants are at substantial risk of serious bacterial infections; however, the current culture-based diagnosis has limitations. Analysis of host expression patterns ("RNA biosignatures") in response to infections may provide an alternative diagnostic approach. OBJECTIVE To assess whether RNA biosignatures can distinguish febrile infants aged 60 days or younger with and without serious bacterial infections. DESIGN, SETTING, AND PARTICIPANTS Prospective observational study involving a convenience sample of febrile infants 60 days or younger evaluated for fever (temperature >38° C) in 22 emergency departments from December 2008 to December 2010 who underwent laboratory evaluations including blood cultures. A random sample of infants with and without bacterial infections was selected for RNA biosignature analysis. Afebrile healthy infants served as controls. Blood samples were collected for cultures and RNA biosignatures. Bioinformatics tools were applied to define RNA biosignatures to classify febrile infants by infection type. EXPOSURE RNA biosignatures compared with cultures for discriminating febrile infants with and without bacterial infections and infants with bacteremia from those without bacterial infections. MAIN OUTCOMES AND MEASURES Bacterial infection confirmed by culture. Performance of RNA biosignatures was compared with routine laboratory screening tests and Yale Observation Scale (YOS) scores. RESULTS Of 1883 febrile infants (median age, 37 days; 55.7% boys), RNA biosignatures were measured in 279 randomly selected infants (89 with bacterial infections-including 32 with bacteremia and 15 with urinary tract infections-and 190 without bacterial infections), and 19 afebrile healthy infants. Sixty-six classifier genes were identified that distinguished infants with and without bacterial infections in the test set with 87% (95% CI, 73%-95%) sensitivity and 89% (95% CI, 81%-93%) specificity. Ten classifier genes distinguished infants with bacteremia from those without bacterial infections in the test set with 94% (95% CI, 70%-100%) sensitivity and 95% (95% CI, 88%-98%) specificity. The incremental C statistic for the RNA biosignatures over the YOS score was 0.37 (95% CI, 0.30-0.43). CONCLUSIONS AND RELEVANCE In this preliminary study, RNA biosignatures were defined to distinguish febrile infants aged 60 days or younger with vs without bacterial infections. Further research with larger populations is needed to refine and validate the estimates of test accuracy and to assess the clinical utility of RNA biosignatures in practice.
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Affiliation(s)
- Prashant Mahajan
- Division of Emergency Medicine, Department of Pediatrics, Children's Hospital of Michigan, Wayne State University, Detroit
| | - Nathan Kuppermann
- Departments of Emergency Medicine and Pediatrics, University of California, Davis, School of Medicine, Sacramento
| | - Asuncion Mejias
- Division of Pediatric Infectious Diseases and Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University, Columbus
| | - Nicolas Suarez
- Division of Pediatric Infectious Diseases and Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University, Columbus
| | - Damien Chaussabel
- Benaroya Research Institute, Virginia Mason and Sidra Medical and Research Center, Seattle, Washington, and Doha, Qatar
| | | | - Bennett Smith
- Division of Pediatric Infectious Diseases and Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University, Columbus
| | - Elizabeth R Alpern
- Division of Emergency Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania7Now at Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jennifer Anders
- Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland
| | - Shireen M Atabaki
- Division of Emergency Medicine, Department of Pediatrics, Children's National Medical Center, George Washington School of Medicine and Health Sciences, Washington, DC
| | - Jonathan E Bennett
- Division of Pediatric Emergency Medicine, Alfred I. DuPont Hospital for Children, Nemours Children's Health System, Wilmington, Delaware
| | - Stephen Blumberg
- Department of Pediatrics, Jacobi Medical Center, Albert Einstein College of Medicine, New York, New York
| | - Bema Bonsu
- Section of Emergency Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio
| | - Dominic Borgialli
- Department of Emergency Medicine, Hurley Medical Center and University of Michigan, Flint
| | - Anne Brayer
- Departments of Emergency Medicine and Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Lorin Browne
- Departments of Pediatrics and Emergency Medicine, Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee
| | - Daniel M Cohen
- Section of Emergency Medicine, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University, Columbus
| | - Ellen F Crain
- Division of Pediatric Emergency Medicine, Alfred I. DuPont Hospital for Children, Nemours Children's Health System, Wilmington, Delaware
| | - Andrea T Cruz
- Sections of Emergency Medicine and Infectious Diseases, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston
| | - Peter S Dayan
- Division of Emergency Medicine, Department of Pediatrics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Rajender Gattu
- Division of Emergency Medicine, Department of Pediatrics, University of Maryland Medical Center, Baltimore
| | - Richard Greenberg
- Department of Pediatrics, Primary Children's Medical Center, University of Utah, Salt Lake City
| | - John D Hoyle
- Department of Emergency Medicine, Helen DeVos Children's Hospital of Spectrum Health, Grand Rapids, Michigan22Now with the Departments of Emergency Medicine and Pediatrics, Western Michigan University Homer Stryker, MD, School of Medicine, Kalamazoo
| | - David M Jaffe
- Department of Pediatrics, St Louis Children's Hospital, Washington University, St Louis, Missouri24Now with the Division of Pediatric Emergency Medicine, University of California San Francisco School of Medicine
| | - Deborah A Levine
- Department of Pediatrics, Bellevue Hospital New York University Langone Center, New York
| | - Kathleen Lillis
- Department of Pediatrics, Women and Children's Hospital of Buffalo, State University of New York at Buffalo
| | - James G Linakis
- Department of Emergency Medicine and Pediatrics, Hasbro Children's Hospital and Brown University, Providence, Rhode Island
| | - Jared Muenzer
- Department of Pediatrics, Bellevue Hospital New York University Langone Center, New York28Now with the Department of Emergency Medicine, Phoenix Children's Hospital, Phoenix, Arizona
| | - Lise E Nigrovic
- Department of Pediatrics, Boston Children's Hospital, Harvard University, Boston, Massachusetts
| | - Elizabeth C Powell
- Division of Emergency Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alexander J Rogers
- Departments of Emergency Medicine and Pediatrics, University of Michigan, Ann Arbor
| | - Genie Roosevelt
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado-Denver, Aurora
| | - Richard M Ruddy
- Division of Emergency Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Mary Saunders
- Department of Pediatrics, Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee35Now with Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora
| | - Michael G Tunik
- Department of Pediatrics, Bellevue Hospital, New York University Langone Medical Center, New York
| | - Leah Tzimenatos
- Department of Emergency Medicine, University of California, Davis School of Medicine, Sacramento
| | - Melissa Vitale
- Division of Pediatric Emergency Medicine, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - J Michael Dean
- Department of Pediatrics, University of Utah, Salt Lake City
| | - Octavio Ramilo
- Division of Pediatric Infectious Diseases and Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University, Columbus
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Fattom A, Matalon A, Buerkert J, Taylor K, Damaso S, Boutriau D. Efficacy profile of a bivalent Staphylococcus aureus glycoconjugated vaccine in adults on hemodialysis: Phase III randomized study. Hum Vaccin Immunother 2015; 11:632-41. [PMID: 25483694 PMCID: PMC4514248 DOI: 10.4161/hv.34414] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In a previous study in end-stage renal disease (ESRD) hemodialysis patients, a single dose of Staphylococcus aureus type 5 and 8 capsular polysaccharides (T5/T8) conjugated to nontoxic recombinant Pseudomonas aeruginosa exotoxin A investigational vaccine showed no efficacy against S. aureus bacteremia 1 year post-vaccination, but a trend for efficacy was observed over the first 40 weeks post-vaccination. Vaccine efficacy (VE) of 2 vaccine doses was therefore evaluated. In a double-blind trial 3359 ESRD patients were randomized (1:1) to receive vaccine or placebo at week 0 and 35. VE in preventing S. aureus bacteremia was assessed between 3–35 weeks and 3–60 weeks post-dose-1. Anti-T5 and anti-T8 antibodies were measured. Serious adverse events (SAEs) were recorded for 42 days post-vaccination and deaths until study end. No significant difference in the incidence of S. aureus bacteremia was observed between vaccine and placebo groups between weeks 3–35 weeks post-dose 1 (VE -23%, 95%CI: -98;23, p = 0.39) or at 3–60 weeks post-dose-1 (VE -8%, 95%CI: -57;26, p = 0.70). Day 42 geometric mean antibody concentrations were 272.4 μg/ml and 242.0 μg/ml (T5 and T8, respectively) in vaccinees. SAEs were reported by 24%/25.3% of vaccinees/placebo recipients. These data do not show a protective effect of either 1 or 2 vaccine doses against S. aureus bacteremia in ESRD patients. The vaccine induced a robust immune response and had an acceptable safety profile. Further investigation suggested possible suboptimal vaccine quality (manufacturing) and a need to expand the antigen composition of the vaccine. This study is registered at www.clinicaltrials.gov NCT00071214.
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Affiliation(s)
- Ali Fattom
- a Nabi Biopharmaceuticals ; Rockville , MD USA
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31
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Nelita GCAFDB, Mir eacute ia ABP, Vany F, Karine QP, Alo iacute sio FCJUN, Artur A. Antimicrobial activity and medicinal biomass of Siparuna guianensis in Brazilian Cerrado forest, a global hotspot. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/jmpr2015.5884] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Ko ER, Yang WE, McClain MT, Woods CW, Ginsburg GS, Tsalik EL. What was old is new again: using the host response to diagnose infectious disease. Expert Rev Mol Diagn 2015; 15:1143-58. [PMID: 26145249 DOI: 10.1586/14737159.2015.1059278] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A century of advances in infectious disease diagnosis and treatment changed the face of medicine. However, challenges continue to develop including multi-drug resistance, globalization that increases pandemic risks and high mortality from severe infections. These challenges can be mitigated through improved diagnostics, focusing on both pathogen discovery and the host response. Here, we review how 'omics' technologies improve sepsis diagnosis, early pathogen identification and personalize therapy. Such host response diagnostics are possible due to the confluence of advanced laboratory techniques (e.g., transcriptomics, metabolomics, proteomics) along with advanced mathematical modeling such as machine learning techniques. The road ahead is promising, but obstacles remain before the impact of such advanced diagnostic modalities is felt at the bedside.
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Affiliation(s)
- Emily R Ko
- a 1 Department of Medicine Center for Applied Genomics & Precision Medicine, Duke University, Durham, NC 27708, USA
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Detecting specific infections in children through host responses: a paradigm shift. Curr Opin Infect Dis 2015; 27:228-35. [PMID: 24739346 DOI: 10.1097/qco.0000000000000065] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW There is a need for improved diagnosis and for optimal classification of patients with infectious diseases. An alternative approach to the pathogen-detection strategy is based on a comprehensive analysis of the host response to the infection. This review focuses on the value of transcriptome analyses of blood leukocytes for the diagnosis and management of patients with infectious diseases. RECENT FINDINGS Initial studies showed that RNA from blood leukocytes of children with acute viral and bacterial infections carried pathogen-specific transcriptional signatures. Subsequently, transcriptional signatures for several other infections have been described and validated in humans with malaria, dengue, salmonella, melioidosis, respiratory syncytial virus, influenza, tuberculosis, and HIV. In addition, transcriptome analyses represent an invaluable tool to understand disease pathogenesis and to objectively classify patients according to the clinical severity. SUMMARY Microarray studies have been shown to be highly reproducible using different platforms, and in different patient populations, confirming the value of blood transcriptome analyses to study pathogen-specific host immune responses in the clinical setting. Combining the detection of the pathogen with a comprehensive assessment of the host immune response will provide a new understanding of the correlations between specific causative agents, the host response, and the clinical manifestations of the disease.
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Suarez NM, Bunsow E, Falsey AR, Walsh EE, Mejias A, Ramilo O. Superiority of transcriptional profiling over procalcitonin for distinguishing bacterial from viral lower respiratory tract infections in hospitalized adults. J Infect Dis 2015; 212:213-22. [PMID: 25637350 PMCID: PMC4565998 DOI: 10.1093/infdis/jiv047] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/26/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Distinguishing between bacterial and viral lower respiratory tract infection (LRTI) remains challenging. Transcriptional profiling is a promising tool for improving diagnosis in LRTI. METHODS We performed whole blood transcriptional analysis in 118 patients (median age [interquartile range], 61 [50-76] years) hospitalized with LRTI and 40 age-matched healthy controls (median age, 60 [46-70] years). We applied class comparisons, modular analysis, and class prediction algorithms to identify and validate diagnostic biosignatures for bacterial and viral LRTI. RESULTS Patients were classified as having bacterial (n = 22), viral (n = 71), or bacterial-viral LRTI (n = 25) based on comprehensive microbiologic testing. Compared with healthy controls, statistical group comparisons (P < .01; multiple-test corrections) identified 3376 differentially expressed genes in patients with bacterial LRTI, 2391 in viral LRTI, and 2628 in bacterial-viral LRTI. Patients with bacterial LRTI showed significant overexpression of inflammation and neutrophil genes (bacterial > bacterial-viral > viral), and those with viral LRTI displayed significantly greater overexpression of interferon genes (viral > bacterial-viral > bacterial). The K-nearest neighbors algorithm identified 10 classifier genes that discriminated between bacterial and viral LRTI with a 95% sensitivity (95% confidence interval, 77%-100%) and 92% specificity (77%-98%), compared with a sensitivity of 38% (18%-62%) and a specificity of 91% (76%-98%) for procalcitonin. CONCLUSIONS Transcriptional profiling is a helpful tool for diagnosis of LRTI.
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Affiliation(s)
- Nicolas M Suarez
- Center for Vaccines and Immunity Division of Pediatric Infectious Diseases, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus
| | - Eleonora Bunsow
- Center for Vaccines and Immunity Division of Pediatric Infectious Diseases, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus
| | - Ann R Falsey
- Department of Medicine, University of Rochester Rochester General Hospital, New York
| | - Edward E Walsh
- Department of Medicine, University of Rochester Rochester General Hospital, New York
| | - Asuncion Mejias
- Center for Vaccines and Immunity Division of Pediatric Infectious Diseases, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus
| | - Octavio Ramilo
- Center for Vaccines and Immunity Division of Pediatric Infectious Diseases, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus
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RNA transcriptional biosignature analysis for identifying febrile infants with serious bacterial infections in the emergency department: a feasibility study. Pediatr Emerg Care 2015; 31:1-5. [PMID: 25526020 PMCID: PMC4300534 DOI: 10.1097/pec.0000000000000324] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To develop the infrastructure and demonstrate the feasibility of conducting microarray-based RNA transcriptional profile analyses for the diagnosis of serious bacterial infections in febrile infants 60 days and younger in a multicenter pediatric emergency research network. METHODS We designed a prospective multicenter cohort study with the aim of enrolling more than 4000 febrile infants 60 days and younger. To ensure success of conducting complex genomic studies in emergency department (ED) settings, we established an infrastructure within the Pediatric Emergency Care Applied Research Network, including 21 sites, to evaluate RNA transcriptional profiles in young febrile infants. We developed a comprehensive manual of operations and trained site investigators to obtain and process blood samples for RNA extraction and genomic analyses. We created standard operating procedures for blood sample collection, processing, storage, shipping, and analyses. We planned to prospectively identify, enroll, and collect 1 mL blood samples for genomic analyses from eligible patients to identify logistical issues with study procedures. Finally, we planned to batch blood samples and determined RNA quantity and quality at the central microarray laboratory and organized data analysis with the Pediatric Emergency Care Applied Research Network data coordinating center. Below we report on establishment of the infrastructure and the feasibility success in the first year based on the enrollment of a limited number of patients. RESULTS We successfully established the infrastructure at 21 EDs. Over the first 5 months we enrolled 79% (74 of 94) of eligible febrile infants. We were able to obtain and ship 1 mL of blood from 74% (55 of 74) of enrolled participants, with at least 1 sample per participating ED. The 55 samples were shipped and evaluated at the microarray laboratory, and 95% (52 of 55) of blood samples were of adequate quality and contained sufficient RNA for expression analysis. CONCLUSIONS It is possible to create a robust infrastructure to conduct genomic studies in young febrile infants in the context of a multicenter pediatric ED research setting. The sufficient quantity and high quality of RNA obtained suggests that whole blood transcriptional profile analysis for the diagnostic evaluation of young febrile infants can be successfully performed in this setting.
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Yeaman MR, Filler SG, Schmidt CS, Ibrahim AS, Edwards JE, Hennessey JP. Applying Convergent Immunity to Innovative Vaccines Targeting Staphylococcus aureus. Front Immunol 2014; 5:463. [PMID: 25309545 PMCID: PMC4176462 DOI: 10.3389/fimmu.2014.00463] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/10/2014] [Indexed: 12/22/2022] Open
Abstract
Recent perspectives forecast a new paradigm for future “third generation” vaccines based on commonalities found in diverse pathogens or convergent immune defenses to such pathogens. For Staphylococcus aureus, recurring infections and a limited success of vaccines containing S. aureus antigens imply that native antigens induce immune responses insufficient for optimal efficacy. These perspectives exemplify the need to apply novel vaccine strategies to high-priority pathogens. One such approach can be termed convergent immunity, where antigens from non-target organisms that contain epitope homologs found in the target organism are applied in vaccines. This approach aims to evoke atypical immune defenses via synergistic processes that (1) afford protective efficacy; (2) target an epitope from one organism that contributes to protective immunity against another; (3) cross-protect against multiple pathogens occupying a common anatomic or immunological niche; and/or (4) overcome immune subversion or avoidance strategies of target pathogens. Thus, convergent immunity has a potential to promote protective efficacy not usually elicited by native antigens from a target pathogen. Variations of this concept have been mainstays in the history of viral and bacterial vaccine development. A more far-reaching example is the pre-clinical evidence that specific fungal antigens can induce cross-kingdom protection against bacterial pathogens. This trans-kingdom protection has been demonstrated in pre-clinical studies of the recombinant Candida albicans agglutinin-like sequence 3 protein (rAls3) where it was shown that a vaccine containing rAls3 provides homologous protection against C. albicans, heterologous protection against several other Candida species, and convergent protection against several strains of S. aureus. Convergent immunity reflects an intriguing new approach to designing and developing vaccine antigens and is considered here in the context of vaccines to target S. aureus.
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Affiliation(s)
- Michael R Yeaman
- Department of Medicine, David Geffen School of Medicine at UCLA , Los Angeles, CA , USA ; Division of Infectious Diseases, Harbor-UCLA Medical Center , Torrance, CA , USA ; Division of Molecular Medicine, Harbor-UCLA Medical Center , Torrance, CA , USA ; St. John's Cardiovascular Research Center, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , USA
| | - Scott G Filler
- Department of Medicine, David Geffen School of Medicine at UCLA , Los Angeles, CA , USA ; Division of Infectious Diseases, Harbor-UCLA Medical Center , Torrance, CA , USA ; St. John's Cardiovascular Research Center, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , USA
| | | | - Ashraf S Ibrahim
- Department of Medicine, David Geffen School of Medicine at UCLA , Los Angeles, CA , USA ; Division of Infectious Diseases, Harbor-UCLA Medical Center , Torrance, CA , USA ; St. John's Cardiovascular Research Center, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , USA
| | - John E Edwards
- Department of Medicine, David Geffen School of Medicine at UCLA , Los Angeles, CA , USA ; Division of Infectious Diseases, Harbor-UCLA Medical Center , Torrance, CA , USA ; St. John's Cardiovascular Research Center, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , USA
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Kaforou M, Wright VJ, Levin M. Host RNA signatures for diagnostics: an example from paediatric tuberculosis in Africa. J Infect 2014; 69 Suppl 1:S28-31. [PMID: 25264160 DOI: 10.1016/j.jinf.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2014] [Indexed: 01/30/2023]
Abstract
Host gene expression profiling is a widely used research tool for assessing the host response to infection in order to provide insight into the immunopathophysiology of disease, as well as the analysis of disease progression and treatment response. It has recently been applied for the diagnosis of tuberculosis in children in Africa, as a result of the implementation of novel statistical methodology that enabled the reduction of a large number of significantly differentially expressed genes into a minimal set, and the development of a 'disease risk score' that could be used to develop a diagnostic test. Whilst the experimental and statistical methodologies are now in place to generate minimal transcriptional signatures that can distinguish disease states, the challenge is how to take these forward into development of a diagnostic test for use in clinical resource-poor settings.
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Affiliation(s)
- Myrsini Kaforou
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, UK; Department of Genomics of Common Disease, School of Public Health, Imperial College London, UK.
| | - Victoria J Wright
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, UK.
| | - Michael Levin
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, UK.
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Smith CL, Dickinson P, Forster T, Craigon M, Ross A, Khondoker MR, France R, Ivens A, Lynn DJ, Orme J, Jackson A, Lacaze P, Flanagan KL, Stenson BJ, Ghazal P. Identification of a human neonatal immune-metabolic network associated with bacterial infection. Nat Commun 2014; 5:4649. [PMID: 25120092 PMCID: PMC4143936 DOI: 10.1038/ncomms5649] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/09/2014] [Indexed: 12/26/2022] Open
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. Infection remains a leading cause of morbidity and mortality in neonates worldwide. Here the authors report disproportionate immune stimulatory, co-inhibitory and metabolic pathway responses that specifically mark bacterial infection and can be used to predict sepsis in neonatal patients at the first clinical signs of infection.
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Affiliation(s)
- Claire L Smith
- 1] Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK [2] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [3]
| | - Paul Dickinson
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK [3]
| | - Thorsten Forster
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK
| | - Marie Craigon
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Alan Ross
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Mizanur R Khondoker
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2]
| | - Rebecca France
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Alasdair Ivens
- 1] Fios Genomics Ltd., ETTC, King's Buildings, Edinburgh EH9 3JL, UK [2]
| | - David J Lynn
- 1] Animal Bioscience Research Department, AGRIC, Teagasc, Grange, Dunsany, Co. Meath, Ireland [2]
| | - Judith Orme
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Allan Jackson
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Paul Lacaze
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Katie L Flanagan
- 1] MRC Research Laboratories, Atlantic Boulevard, PO Box 273, Fajara, Gambia [2]
| | - Benjamin J Stenson
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Peter Ghazal
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK
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Gaviria-Agudelo C, Carter K, Tareen N, Pascual V, Copley LA. Gene expression analysis of children with acute hematogenous osteomyelitis caused by Methicillin-resistant Staphylococcus aureus: correlation with clinical severity of illness. PLoS One 2014; 9:e103523. [PMID: 25076205 PMCID: PMC4116206 DOI: 10.1371/journal.pone.0103523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/03/2014] [Indexed: 12/22/2022] Open
Abstract
Children with acute hematogenous osteomyelitis (AHO) demonstrate a broad spectrum of clinical manifestations, ranging from mild to severe. Several advances have been achieved in the study of host immune response to acute invasive Staphylococcus aureus infections through gene expression analysis. However, previous research has neither attempted to evaluate the response of children with AHO specific to Methicillin-resistant Staphylococcus aureus (MRSA) nor to correlate gene expression with clinical phenotype. Study objective was to correlate gene expression of children with AHO due to MRSA with clinical severity of illness. Whole blood samples were obtained in Tempus tubes from 12 children with osteomyelitis once cultures obtained directly from the site of infection confirmed to be positive for MRSA. Using an Illumina platform and a systems-wide modular analysis, microarray findings from ten of these children were compared to that of nine healthy (age, ethnicity and gender) matched controls and correlated with clinical severity of illness. Children with AHO from MRSA demonstrated over-expression of innate immunity with respect to neutrophil activity, coagulation, inflammatory response, and erythrocyte development. Concurrently, these children demonstrated under-expression of adaptive immunity with respect to lymphocyte activation and activity of T-cell, cytotoxic or NK cell, and B-cell lines. Three over-expressed genes, P2RX1, SORT1, and RETN, and two under-expressed genes, LOC641788 and STAT 4, were significantly correlated with severity of illness. STAT 4 showed the strongest correlation (R2 = –0.83). STAT4 downregulation could potentially explain under-expression of genes related to adaptive immunity in this cohort of patients with AHO. This study identified specific genes which correspond to disease severity during the early hospitalization of children with AHO from MRSA. Pattern recognition of this combination of genes could help to identify in the future severe clinical phenotypes before the disease is fully manifest and direct appropriate attention and resources to those children.
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Affiliation(s)
- Claudia Gaviria-Agudelo
- Department of Pediatrics Infectious Disease, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Children’s Medical Center, Dallas, Texas, United States of America
- * E-mail:
| | - Kristen Carter
- University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Naureen Tareen
- Children’s Medical Center, Dallas, Texas, United States of America
| | - Virginia Pascual
- Baylor Institute for Immunology Research, Dallas, Texas, United States of America
- Texas Scottish Rite Hospital, Dallas, Texas, United States of America
| | - Lawson A. Copley
- Children’s Medical Center, Dallas, Texas, United States of America
- Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Texas Scottish Rite Hospital, Dallas, Texas, United States of America
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40
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Chaussabel D, Baldwin N. Democratizing systems immunology with modular transcriptional repertoire analyses. Nat Rev Immunol 2014; 14:271-80. [PMID: 24662387 DOI: 10.1038/nri3642] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Individual elements that constitute the immune system have been characterized over the few past decades, mostly through reductionist approaches. The introduction of large-scale profiling platforms has more recently facilitated the assessment of these elements on a global scale. However, the analysis and the interpretation of such large-scale datasets remains a challenge and a barrier for the wider adoption of systems approaches in immunological and clinical studies. In this Innovation article, we describe an analytical strategy that relies on the a priori determination of co-dependent gene sets for a given biological system. Such modular transcriptional repertoires can in turn be used to simplify the analysis and the interpretation of large-scale datasets, and to design targeted immune fingerprinting assays and web applications that will further facilitate the dissemination of systems approaches in immunology.
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Affiliation(s)
- Damien Chaussabel
- Benaroya Research Institute Systems Immunology Division, 1201 Ninth Street, Seattle, Washington, 98101-2795, USA
| | - Nicole Baldwin
- Baylor Institute for Immunology Research, Baylor Research Institute, 3434 Live Oak St, Dallas, Texas, 75204, USA
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41
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Blankley S, Berry MPR, Graham CM, Bloom CI, Lipman M, O'Garra A. The application of transcriptional blood signatures to enhance our understanding of the host response to infection: the example of tuberculosis. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130427. [PMID: 24821914 PMCID: PMC4024221 DOI: 10.1098/rstb.2013.0427] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Despite advances in antimicrobials, vaccination and public health measures, infectious diseases remain a leading cause of morbidity and mortality worldwide. With the increase in antimicrobial resistance and the emergence of new pathogens, there remains a need for new and more accurate diagnostics, the ability to monitor adequate treatment response as well as the ability to predict prognosis for an individual. Transcriptional approaches using blood signatures have enabled a better understanding of the host response to diseases, leading not only to new avenues of basic research, but also to the identification of potential biomarkers for use in diagnosis, prognosis and treatment monitoring.
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Affiliation(s)
- Simon Blankley
- Division of Immunoregulation, MRC National Institute for Medical Research, , London NW7 1AA, UK
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42
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Brown AF, Leech JM, Rogers TR, McLoughlin RM. Staphylococcus aureus Colonization: Modulation of Host Immune Response and Impact on Human Vaccine Design. Front Immunol 2014; 4:507. [PMID: 24409186 PMCID: PMC3884195 DOI: 10.3389/fimmu.2013.00507] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 12/21/2013] [Indexed: 12/15/2022] Open
Abstract
In apparent contrast to its invasive potential Staphylococcus aureus colonizes the anterior nares of 20–80% of the human population. The relationship between host and microbe appears particularly individualized and colonization status seems somehow predetermined. After decolonization, persistent carriers often become re-colonized with their prior S. aureus strain, whereas non-carriers resist experimental colonization. Efforts to identify factors facilitating colonization have thus far largely focused on the microorganism rather than on the human host. The host responds to S. aureus nasal colonization via local expression of anti-microbial peptides, lipids, and cytokines. Interplay with the co-existing microbiota also influences colonization and immune regulation. Transient or persistent S. aureus colonization induces specific systemic immune responses. Humoral responses are the most studied of these and little is known of cellular responses induced by colonization. Intriguingly, colonized patients who develop bacteremia may have a lower S. aureus-attributable mortality than their non-colonized counterparts. This could imply a staphylococcal-specific immune “priming” or immunomodulation occurring as a consequence of colonization and impacting on the outcome of infection. This has yet to be fully explored. An effective vaccine remains elusive. Anti-S. aureus vaccine strategies may need to drive both humoral and cellular immune responses to confer efficient protection. Understanding the influence of colonization on adaptive response is essential to intelligent vaccine design, and may determine the efficacy of vaccine-mediated immunity. Clinical trials should consider colonization status and the resulting impact of this on individual patient responses. We urgently need an increased appreciation of colonization and its modulation of host immunity.
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Affiliation(s)
- Aisling F Brown
- Host-Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute , Dublin , Ireland
| | - John M Leech
- Host-Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute , Dublin , Ireland
| | - Thomas R Rogers
- Sir Patrick Dun Laboratory, Department of Clinical Microbiology, Trinity College Dublin, St James's Hospital , Dublin , Ireland
| | - Rachel M McLoughlin
- Host-Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute , Dublin , Ireland
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Mejias A, Dimo B, Suarez NM, Garcia C, Suarez-Arrabal MC, Jartti T, Blankenship D, Jordan-Villegas A, Ardura MI, Xu Z, Banchereau J, Chaussabel D, Ramilo O. Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection. PLoS Med 2013; 10:e1001549. [PMID: 24265599 PMCID: PMC3825655 DOI: 10.1371/journal.pmed.1001549] [Citation(s) in RCA: 237] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 09/30/2013] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the leading cause of viral lower respiratory tract infection (LRTI) and hospitalization in infants. Mostly because of the incomplete understanding of the disease pathogenesis, there is no licensed vaccine, and treatment remains symptomatic. We analyzed whole blood transcriptional profiles to characterize the global host immune response to acute RSV LRTI in infants, to characterize its specificity compared with influenza and human rhinovirus (HRV) LRTI, and to identify biomarkers that can objectively assess RSV disease severity. METHODS AND FINDINGS This was a prospective observational study over six respiratory seasons including a cohort of infants hospitalized with RSV (n = 135), HRV (n = 30), and influenza (n = 16) LRTI, and healthy age- and sex-matched controls (n = 39). A specific RSV transcriptional profile was identified in whole blood (training cohort, n = 45 infants; Dallas, Texas, US) and validated in three different cohorts (test cohort, n = 46, Dallas, Texas, US; validation cohort A, n = 16, Turku, Finland; validation cohort B, n = 28, Columbus, Ohio, US) with high sensitivity (94% [95% CI 87%-98%]) and specificity (98% [95% CI 88%-99%]). It classified infants with RSV LRTI versus HRV or influenza LRTI with 95% accuracy. The immune dysregulation induced by RSV (overexpression of neutrophil, inflammation, and interferon genes, and suppression of T and B cell genes) persisted beyond the acute disease, and immune dysregulation was greatly impaired in younger infants (<6 mo). We identified a genomic score that significantly correlated with outcomes of care including a clinical disease severity score and, more importantly, length of hospitalization and duration of supplemental O2. CONCLUSIONS Blood RNA profiles of infants with RSV LRTI allow specific diagnosis, better understanding of disease pathogenesis, and assessment of disease severity. This study opens new avenues for biomarker discovery and identification of potential therapeutic or preventive targets, and demonstrates that large microarray datasets can be translated into a biologically meaningful context and applied to the clinical setting. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Asuncion Mejias
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail: (AM); (OR)
| | - Blerta Dimo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Nicolas M. Suarez
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Carla Garcia
- Division of Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - M. Carmen Suarez-Arrabal
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Tuomas Jartti
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Derek Blankenship
- Department of Statistics, Baylor Research Institute, Dallas, Texas, United States of America
| | - Alejandro Jordan-Villegas
- Division of Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Monica I. Ardura
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Zhaohui Xu
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
| | - Jacques Banchereau
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
| | - Damien Chaussabel
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
- Benaroya Research Institute, Seattle, Washington, United States of America
| | - Octavio Ramilo
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail: (AM); (OR)
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44
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Nygaard TK, Pallister KB, Zurek OW, Voyich JM. The impact of α-toxin on host cell plasma membrane permeability and cytokine expression during human blood infection by CA-MRSA USA300. J Leukoc Biol 2013; 94:971-9. [PMID: 24026286 DOI: 10.1189/jlb.0213080] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This investigation examines the influence of α-toxin (Hla) expression by CA-MRSA on host immune cell integrity and cytokine expression during infection of human blood. Flow cytometry analysis of human blood infected by Staphylococcus aureus PFGE type USA300 or a USA300Δhla demonstrated that Hla expression significantly increased plasma membrane permeability of human CD14(+) monocytes. The increased susceptibility of human CD14(+) monocytes to Hla toxicity paralleled the high cell-surface expression on these cell types of ADAM10. USA300 rapidly associated with PMNs and monocytes but not T cells following inoculation of human blood. Transcription analysis indicated a strong up-regulation of proinflammatory cytokine transcription following infection of human blood by USA300 and USA300Δhla. CBAs and ELISAs determined that IL-6, IL-10, TNF-α, IFN-γ, IL-1β, IL-8, and IL-4 are significantly up-regulated during the initial phases of human blood infection by USA300 relative to mock-infected blood but failed to distinguish any significant differences in secreted cytokine protein concentrations during infection by USA300Δhla relative to USA300. Collectively, these findings demonstrate that expression of Hla by USA300 has a significant impact on human CD14(+) monocyte plasma membrane integrity but is not exclusively responsible for the proinflammatory cytokine profile induced by USA300 during the initial stages of human blood infection.
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Affiliation(s)
- Tyler K Nygaard
- 1.Lewis Hall, Montana State University, Bozeman, MT 59717, USA.
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45
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Bloom CI, Graham CM, Berry MPR, Rozakeas F, Redford PS, Wang Y, Xu Z, Wilkinson KA, Wilkinson RJ, Kendrick Y, Devouassoux G, Ferry T, Miyara M, Bouvry D, Valeyre D, Dominique V, Gorochov G, Blankenship D, Saadatian M, Vanhems P, Beynon H, Vancheeswaran R, Wickremasinghe M, Chaussabel D, Banchereau J, Pascual V, Ho LP, Lipman M, O'Garra A. Transcriptional blood signatures distinguish pulmonary tuberculosis, pulmonary sarcoidosis, pneumonias and lung cancers. PLoS One 2013; 8:e70630. [PMID: 23940611 PMCID: PMC3734176 DOI: 10.1371/journal.pone.0070630] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 06/20/2013] [Indexed: 01/08/2023] Open
Abstract
RATIONALE New approaches to define factors underlying the immunopathogenesis of pulmonary diseases including sarcoidosis and tuberculosis are needed to develop new treatments and biomarkers. Comparing the blood transcriptional response of tuberculosis to other similar pulmonary diseases will advance knowledge of disease pathways and help distinguish diseases with similar clinical presentations. OBJECTIVES To determine the factors underlying the immunopathogenesis of the granulomatous diseases, sarcoidosis and tuberculosis, by comparing the blood transcriptional responses in these and other pulmonary diseases. METHODS We compared whole blood genome-wide transcriptional profiles in pulmonary sarcoidosis, pulmonary tuberculosis, to community acquired pneumonia and primary lung cancer and healthy controls, before and after treatment, and in purified leucocyte populations. MEASUREMENTS AND MAIN RESULTS An Interferon-inducible neutrophil-driven blood transcriptional signature was present in both sarcoidosis and tuberculosis, with a higher abundance and expression in tuberculosis. Heterogeneity of the sarcoidosis signature correlated significantly with disease activity. Transcriptional profiles in pneumonia and lung cancer revealed an over-abundance of inflammatory transcripts. After successful treatment the transcriptional activity in tuberculosis and pneumonia patients was significantly reduced. However the glucocorticoid-responsive sarcoidosis patients showed a significant increase in transcriptional activity. 144-blood transcripts were able to distinguish tuberculosis from other lung diseases and controls. CONCLUSIONS Tuberculosis and sarcoidosis revealed similar blood transcriptional profiles, dominated by interferon-inducible transcripts, while pneumonia and lung cancer showed distinct signatures, dominated by inflammatory genes. There were also significant differences between tuberculosis and sarcoidosis in the degree of their transcriptional activity, the heterogeneity of their profiles and their transcriptional response to treatment.
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Affiliation(s)
- Chloe I Bloom
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom.
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46
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Gene expression profiles in febrile children with defined viral and bacterial infection. Proc Natl Acad Sci U S A 2013; 110:12792-7. [PMID: 23858444 DOI: 10.1073/pnas.1302968110] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Viral infections are common causes of fever without an apparent source in young children. Despite absence of bacterial infection, many febrile children are treated with antibiotics. Virus and bacteria interact with different pattern recognition receptors in circulating blood leukocytes, triggering specific host transcriptional programs mediating immune response. Therefore, unique transcriptional signatures may be defined that discriminate viral from bacterial causes of fever without an apparent source. Gene expression microarray analyses were conducted on blood samples from 30 febrile children positive for adenovirus, human herpesvirus 6, or enterovirus infection or with acute bacterial infection and 22 afebrile controls. Blood leukocyte transcriptional profiles clearly distinguished virus-positive febrile children from both virus-negative afebrile controls and afebrile children with the same viruses present in the febrile children. Virus-specific gene expression profiles could be defined. The IFN signaling pathway was uniquely activated in febrile children with viral infection, whereas the integrin signaling pathway was uniquely activated in children with bacterial infection. Transcriptional profiles classified febrile children with viral or bacterial infection with better accuracy than white blood cell count in the blood. Similarly accurate classification was shown with data from an independent study using different microarray platforms. Our results support the paradigm of using host response to define the etiology of childhood infections. This approach could be an important supplement to highly sensitive tests that detect the presence of a possible pathogen but do not address its pathogenic role in the patient being evaluated.
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Abstract
Developing a universal vaccine for S. aureus is a top priority but to date we have only had failures in human clinical trials. Given the plethora of bacterial virulence factors, broad range of the health of humans at-risk for infections, lack of any information regarding immune effectors mediating protection for any manifestation of S. aureus infection and overall competence of this organism as a colonizer, commensal and pathogen, we may just simply have to accept the fact that we will not get a universal vaccine. Antigenic variation is a major challenge for some vaccine targets and for many conserved targets the organism can easily decrease or even eliminate expression to avoid immune effectors without compromise to infectivity and ability to cause disease. Studies of human immune responses similarly have been unable to identify any clear mediators of immunity and data from such studies can only eliminate those found not to be associated with protection or that might serve as a marker for individuals with a higher level of resistance to infection. Animal studies are not predictive of success in humans and unlikely will be except in hindsight if and when we develop an efficacious vaccine. Successful vaccines for other bacteria based on capsular polysaccharides have not worked to date for S. aureus, and laboratory studies combining antibody to the major capsular serotypes and the other S. aureus surface polysaccharide, poly-N-acetyl glucosamine, unexpectedly showed interference not augmentation of immunity. Potential pathways toward vaccine development do exist but for the foreseeable future will be based on empiric approaches derived from laboratory-based in vitro and animal tests and not on inducing a known immune effector that predicts human resistance to infection.
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Affiliation(s)
- Gerald B Pier
- Division of Infectious Diseases; Department of Medicine; Brigham and Women's Hospital; Harvard Medical School; Boston, MA USA
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48
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Sharma-Kuinkel BK, Zhang Y, Yan Q, Ahn SH, Fowler VG. Host gene expression profiling and in vivo cytokine studies to characterize the role of linezolid and vancomycin in methicillin-resistant Staphylococcus aureus (MRSA) murine sepsis model. PLoS One 2013; 8:e60463. [PMID: 23565251 PMCID: PMC3614971 DOI: 10.1371/journal.pone.0060463] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/26/2013] [Indexed: 01/11/2023] Open
Abstract
Linezolid (L), a potent antibiotic for Methicillin Resistant Staphylococcus aureus (MRSA), inhibits bacterial protein synthesis. By contrast, vancomycin (V) is a cell wall active agent. Here, we used a murine sepsis model to test the hypothesis that L treatment is associated with differences in bacterial and host characteristics as compared to V. Mice were injected with S. aureus USA300, and then intravenously treated with 25 mg/kg of either L or V at 2 hours post infection (hpi). In vivo alpha-hemolysin production was reduced in both L and V-treated mice compared to untreated mice but the reduction did not reach the statistical significance [P = 0.12 for L; P = 0.70 for V). PVL was significantly reduced in L-treated mice compared to untreated mice (P = 0.02). However the reduction of in vivo PVL did not reach the statistical significance in V- treated mice compared to untreated mice (P = 0.27). Both antibiotics significantly reduced IL-1β production [P = 0.001 for L; P = 0.006 for V]. IL-6 was significantly reduced with L but not V antibiotic treatment [P<0.001 for L; P = 0.11 for V]. Neither treatment significantly reduced production of TNF-α. Whole-blood gene expression profiling showed no significant effect of L and V on uninfected mice. In S. aureus-infected mice, L altered the expression of a greater number of genes than V (95 vs. 42; P = 0.001). Pathway analysis for the differentially expressed genes identified toll-like receptor signaling pathway to be common to each S. aureus-infected comparison. Expression of immunomodulatory genes like Cxcl9, Cxcl10, Il1r2, Cd14 and Nfkbia was different among the treatment groups. Glycerolipid metabolism pathway was uniquely associated with L treatment in S. aureus infection. This study demonstrates that, as compared to V, treatment with L is associated with reduced levels of toxin production, differences in host inflammatory response, and distinct host gene expression characteristics in MRSA sepsis.
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Affiliation(s)
- Batu K. Sharma-Kuinkel
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (BKSK); (SHA)
| | - Yurong Zhang
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Qin Yan
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sun Hee Ahn
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (BKSK); (SHA)
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
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49
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Ahn SH, Tsalik EL, Cyr DD, Zhang Y, van Velkinburgh JC, Langley RJ, Glickman SW, Cairns CB, Zaas AK, Rivers EP, Otero RM, Veldman T, Kingsmore SF, Lucas J, Woods CW, Ginsburg GS, Fowler VG. Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans. PLoS One 2013; 8:e48979. [PMID: 23326304 PMCID: PMC3541361 DOI: 10.1371/journal.pone.0048979] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 09/27/2012] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureus causes a spectrum of human infection. Diagnostic delays and uncertainty lead to treatment delays and inappropriate antibiotic use. A growing literature suggests the host’s inflammatory response to the pathogen represents a potential tool to improve upon current diagnostics. The hypothesis of this study is that the host responds differently to S. aureus than to E. coli infection in a quantifiable way, providing a new diagnostic avenue. This study uses Bayesian sparse factor modeling and penalized binary regression to define peripheral blood gene-expression classifiers of murine and human S. aureus infection. The murine-derived classifier distinguished S. aureus infection from healthy controls and Escherichia coli-infected mice across a range of conditions (mouse and bacterial strain, time post infection) and was validated in outbred mice (AUC>0.97). A S. aureus classifier derived from a cohort of 94 human subjects distinguished S. aureus blood stream infection (BSI) from healthy subjects (AUC 0.99) and E. coli BSI (AUC 0.84). Murine and human responses to S. aureus infection share common biological pathways, allowing the murine model to classify S. aureus BSI in humans (AUC 0.84). Both murine and human S. aureus classifiers were validated in an independent human cohort (AUC 0.95 and 0.92, respectively). The approach described here lends insight into the conserved and disparate pathways utilized by mice and humans in response to these infections. Furthermore, this study advances our understanding of S. aureus infection; the host response to it; and identifies new diagnostic and therapeutic avenues.
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Affiliation(s)
- Sun Hee Ahn
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Ephraim L. Tsalik
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Section on Infectious Diseases, Durham Veteran’s Affairs Medical Center, Durham, North Carolina, United States of America
| | - Derek D. Cyr
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Yurong Zhang
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Jennifer C. van Velkinburgh
- van Velkinburgh Initiative for Collaborative BioMedical Research, Santa Fe, New Mexico, United States of America
| | - Raymond J. Langley
- Immunology Division, Lovelace Respiratory Research Institute, Albuquerque, New Mexico, United States of America
| | - Seth W. Glickman
- Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Charles B. Cairns
- Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Aimee K. Zaas
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Emanuel P. Rivers
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, Michigan, United States of America
| | - Ronny M. Otero
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, Michigan, United States of America
| | - Tim Veldman
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Stephen F. Kingsmore
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospitals and Clinics, Kansas City, Missouri, United States of America
| | - Joseph Lucas
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Christopher W. Woods
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Section on Infectious Diseases, Durham Veteran’s Affairs Medical Center, Durham, North Carolina, United States of America
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Geoffrey S. Ginsburg
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
- * E-mail: (GSG); (VGF)
| | - Vance G. Fowler
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
- * E-mail: (GSG); (VGF)
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Ginsburg GS, Woods CW. The host response to infection: advancing a novel diagnostic paradigm. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2012; 16:168. [PMID: 23134694 PMCID: PMC3672566 DOI: 10.1186/cc11685] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Capturing the host response by using genomic technologies such as transcriptional profiling provides a new paradigm for classifying and diagnosing infectious disease and for potentially distinguishing infection from other causes of serious respiratory illness. This strategy has been used to define a blood-based RNA signature as a classifier for pandemic H1N1 influenza infection that is distinct from bacterial pneumonia and other inflammatory causes of respiratory disease. To realize the full potential of this approach as a diagnostic test will require additional independent validation of the results and studies to examine the specificity of this signature for viral versus bacterial infection or co-infection.
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