201
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Jackson DJ, Lemanske RF, Gern JE. Infections and Asthma. PEDIATRIC ALLERGY: PRINCIPLES AND PRACTICE 2016. [PMCID: PMC7173469 DOI: 10.1016/b978-0-323-29875-9.00031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Wheezing viral respiratory illnesses are the most common initial presentation of childhood asthma. Once asthma is established, viral infections, most notably rhinovirus (RV), are the most frequent trigger of severe asthma exacerbations. RV-C appears to be a particularly pathogenic virus in children with asthma. Evidence has recently emerged to suggest that bacterial pathogens in the lower airway may contribute to the expression of asthma. Ongoing studies are critical to our understanding of the role of the airway microbiome in asthma inception and exacerbation. Synergistic interactions between underlying allergy and virus infections play an important mechanistic role in asthma inception and exacerbation, and are an important therapeutic target. Novel therapies are needed to prevent and treat virus-induced wheezing and asthma exacerbations.
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202
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Biomarkers of Gastrointestinal Host Responses to Microbial Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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203
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Abraha HY, Lanctôt KL, Paes B. Risk of respiratory syncytial virus infection in preterm infants: reviewing the need for prevention. Expert Rev Respir Med 2015; 9:779-99. [PMID: 26457970 DOI: 10.1586/17476348.2015.1098536] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Premature infants are at substantial risk for a spectrum of morbidities that are gestational age dependent. Respiratory syncytial virus (RSV) infection is most common in the first two years of life with the highest burden in children aged <6 months. Preterm infants ≤35 weeks' gestation are handicapped by incomplete immunological and pulmonary maturation and immature premorbid lung function with the added risk of bronchopulmonary dysplasia. Superimposed RSV infection incites marked neutrophilic airway inflammation and innate immunological responses that further compromise normal airway modeling. This review addresses the epidemiology and burden of RSV disease, focusing on the preterm population. Risk factors that determine RSV-disease severity and hospitalization and the impact on healthcare resource utilization and potential long-term respiratory sequelae are discussed. The importance of disease prevention and the evidence-based rationale for prophylaxis with palivizumab is explored, while awaiting the development of a universal vaccine.
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Affiliation(s)
- Haben Y Abraha
- a Medical Outcomes and Research in Economics (MORE®) Research Group, Sunnybrook Health Sciences Centre , University of Toronto , Toronto , Ontario , Canada
| | - Krista L Lanctôt
- a Medical Outcomes and Research in Economics (MORE®) Research Group, Sunnybrook Health Sciences Centre , University of Toronto , Toronto , Ontario , Canada
| | - Bosco Paes
- b Division of Neonatology, Department of Pediatrics , McMaster University , Hamilton , Ontario , Canada
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204
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Brown PM, Schneeberger DL, Piedimonte G. Biomarkers of respiratory syncytial virus (RSV) infection: specific neutrophil and cytokine levels provide increased accuracy in predicting disease severity. Paediatr Respir Rev 2015; 16:232-40. [PMID: 26074450 PMCID: PMC4656140 DOI: 10.1016/j.prrv.2015.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 12/17/2022]
Abstract
Despite fundamental advances in the research on respiratory syncytial virus (RSV) since its initial identification almost 60 years ago, recurring failures in developing vaccines and pharmacologic strategies effective in controlling the infection have allowed RSV to become a leading cause of global infant morbidity and mortality. Indeed, the burden of this infection on families and health care organizations worldwide continues to escalate and its financial costs are growing. Furthermore, strong epidemiologic evidence indicates that early-life lower respiratory tract infections caused by RSV lead to the development of recurrent wheezing and childhood asthma. While some progress has been made in the identification of reliable biomarkers for RSV bronchiolitis, a "one size fits all" biomarker capable of accurately and consistently predicting disease severity and post-acute outcomes has yet to be discovered. Therefore, it is of great importance on a global scale to identify useful biomarkers for this infection that will allow pediatricians to cost-effectively predict the clinical course of the disease, as well as monitor the efficacy of new therapeutic strategies.
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Affiliation(s)
| | | | - Giovanni Piedimonte
- Center for Pediatric Research, Pediatric Institute and Children's Hospitals, The Cleveland Clinic.
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205
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Shah SS, Ambroggio L, Florin TA. Biomarkers for Predicting Illness Severity in Children With Acute Lower Respiratory Tract Infections. J Pediatric Infect Dis Soc 2015; 4:189-91. [PMID: 26336602 PMCID: PMC4554202 DOI: 10.1093/jpids/piu041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Samir S. Shah
- Division of Infectious Diseases;,Division of Hospital Medicine
| | - Lilliam Ambroggio
- Division of Hospital Medicine;,Division of Biostatistics and Epidemiology
| | - Todd A. Florin
- Division of Emergency Medicine,Cincinnati Children's Hospital Medical Center, Ohio
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206
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Shrivastava P, Atanley E, Sarkar I, Watkiss E, Gomis S, van Drunen Littel-van den Hurk S. Blunted inflammatory and mucosal IgA responses to pneumonia virus of mice in C57BL/6 neonates are correlated to reduced protective immunity upon re-infection as elderly mice. Virology 2015; 485:233-43. [PMID: 26298860 DOI: 10.1016/j.virol.2015.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 11/17/2022]
Abstract
Respiratory syncytial virus is a major cause of bronchiolitis in infants and pneumonia virus of mice (PVM) causes similar disease in mice. The impact of PVM infection in BALB/c and C57BL/6 neonates, and upon re-infection as elderly mice, was compared. As previously shown for adult mice, PVM caused more disease in BALB/c than in C57BL/6 neonates. After PVM-15 infection BALB/c neonates showed higher production of inflammatory mediators, more influx of plasmacytoid dendritic cells and higher IFN-α expression, and more IgA in the lungs than C57BL/6 neonates. After re-infection as elderly, BALB/c mice developed virus neutralizing antibodies in serum and lung, and were protected from clinical disease, whereas C57BL/6 mice did not develop an anamnestic response and were not protected. These results suggest that an effective local innate response, as well as priming of mucosal adaptive responses in neonates after PVM-15 infection is correlated to decreased susceptibility and protection upon re-infection.
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Affiliation(s)
- Pratima Shrivastava
- VIDO-InterVac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, Canada S7N 5E3
| | - Ethel Atanley
- VIDO-InterVac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, Canada S7N 5E3; Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Indranil Sarkar
- VIDO-InterVac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, Canada S7N 5E3; Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Ellen Watkiss
- VIDO-InterVac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, Canada S7N 5E3; Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan, Canada S7N 5B4
| | - Susantha Gomis
- Veterinary Pathology, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan, Canada S7N 5B4
| | - Sylvia van Drunen Littel-van den Hurk
- VIDO-InterVac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, Canada S7N 5E3; Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5.
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207
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van den Kieboom CH, Ferwerda G, de Baere I, Vermeiren H, de Groot R, Rossau R, de Jonge MI. Assessment of a molecular diagnostic platform for integrated isolation and quantification of mRNA in whole blood. Eur J Clin Microbiol Infect Dis 2015; 34:2209-12. [PMID: 26298058 PMCID: PMC4607718 DOI: 10.1007/s10096-015-2470-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/02/2015] [Indexed: 11/24/2022]
Abstract
Implementation of point-of-care tests may facilitate the health management of infectious diseases by reducing the timeframe on pathogen identification and host response measurements, allowing for immediate diagnosis and guided clinical intervention. In this feasibility study, a novel totally integrated and fully automated real-time polymerase chain reaction (PCR) platform (Idylla™, Biocartis) was assessed to determine the mRNA expression levels of multiple genes from 1 mL of whole blood. To this purpose, a sample-in result-out assay, including mRNA extraction and RT-qPCR-based detection, was ported to the platform. The genes used (matrix metallopeptidase 9, olfactomedin 4, NB1 glycoprotein and lipocalin 2) were previously identified as predictive for severity of disease caused by infection with respiratory syncytial virus (RSV). The reproducibility and robustness of the prototype assay was determined using the blood samples of 21 healthy donors. The data showed that the Idylla™ platform allows for a fast and user-friendly determination of the relative expression levels of the four selected mRNA markers.
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Affiliation(s)
- C H van den Kieboom
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands. .,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
| | - G Ferwerda
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - I de Baere
- R&D Department, Biocartis N.V., Mechelen, Belgium
| | - H Vermeiren
- R&D Department, Biocartis N.V., Mechelen, Belgium
| | - R de Groot
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Rossau
- R&D Department, Biocartis N.V., Mechelen, Belgium
| | - M I de Jonge
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
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208
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Geerdink RJ, Pillay J, Meyaard L, Bont L. Neutrophils in respiratory syncytial virus infection: A target for asthma prevention. J Allergy Clin Immunol 2015; 136:838-47. [PMID: 26277597 PMCID: PMC7112351 DOI: 10.1016/j.jaci.2015.06.034] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/30/2015] [Accepted: 06/05/2015] [Indexed: 12/25/2022]
Abstract
Lower respiratory tract infections by respiratory syncytial virus (RSV) are the foremost cause of infant hospitalization and are implicated in lasting pulmonary impairment and the development of asthma. Neutrophils infiltrate the airways of pediatric patients with RSV-induced bronchiolitis in vast numbers: approximately 80% of infiltrated cells are neutrophils. However, why neutrophils are recruited to the site of viral respiratory tract infection is not clear. In this review we discuss the beneficial and pathologic contributions of neutrophils to the immune response against RSV infection. Neutrophils can limit viral replication and spread, as well as stimulate an effective antiviral adaptive immune response. However, low specificity of neutrophil antimicrobial armaments allows for collateral tissue damage. Neutrophil-induced injury to the airways during the delicate period of infant lung development has lasting adverse consequences for pulmonary architecture and might promote the onset of asthma in susceptible subjects. We suggest that pharmacologic modulation of neutrophils should be explored as a viable future therapy for severe RSV-induced bronchiolitis and thereby prevent the inception of subsequent asthma. The antiviral functions of neutrophils suggest that targeting of neutrophils in patients with RSV-induced bronchiolitis is best performed under the umbrella of antiviral treatment.
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Affiliation(s)
- Ruben J Geerdink
- Department of Immunology, Laboratory for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Janesh Pillay
- Department of Respiratory Medicine, Laboratory for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands; Department of Anaesthesiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Linde Meyaard
- Department of Immunology, Laboratory for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Louis Bont
- Department of Immunology, Laboratory for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands; Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.
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209
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Groen N, Tahmasebi N, Shimizu F, Sano Y, Kanda T, Barbieri D, Yuan H, Habibovic P, van Blitterswijk CA, de Boer J. Exploring the Material-Induced Transcriptional Landscape of Osteoblasts on Bone Graft Materials. Adv Healthc Mater 2015; 4:1691-700. [PMID: 26046651 DOI: 10.1002/adhm.201500171] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/30/2015] [Indexed: 01/14/2023]
Abstract
During the past decades, there have been major advances in the field of biomaterials, thereby generating a vast variety of materials for a broad range of tissue engineering and regeneration applications. Although gene expression profiling has been used occasionally in biomaterial research, its usefulness for understanding cell-biomaterial interactions should be further explored for it to fulfill its promise as a tool to assess and improve material properties. Here, the transcriptional landscape induced by 23 materials is explored with a variety of properties within the scope of bone regeneration. An osteoblast cell line is used to identify the gene expression profiles that can be adopted in response to biophysical and chemical cues. It is shown that TGF-β and WNT signaling may be involved in the cellular response to osteoinductive materials along with differential cell adhesion kinetics via attenuated FAK signaling. The previously reported effect of calcium and phosphate on BMP2 and TGF-β signaling is confirmed and the biological effect of the addition of nanohydroxyapatite in poly (d,l-lactic acid) polymer particles is studied. Together with future applications, this approach will help researchers understand cellular responses in relation to material properties, which will promote the development of more effective biomaterials for applications in tissue regeneration.
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Affiliation(s)
- Nathalie Groen
- Department of Tissue Regeneration; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; Enschede 7500 AE The Netherlands
| | - Niloofar Tahmasebi
- Department of Tissue Regeneration; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; Enschede 7500 AE The Netherlands
| | - Fumitaka Shimizu
- Department of Neurology and Clinical Neuroscience; Yamaguchi University Graduate School of Medicine; Yamaguchi 755-8505 Japan
| | - Yasuteru Sano
- Department of Neurology and Clinical Neuroscience; Yamaguchi University Graduate School of Medicine; Yamaguchi 755-8505 Japan
| | - Takashi Kanda
- Department of Neurology and Clinical Neuroscience; Yamaguchi University Graduate School of Medicine; Yamaguchi 755-8505 Japan
| | - Davide Barbieri
- Department of Tissue Regeneration; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; Enschede 7500 AE The Netherlands
- Xpand Biotechnology BV; Prof. Bronkhorstlaan 10-D 3723 MB Bilthoven The Netherlands
| | - Huipin Yuan
- Department of Tissue Regeneration; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; Enschede 7500 AE The Netherlands
- Xpand Biotechnology BV; Prof. Bronkhorstlaan 10-D 3723 MB Bilthoven The Netherlands
| | - Pamela Habibovic
- Department of Tissue Regeneration; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; Enschede 7500 AE The Netherlands
- MERLN Institute for Technology-Inspired Regenerative Medicine; Maastricht University; 6200 MD Maastricht The Netherlands
| | - Clemens A van Blitterswijk
- Department of Tissue Regeneration; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; Enschede 7500 AE The Netherlands
- MERLN Institute for Technology-Inspired Regenerative Medicine; Maastricht University; 6200 MD Maastricht The Netherlands
| | - Jan de Boer
- Department of Tissue Regeneration; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; Enschede 7500 AE The Netherlands
- MERLN Institute for Technology-Inspired Regenerative Medicine; Maastricht University; 6200 MD Maastricht The Netherlands
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210
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Guo X, Liu T, Shi H, Wang J, Ji P, Wang H, Hou Y, Tan RX, Li E. Respiratory Syncytial Virus Infection Upregulates NLRC5 and Major Histocompatibility Complex Class I Expression through RIG-I Induction in Airway Epithelial Cells. J Virol 2015; 89:7636-45. [PMID: 25972545 PMCID: PMC4505675 DOI: 10.1128/jvi.00349-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/06/2015] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED Respiratory syncytial virus (RSV) is the leading cause of acute respiratory tract viral infection in infants, causing bronchiolitis and pneumonia. The host antiviral response to RSV acts via retinoic acid-inducible gene I (RIG-I). We show here that RSV infection upregulates major histocompatibility complex class I (MHC-I) expression through the induction of NLRC5, a NOD-like, CARD domain-containing intracellular protein that has recently been identified as a class I MHC transactivator (CITA). RSV infection of A549 cells promotes upregulation of NLRC5 via beta interferon (IFN-β) production, since the NLRC5-inducing activity in a conditioned medium from RSV-infected A549 cells was removed by antibody to IFN-β, but not by antibody to IFN-γ. RSV infection resulted in RIG-I upregulation and induction of NLRC5 and MHC-I. Suppression of RIG-I induction significantly blocked NLRC5, as well as MHC-I, upregulation and diminished IRF3 activation. Importantly, Vero cells deficient in interferon production still upregulated MHC-I following introduction of the RSV genome by infection or transfection, further supporting a key role for RIG-I. A model is therefore proposed in which the host upregulates MHC-I expression during RSV infection directly via the induction of RIG-I and NLRC5 expression. Since elevated expression of MHC-I molecules can sensitize host cells to T lymphocyte-mediated cytotoxicity or immunopathologic damage, the results have significant implications for the modification of immunity in RSV disease. IMPORTANCE Human respiratory syncytial virus (RSV) is the leading cause of bronchiolitis and pneumonia in infants and young children worldwide. Infection early in life is linked to persistent wheezing and allergic asthma in later life, possibly related to upregulation of major histocompatibility class I (MHC-I) on the cell surface, which facilitates cytotoxic T cell activation and antiviral immunity. Here, we show that RSV infection of lung epithelial cells induces expression of RIG-I, resulting in induction of a class I MHC transactivator, NLRC5, and subsequent upregulation of MHC-I. Suppression of RIG-I induction blocked RSV-induced NLRC5 expression and MHC-I upregulation. Increased MHC-I expression may exacerbate the RSV disease condition due to immunopathologic damage, linking the innate immune response to RSV disease.
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Affiliation(s)
- Xuancheng Guo
- State Key Laboratory of Pharmaceutical Biotechnology and School of Medicine, Nanjing University, Nanjing, Jiangsu, China Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Taixiang Liu
- Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, China Jiangsu Province Blood Center, Nanjing, Jiangsu, China
| | - Hengfei Shi
- State Key Laboratory of Pharmaceutical Biotechnology and School of Medicine, Nanjing University, Nanjing, Jiangsu, China Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Jingjing Wang
- State Key Laboratory of Pharmaceutical Biotechnology and School of Medicine, Nanjing University, Nanjing, Jiangsu, China College of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Ping Ji
- State Key Laboratory of Pharmaceutical Biotechnology and School of Medicine, Nanjing University, Nanjing, Jiangsu, China Jiangsu Province Blood Center, Nanjing, Jiangsu, China
| | - Hongwei Wang
- Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Yayi Hou
- State Key Laboratory of Pharmaceutical Biotechnology and School of Medicine, Nanjing University, Nanjing, Jiangsu, China Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology and School of Medicine, Nanjing University, Nanjing, Jiangsu, China College of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Erguang Li
- State Key Laboratory of Pharmaceutical Biotechnology and School of Medicine, Nanjing University, Nanjing, Jiangsu, China Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, China
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211
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Brand HK, Ahout IML, de Ridder D, van Diepen A, Li Y, Zaalberg M, Andeweg A, Roeleveld N, de Groot R, Warris A, Hermans PWM, Ferwerda G, Staal FJT. Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection. PLoS One 2015; 10:e0131927. [PMID: 26162090 PMCID: PMC4498630 DOI: 10.1371/journal.pone.0131927] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/08/2015] [Indexed: 12/20/2022] Open
Abstract
Background Respiratory viral infections follow an unpredictable clinical course in young children ranging from a common cold to respiratory failure. The transition from mild to severe disease occurs rapidly and is difficult to predict. The pathophysiology underlying disease severity has remained elusive. There is an urgent need to better understand the immune response in this disease to come up with biomarkers that may aid clinical decision making. Methods In a prospective study, flow cytometric and genome-wide gene expression analyses were performed on blood samples of 26 children with a diagnosis of severe, moderate or mild Respiratory Syncytial Virus (RSV) infection. Differentially expressed genes were validated using Q-PCR in a second cohort of 80 children during three consecutive winter seasons. FACS analyses were also performed in the second cohort and on recovery samples of severe cases in the first cohort. Results Severe RSV infection was associated with a transient but marked decrease in CD4+ T, CD8+ T, and NK cells in peripheral blood. Gene expression analyses in both cohorts identified Olfactomedin4 (OLFM4) as a fully discriminative marker between children with mild and severe RSV infection, giving a PAM cross-validation error of 0%. Patients with an OLFM4 gene expression level above -7.5 were 6 times more likely to develop severe disease, after correction for age at hospitalization and gestational age. Conclusion By combining genome-wide expression profiling of blood cell subsets with clinically well-annotated samples, OLFM4 was identified as a biomarker for severity of pediatric RSV infection.
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Affiliation(s)
- H. K. Brand
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - I. M. L. Ahout
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - D. de Ridder
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - A. van Diepen
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Y. Li
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M. Zaalberg
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
| | - A. Andeweg
- Department of Virology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - N. Roeleveld
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Department for Health Evidence, Radboud university medical center, Nijmegen, the Netherlands
| | - R. de Groot
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - A. Warris
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - P. W. M. Hermans
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - G. Ferwerda
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud university medical center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
- * E-mail:
| | - F. J. T. Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
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212
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213
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Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism. Mol Ther 2015; 23:1622-9. [PMID: 26156244 DOI: 10.1038/mt.2015.124] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/27/2015] [Indexed: 11/08/2022] Open
Abstract
Target identification is highly instructive in defining the biological roles of microRNAs. However, little is known about other small noncoding RNAs; for example, tRNA-derived RNA Fragments (tRFs). Some tRFs exhibit a gene-silencing mechanism distinctly different from that of typical microRNAs. We recently demonstrated that a respiratory syncytial virus (RSV)-induced tRF, called tRF5-GluCTC, promotes RSV replication. RSV is the single most important cause of lower respiratory tract infection in children. By using biochemical screening and bioinformatics analyses, we have identified apolipoprotein E receptor 2 (APOER2) as a target of tRF5-GluCTC. The 3'-portion of tRF5-GluCTC recognizes a target site in the 3'-untranslated region of APOER2 and suppresses its expression. We have also discovered that APOER2 is an anti-RSV protein whose suppression by tRF5-GluCTC promotes RSV replication. Our report represents the first identification of a natural target of a tRF and illustrates how a virus utilizes a host tRF to control a host gene to favor its replication.
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214
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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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Nasopharyngeal bacterial burden and antibiotics: Influence on inflammatory markers and disease severity in infants with respiratory syncytial virus bronchiolitis. J Infect 2015; 71:458-69. [PMID: 26149186 DOI: 10.1016/j.jinf.2015.06.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 06/23/2015] [Accepted: 06/27/2015] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Animal studies suggest that RSV increases nasopharyngeal (NP) bacterial colonization facilitating bacterial infections. We investigated the influence of antibiotic treatment and colonization with potentially pathogenic bacteria on inflammatory markers and disease severity in RSV-infected in infants. METHODS Healthy young infants hospitalized with RSV bronchiolitis (n = 136) and age-matched healthy controls (n = 23) were enrolled and NP samples cultured for potentially pathogenic bacteria including: Gram-positive bacteria (GPB): Staphylococcus aureus, Streptococcus pneumoniae, β-hemolytic Streptococcus; and Gram-negative bacteria (GNB): Moraxella catarrhalis and Haemophilus influenzae. Clinical parameters and plasma IL-8, IL-6 and TNF-α concentrations were compared according to the bacterial class and antibiotic treatment. RESULTS Antibiotic treatment decreased by 10-fold NP bacterial recovery. Eighty-one percent of RSV infants who did not receive antibiotics before sample collection were colonized with pathogenic bacteria. Overall, GNB were identified in 21% of patients versus 4% of controls who were mostly colonized with GPB. Additionally, in RSV patients NP white blood cell counts (p = 0.026), and blood neutrophils (p = 0.02) were higher in those colonized with potentially pathogenic bacteria versus respiratory flora. RSV patients colonized with GNB had higher plasma IL-8 (p = 0.01) and IL-6 (p < 0.01) concentrations than controls, and required longer duration of oxygen (p = 0.049). CONCLUSIONS Infants with RSV bronchiolitis colonized with potentially pathogenic bacteria had increased numbers of mucosal and systemic inflammatory cells. Specifically, colonization with GNB was associated with higher concentrations of proinflammatory cytokines and a trend towards increased disease severity.
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O'Ryan ML, Lucero Y, Rabello M, Mamani N, Salinas AM, Peña A, Torres-Torreti JP, Mejías A, Ramilo O, Suarez N, Reynolds HE, Orellana A, Lagomarcino AJ. Persistent and transient Helicobacter pylori infections in early childhood. Clin Infect Dis 2015; 61:211-8. [PMID: 25838286 DOI: 10.1093/cid/civ256] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/21/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Helicobacter pylori, the main cause of peptic ulcer disease and gastric cancer in adult populations, is generally acquired during the first years of life. Infection can be persistent or transient and bacterial and host factors determining persistence are largely unknown and may prove relevant for future disease. METHODS Two cohorts of healthy Chilean infants (313 total) were evaluated every 3 months for 18-57 months to determine pathogen- and host-factors associated with persistent and transient infection. RESULTS One-third had at least one positive stool ELISA by age 3, with 20% overall persistence. Persistent infections were acquired at an earlier age, associated with more household members, decreased duration of breastfeeding, and nonsecretor status compared to transient infections. The cagA positive strains were more common in persistent stools, and nearly 60% of fully characterized persistent stool samples amplified cagA/vacAs1m1. Persistent children were more likely to elicit a serologic immune response, and both infection groups had differential gene expression profiles, including genes associated with cancer suppression when compared to healthy controls. CONCLUSIONS These results indicate that persistent H. pylori infections acquired early in life are associated with specific host and/or strain profiles possibly associated with future disease occurrence.
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Affiliation(s)
- Miguel L O'Ryan
- Microbiology and Mycology Program, Institute of Biomedical Sciences
| | - Yalda Lucero
- Luis Calvo Mackenna Hospital, Department of Pediatrics and Pediatric Surgery (Eastern Campus), Faculty of Medicine, Universidad de Chile
| | - Marcela Rabello
- Luis Calvo Mackenna Hospital, Department of Pediatrics and Pediatric Surgery (Eastern Campus), Faculty of Medicine, Universidad de Chile
| | - Nora Mamani
- Microbiology and Mycology Program, Institute of Biomedical Sciences
| | - Ana María Salinas
- School of Medical Technology, Faculty of Health, Universidad Santo Tomás
| | - Alfredo Peña
- Pediatric Service, Sótero del Río Hospital, Santiago, Chile
| | - Juan Pablo Torres-Torreti
- Luis Calvo Mackenna Hospital, Department of Pediatrics and Pediatric Surgery (Eastern Campus), Faculty of Medicine, Universidad de Chile
| | - Asunción Mejías
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University School of Medicine, Columbus
| | - Octavio Ramilo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University School of Medicine, Columbus
| | - Nicolas Suarez
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University School of Medicine, Columbus
| | - Henry E Reynolds
- Physiopathology Program Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago
| | - Andrea Orellana
- Microbiology and Mycology Program, Institute of Biomedical Sciences
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Gardeux V, Bosco A, Li J, Halonen MJ, Jackson D, Martinez FD, Lussier YA. Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. J Biomed Inform 2015; 55:94-103. [PMID: 25797143 DOI: 10.1016/j.jbi.2015.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/25/2015] [Accepted: 03/13/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Understanding individual patient host-response to viruses is key to designing optimal personalized therapy. Unsurprisingly, in vivo human experimentation to understand individualized dynamic response of the transcriptome to viruses are rarely studied because of the obvious limitations stemming from ethical considerations of the clinical risk. OBJECTIVE In this rhinovirus study, we first hypothesized that ex vivo human cells response to virus can serve as a proxy for otherwise controversial in vivo human experimentation. We further hypothesized that the N-of-1-pathways framework, previously validated in cancer, can be effective in understanding the more subtle individual transcriptomic response to viral infection. METHOD N-of-1-pathways computes a significance score for a given list of gene sets at the patient level, using merely the 'omics profiles of two paired samples as input. We extracted the peripheral blood mononuclear cells (PBMC) of four human subjects, aliquoted in two paired samples, one subjected to ex vivo rhinovirus infection. Their dysregulated genes and pathways were then compared to those of 9 human subjects prior and after intranasal inoculation in vivo with rhinovirus. Additionally, we developed the Similarity Venn Diagram, a novel visualization method that goes beyond conventional overlap to show the similarity between two sets of qualitative measures. RESULTS We evaluated the individual N-of-1-pathways results using two established cohort-based methods: GSEA and enrichment of differentially expressed genes. Similarity Venn Diagrams and individual patient ROC curves illustrate and quantify that the in vivo dysregulation is recapitulated ex vivo both at the gene and pathway level (p-values⩽0.004). CONCLUSION We established the first evidence that an interpretable dynamic transcriptome metric, conducted as an ex vivo assays for a single subject, has the potential to predict individualized response to infectious disease without the clinical risks otherwise associated to in vivo challenges. These results serve as a foundational work for personalized "virograms".
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Affiliation(s)
- Vincent Gardeux
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Anthony Bosco
- Telethon Institute for Child Health Research, Perth, Australia
| | - Jianrong Li
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | | | - Daniel Jackson
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA; The Childhood Asthma Research and Education Network (CARE)
| | - Fernando D Martinez
- The Childhood Asthma Research and Education Network (CARE); Department of Pediatrics, University of Arizona, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA.
| | - Yves A Lussier
- Department of Medicine, University of Arizona, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA; UA Cancer Center, University of Arizona, Tucson, AZ, USA.
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Zhu H, Xin X. Common Dysregulation of Ribosomal Genes Present in Infants with Acute Respiratory Infection of Respiratory Syncytial Virus, Rhinovirus, and Influenza A. PEDIATRIC ALLERGY, IMMUNOLOGY, AND PULMONOLOGY 2015. [DOI: 10.1089/ped.2014.0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Huilan Zhu
- Department of Pediatrics, First People's Hospital of Ji'nan City, Jinan, China
| | - Xinxin Xin
- Department of Orthopedics, 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
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Shurtleff AC, Whitehouse CA, Ward MD, Cazares LH, Bavari S. Pre-symptomatic diagnosis and treatment of filovirus diseases. Front Microbiol 2015; 6:108. [PMID: 25750638 PMCID: PMC4335271 DOI: 10.3389/fmicb.2015.00108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/28/2015] [Indexed: 01/01/2023] Open
Abstract
Filoviruses are virulent human pathogens which cause severe illness with high case fatality rates and for which there are no available FDA-approved vaccines or therapeutics. Diagnostic tools including antibody- and molecular-based assays, mass spectrometry, and next-generation sequencing are continually under development. Assays using the polymerase chain reaction (PCR) have become the mainstay for the detection of filoviruses in outbreak settings. In many cases, real-time reverse transcriptase-PCR allows for the detection of filoviruses to be carried out with minimal manipulation and equipment and can provide results in less than 2 h. In cases of novel, highly diverse filoviruses, random-primed pyrosequencing approaches have proved useful. Ideally, diagnostic tests would allow for diagnosis of filovirus infection as early as possible after infection, either before symptoms begin, in the event of a known exposure or epidemiologic outbreak, or post-symptomatically. If tests could provide an early definitive diagnosis, then this information may be used to inform the choice of possible therapeutics. Several exciting new candidate therapeutics have been described recently; molecules that have therapeutic activity when administered to animal models of infection several days post-exposure, once signs of disease have begun. The latest data for candidate nucleoside analogs, small interfering RNA (siRNA) molecules, phosphorodiamidate (PMO) molecules, as well as antibody and blood-product therapeutics and therapeutic vaccines are discussed. For filovirus researchers and government agencies interested in making treatments available for a nation's defense as well as its general public, having the right diagnostic tools to identify filovirus infections, as well as a panel of available therapeutics for treatment when needed, is a high priority. Additional research in both areas is required for ultimate success, but significant progress is being made to reach these goals.
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Affiliation(s)
- Amy C Shurtleff
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases Fort Detrick, MD, USA
| | - Chris A Whitehouse
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases Fort Detrick, MD, USA
| | - Michael D Ward
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases Fort Detrick, MD, USA
| | - Lisa H Cazares
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases Fort Detrick, MD, USA
| | - Sina Bavari
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases Fort Detrick, MD, 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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Lee Y, Kim YJ, Jung YJ, Kim KH, Kwon YM, Kim SI, Kang SM. Systems biology from virus to humans. J Anal Sci Technol 2015; 6:3. [PMID: 26269748 PMCID: PMC4527316 DOI: 10.1186/s40543-015-0047-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/15/2015] [Indexed: 12/19/2022] Open
Abstract
Natural infection and then recovery are considered to be the most effective means for hosts to build protective immunity. Thus, mimicking natural infection of pathogens, many live attenuated vaccines such as influenza virus, and yellow fever vaccine 17D were developed and have been successfully used to induce protective immunity. However, humans fail to generate long-term protective immunity to some pathogens after natural infection such as influenza virus, respiratory syncytial virus (RSV), and human immunodeficiency virus (HIV) even if they survive initial infections. Many vaccines are suboptimal since much mortality is still occurring, which is exampled by influenza and tuberculosis. It is critically important to increase our understanding on protein components of pathogens and vaccines as well as cellular and host responses to infections and vaccinations. Here, we highlight recent advances in gene transcripts and protein analysis results in the systems biology to enhance our understanding of viral pathogens, vaccines, and host cell responses.
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Affiliation(s)
- Youri Lee
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Yu-Jin Kim
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Yu-Jin Jung
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Ki-Hye Kim
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Young-Man Kwon
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Seung Il Kim
- Division of Life Science, Korea Basic Science Institute, Daejeon, 305-333 South Korea
| | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
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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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Tsalik EL, McClain M, Zaas AK. Moving toward prime time: host signatures for diagnosis of respiratory infections. J Infect Dis 2015; 212:173-5. [PMID: 25637349 DOI: 10.1093/infdis/jiv032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 01/12/2023] Open
Affiliation(s)
- Ephraim L Tsalik
- Institute for Genome Sciences and Precision Medicine, Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Micah McClain
- Institute for Genome Sciences and Precision Medicine, Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Aimee K Zaas
- Institute for Genome Sciences and Precision Medicine, Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
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225
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Yang WE, Woods CW, Tsalik EL. Host-Based Diagnostics for Detection and Prognosis of Infectious Diseases. J Microbiol Methods 2015. [DOI: 10.1016/bs.mim.2015.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hoang LT, Tolfvenstam T, Ooi EE, Khor CC, Naim ANM, Ho EXP, Ong SH, Wertheim HF, Fox A, Van Vinh Nguyen C, Nghiem NM, Ha TM, Thi Ngoc Tran A, Tambayah P, Lin R, Sangsajja C, Manosuthi W, Chuchottaworn C, Sansayunh P, Chotpitayasunondh T, Suntarattiwong P, Chokephaibulkit K, Puthavathana P, de Jong MD, Farrar J, van Doorn HR, Hibberd ML. Patient-based transcriptome-wide analysis identify interferon and ubiquination pathways as potential predictors of influenza A disease severity. PLoS One 2014; 9:e111640. [PMID: 25365328 PMCID: PMC4218794 DOI: 10.1371/journal.pone.0111640] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/19/2014] [Indexed: 12/21/2022] Open
Abstract
Background The influenza A virus is an RNA virus that is responsible for seasonal epidemics worldwide with up to five million cases of severe illness and 500,000 deaths annually according to the World Health Organization estimates. The factors associated with severe diseases are not well defined, but more severe disease is more often seen among persons aged >65 years, infants, pregnant women, and individuals of any age with underlying health conditions. Methodology/Principal Findings Using gene expression microarrays, the transcriptomic profiles of influenza-infected patients with severe (N = 11), moderate (N = 40) and mild (N = 83) symptoms were compared with the febrile patients of unknown etiology (N = 73). We found that influenza-infected patients, regardless of their clinical outcomes, had a stronger induction of antiviral and cytokine responses and a stronger attenuation of NK and T cell responses in comparison with those with unknown etiology. More importantly, we found that both interferon and ubiquitination signaling were strongly attenuated in patients with the most severe outcomes in comparison with those with moderate and mild outcomes, suggesting the protective roles of these pathways in disease pathogenesis. Conclusion/Significances The attenuation of interferon and ubiquitination pathways may associate with the clinical outcomes of influenza patients.
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Affiliation(s)
| | - Thomas Tolfvenstam
- Infection Immunology, Respiratory Infections, Karolinska Institutet, Solna, Sweden
| | - Eng Eong Ooi
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Swee Hoe Ong
- Genome Institute of Singapore, Singapore, Singapore
| | - Heiman F. Wertheim
- National Hospital of Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam, and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Annette Fox
- National Hospital of Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam, and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Ngoc My Nghiem
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | | | - Raymond Lin
- National University Hospital, Singapore, Singapore
| | | | | | | | | | | | | | | | | | - Menno D. de Jong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam, and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeremy Farrar
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam, and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - H. Rogier van Doorn
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam, and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Abstract
Community-acquired pneumonia is one of the most common reasons for emergency department (ED) visits in children and adults. Despite its prevalence, there are many challenges to proper diagnosis and management of pneumonia. There is no accurate and timely etiologic gold standard to differentiate bacterial from viral disease, and there are limitations with precise risk stratification of patients to ensure appropriate site-of-care decisions. Clinical factors obtained by history and physical examination have limited the ability to diagnose pneumonia etiology and severity. Biomarkers offer information about the host response to infection and pathogen activity within the host that can serve to augment clinical features in decision-making. As science and technology progress, novel biomarkers offer great potential in aiding critical decisions for patients with pneumonia. This review summarizes existing knowledge about biomarkers of host response and pathogen activity, in addition to briefly reviewing emerging biomarkers using novel technologies.
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Davenport EE, Antrobus RD, Lillie PJ, Gilbert S, Knight JC. Transcriptomic profiling facilitates classification of response to influenza challenge. J Mol Med (Berl) 2014; 93:105-14. [PMID: 25345603 PMCID: PMC4281383 DOI: 10.1007/s00109-014-1212-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 09/25/2014] [Accepted: 10/14/2014] [Indexed: 11/16/2022]
Abstract
Abstract Despite increases in vaccination coverage, reductions in influenza-related mortality have not been observed. Better vaccines are therefore required and influenza challenge studies can be used to test the efficacy of new vaccines. However, this requires the accurate post-challenge classification of subjects by outcome, which is limited in current methods that use artificial thresholds to assign ‘symptomatic’ and ‘asymptomatic’ phenotypes. We present data from an influenza challenge study in which 22 healthy adults (11 vaccinated) were inoculated with H3N2 influenza (A/Wisconsin/67/2005). We generated genome-wide gene expression data from peripheral blood taken immediately before the challenge and at 12, 24 and 48 h post-challenge. Variation in symptomatic scoring was found amongst those with laboratory confirmed influenza. By combining the dynamic transcriptomic data with the clinical parameters this variability can be reduced. We identified four subjects with severe laboratory confirmed influenza that show differential gene expression in 1103 probes 48 h post-challenge compared to the remaining subjects. We have further reduced this profile to six genes (CCL2, SEPT4, LAMP3, RTP4, MT1G and OAS3) that can be used to define these subjects. We have used this gene set to predict symptomatic infection from an independent study. This analysis gives further insight into host-pathogen interactions during influenza infection. However, the major potential value is in the clinical trial setting by providing a more quantitative method to better classify symptomatic individuals post influenza challenge. Key message Differential gene expression signatures are seen following influenza challenge. Expression of six predictive genes can classify response to influenza challenge. The genomic influenza response classification replicates in an independent dataset.
Electronic supplementary material The online version of this article (doi:10.1007/s00109-014-1212-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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Early-life viral infections and the development of asthma: a target for asthma prevention? Curr Opin Allergy Clin Immunol 2014; 14:131-6. [PMID: 24569522 DOI: 10.1097/aci.0000000000000047] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW To discuss the recent insights into the relationships between viral respiratory infections and asthma inception in the context of a long-term goal of moving toward prevention strategies for childhood asthma. RECENT FINDINGS There is strong evidence for respiratory syncytial virus and human rhinovirus wheezing illnesses as important risk factors for asthma inception. The mechanisms underlying these relationships have been an intense area of study. Novel approaches for the prevention of virus infections and/or lessening the severity of associated illnesses are at various stages of development, and are important potential tools in efforts aimed at primary and secondary prevention of asthma. SUMMARY Viral respiratory infections in early life are a major source of morbidity and are critical in the development of asthma. Mechanisms by which these infections lead to asthma inception in susceptible individuals are emerging. Further, there are promising potential interventions currently available that should be tested in clinical trials. The goal of prevention of disease inception is clearly on the horizon.
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230
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Ronchi A, Michelow IC, Chapin KC, Bliss JM, Pugni L, Mosca F, Sánchez PJ. Viral respiratory tract infections in the neonatal intensive care unit: the VIRIoN-I study. J Pediatr 2014; 165:690-6. [PMID: 25027362 PMCID: PMC7094497 DOI: 10.1016/j.jpeds.2014.05.054] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/12/2014] [Accepted: 05/29/2014] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To determine the frequency of respiratory viral infections among infants who were evaluated for late-onset sepsis in the neonatal intensive care units (NICUs) of Parkland Memorial Hospital, Dallas, Texas; and Women & Infants Hospital, Providence, Rhode Island. STUDY DESIGN Prospective cohort study conducted from January 15, 2012 to January 31, 2013. Infants in the NICU were enrolled if they were inborn, had never been discharged home, and were evaluated for sepsis (at >72 hours of age) and antibiotic therapy was initiated. Infants had a nasopharyngeal specimen collected for detection of respiratory viruses by multiplex polymerase chain reaction within 72 hours of the initiation of antibiotic therapy. Their medical records were reviewed for demographic, clinical, radiographic, and laboratory data until NICU discharge. RESULTS During the 13-month study, 8 of 100 infants, or 8 (6%) of the 135 sepsis evaluations, had a respiratory virus detected by polymerase chain reaction (2, enterovirus/rhinovirus; 2, rhinovirus; 2, coronaviruses; and 2, parainfluenza-3 virus). By bivariate analysis, the infants with viral detection were older (41 vs 11 days; P = .007), exposed to individuals with respiratory tract viral symptoms (37% vs 2%; P = .003), tested for respiratory viruses by provider (75% vs 11%; P < .001), and had lower total neutrophil counts (P = .02). In multivariate regression analysis, the best predictor of viral infection was the caregivers' clinical suspicion of viral infection (P = .006). CONCLUSIONS A total of 8% of infants, or 6% of all NICU sepsis evaluations, had a respiratory virus detected when evaluated for bacterial sepsis. These findings argue for more respiratory viral testing of infants with suspected sepsis using optimal molecular assays to establish accurate diagnoses, prevent transmission, and inform antibiotic stewardship efforts.
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Affiliation(s)
- Andrea Ronchi
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX; Neonatal Intensive Care Unit, Department of Clinical Sciences and Community Health, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Ian C Michelow
- Department of Pediatrics, Rhode Island Hospital, Providence, RI; Alpert Medical School of Brown University, Providence, RI
| | - Kimberle C Chapin
- Alpert Medical School of Brown University, Providence, RI; Department of Pathology and Medicine, Rhode Island Hospital, Providence, RI
| | - Joseph M Bliss
- Alpert Medical School of Brown University, Providence, RI; Department of Pediatrics, Women & Infants Hospital, Providence, RI
| | - Lorenza Pugni
- Neonatal Intensive Care Unit, Department of Clinical Sciences and Community Health, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Fabio Mosca
- Neonatal Intensive Care Unit, Department of Clinical Sciences and Community Health, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Pablo J Sánchez
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX; Department of Pediatrics, Center for Perinatal Research, Nationwide Children's Hospital - The Ohio State University, Columbus, OH.
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231
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van den Kieboom CH, Ahout IML, Zomer A, Brand KH, de Groot R, Ferwerda G, de Jonge MI. Nasopharyngeal gene expression, a novel approach to study the course of respiratory syncytial virus infection. Eur Respir J 2014; 45:718-25. [PMID: 25261323 DOI: 10.1183/09031936.00085614] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Respiratory syncytial virus (RSV) causes mild infections in the vast majority of children. However, in some cases, it causes severe disease, such as bronchiolitis and pneumonia. Development of severe RSV infection is determined by the host response. Therefore, the main aim of this study was to identify biomarkers associated with severe RSV infection. To identify biomarkers, nasopharyngeal gene expression was profiled by microarray studies, resulting in the selection of five genes: ubiquitin D, tetraspanin 8, mucin 13, β-microseminoprotein and chemokine ligand 7. These genes were validated by real-time quantitative PCR in an independent validation cohort, which confirmed significant differences in gene expression between mildly and severely infected and between recovery and acute patients. Nasopharyngeal aspirate samples are regularly taken when a viral respiratory tract infection is suspected. In this article, we describe a method to discriminate between mild and severe RSV infection based on differential host gene expression. The combination of pathogen detection and host gene expression analysis in nasopharyngeal aspirates will significantly improve the diagnosis and prognosis of respiratory tract infections.
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Affiliation(s)
- Corné H van den Kieboom
- Laboratory of Pediatric Infectious Diseases, Dept of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands Laboratory of Medical Immunology, Dept of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Inge M L Ahout
- Laboratory of Pediatric Infectious Diseases, Dept of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands Laboratory of Medical Immunology, Dept of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aldert Zomer
- Laboratory of Pediatric Infectious Diseases, Dept of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands Laboratory of Medical Immunology, Dept of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kim H Brand
- Laboratory of Pediatric Infectious Diseases, Dept of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald de Groot
- Laboratory of Pediatric Infectious Diseases, Dept of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands Laboratory of Medical Immunology, Dept of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerben Ferwerda
- Laboratory of Pediatric Infectious Diseases, Dept of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands Laboratory of Medical Immunology, Dept of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Dept of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands Laboratory of Medical Immunology, Dept of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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232
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Wallihan R, Ramilo O. Community-acquired pneumonia in children: current challenges and future directions. J Infect 2014; 69 Suppl 1:S87-90. [PMID: 25264163 DOI: 10.1016/j.jinf.2014.07.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 12/14/2022]
Abstract
Pneumonia is a commonly encountered illness and the leading cause of death in children under 5 years of age. Our current management strategies remain less than optimal in part because we do not have adequate tools to determine etiology, classify patients and predict their outcomes. Studies in the last decade have demonstrated that viruses are commonly detected in children with pneumonia, but on many occasions this is not sufficient to establish a clear etiologic diagnosis since bacterial coinfection cannot be excluded. Gene expression profile analysis provides a comprehensive assessment of the host response to infection. Preliminary data suggest that transcriptional profile analysis and measurement of Molecular Distance to Health (MDTH) scores allows more precise patient classification than current diagnostic techniques and laboratory markers. Application of this tool to the evaluation of children with pneumonia may enhance our clinical decision making process and ultimately improve patient outcomes.
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Affiliation(s)
- Rebecca Wallihan
- Section of Infectious Diseases, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, 370 W. 9th Ave., Columbus, OH 43210, USA.
| | - Octavio Ramilo
- Section of Infectious Diseases, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, 370 W. 9th Ave., Columbus, OH 43210, USA.
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233
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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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234
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Zaas AK, Garner BH, Tsalik EL, Burke T, Woods CW, Ginsburg GS. The current epidemiology and clinical decisions surrounding acute respiratory infections. Trends Mol Med 2014; 20:579-88. [PMID: 25201713 DOI: 10.1016/j.molmed.2014.08.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 12/15/2022]
Abstract
Acute respiratory infection (ARI) is a common diagnosis in outpatient and emergent care settings. Currently available diagnostics are limited, creating uncertainty in the use of antibacterial, antiviral, or supportive care. Up to 72% of ambulatory care patients with ARI are treated with an antibacterial, despite only a small fraction actually needing one. Antibiotic overuse is not restricted to ambulatory care: ARI accounts for approximately 5 million emergency department (ED) visits annually in the USA, where 52-61% of such patients receive antibiotics. Thus, an accurate test for the presence or absence of viral or bacterial infection is needed. In this review, we focus on recent research showing that the host-response (genomic, proteomic, or miRNA) can accomplish this task.
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Affiliation(s)
- Aimee K Zaas
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
| | - Bronwen H Garner
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Thomas Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
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235
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Ferreira RC, Guo H, Coulson RMR, Smyth DJ, Pekalski ML, Burren OS, Cutler AJ, Doecke JD, Flint S, McKinney EF, Lyons PA, Smith KGC, Achenbach P, Beyerlein A, Dunger DB, Clayton DG, Wicker LS, Todd JA, Bonifacio E, Wallace C, Ziegler AG. A type I interferon transcriptional signature precedes autoimmunity in children genetically at risk for type 1 diabetes. Diabetes 2014; 63:2538-50. [PMID: 24561305 PMCID: PMC4066333 DOI: 10.2337/db13-1777] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Diagnosis of the autoimmune disease type 1 diabetes (T1D) is preceded by the appearance of circulating autoantibodies to pancreatic islets. However, almost nothing is known about events leading to this islet autoimmunity. Previous epidemiological and genetic data have associated viral infections and antiviral type I interferon (IFN) immune response genes with T1D. Here, we first used DNA microarray analysis to identify IFN-β-inducible genes in vitro and then used this set of genes to define an IFN-inducible transcriptional signature in peripheral blood mononuclear cells from a group of active systemic lupus erythematosus patients (n = 25). Using this predefined set of 225 IFN signature genes, we investigated the expression of the signature in cohorts of healthy controls (n = 87), patients with T1D (n = 64), and a large longitudinal birth cohort of children genetically predisposed to T1D (n = 109; 454 microarrayed samples). Expression of the IFN signature was increased in genetically predisposed children before the development of autoantibodies (P = 0.0012) but not in patients with established T1D. Upregulation of IFN-inducible genes was transient, temporally associated with a recent history of upper respiratory tract infections (P = 0.0064), and marked by increased expression of SIGLEC-1 (CD169), a lectin-like receptor expressed on CD14(+) monocytes. DNA variation in IFN-inducible genes altered T1D risk (P = 0.007), as exemplified by IFIH1, one of the genes in our IFN signature for which increased expression is a known risk factor for disease. These findings identify transient increased expression of type I IFN genes in preclinical diabetes as a risk factor for autoimmunity in children with a genetic predisposition to T1D.
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Affiliation(s)
- Ricardo C Ferreira
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - Hui Guo
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - Richard M R Coulson
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K.Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Deborah J Smyth
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - Marcin L Pekalski
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - Oliver S Burren
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - Antony J Cutler
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - James D Doecke
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K.The Australian E-Health Research Centre, Royal Brisbane and Women's Hospital, Queensland, AustraliaThe Commonwealth Scientific and Industrial Research Organisation (CSIRO) Preventative Health Flagship, Victoria, AustraliaCSIRO Mathematics and Information Sciences, Macquarie University, New South Wales, Australia
| | - Shaun Flint
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Eoin F McKinney
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Paul A Lyons
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Kenneth G C Smith
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Peter Achenbach
- Institute of Diabetes Research, Helmholtz Zentrum München, Neuherberg, and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Andreas Beyerlein
- Institute of Diabetes Research, Helmholtz Zentrum München, Neuherberg, and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - David B Dunger
- Department of Paediatrics, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - David G Clayton
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - Linda S Wicker
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K
| | - John A Todd
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K.
| | - Ezio Bonifacio
- CRTD-DFG Research Center for Regenerative Therapies Dresden and Paul Langerhans Institute Dresden, Technische Universität Dresden, Dresden, Germany
| | - Chris Wallace
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, U.K.
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Neuherberg, and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, München, Germany
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236
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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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237
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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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238
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Ramilo O, Mejias A. It Is Time for a Comprehensive Analytical Approach in Clinical Studies. Virus-versus-Host Interaction and Influenza Disease Severity. Am J Respir Crit Care Med 2014; 189:385-6. [DOI: 10.1164/rccm.201401-0008ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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239
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Blanco JC, Boukhvalova MS, Perez DR, Vogel SN, Kajon A. Modeling Human Respiratory Viral Infections in the Cotton Rat ( Sigmodon hispidus). ACTA ACUST UNITED AC 2014; 6:40-42. [PMID: 25635205 DOI: 10.4172/jaa.1000093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For over three decades, cotton rats have been a preferred model for human Respiratory Syncytial Virus (RSV) infection and pathogenesis, and a reliable model for an impressive list of human respiratory pathogens including adenoviruses, para influenza virus, measles, and human metapneumo virus. The most significant contribution of the cotton rat to biomedical research has been the development of anti-RSV antibodies for prophylactic use in high-risk infants. More recently, however, the cotton rat model has been further explored as a model for infection with other respiratory viral pathogens including influenza and rhinovirus.Together with RSV, these viruses inflict the greatest impact on the human respiratory health.This review will focus on the characteristics of these new models and their potential contribution to the development of new therapies.
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Affiliation(s)
| | | | - Daniel R Perez
- Department of Veterinary Medicine, University of Maryland, Collage Park, USA
| | - Stefanie N Vogel
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, USA
| | - Adriana Kajon
- Infectious Disease Program, Lovelace Respiratory Research Institute, Albuquerque, USA
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