1
|
Cruz PD, Wargowsky R, Gonzalez-Almada A, Sifontes EP, Shaykhinurov E, Jaatinen K, Jepson T, Lafleur JE, Yamane D, Perkins J, Pasquale M, Giang B, McHarg M, Falk Z, McCaffrey TA. Blood RNA Biomarkers Identify Bacterial and Biofilm Coinfections in COVID-19 Intensive Care Patients. J Intensive Care Med 2024:8850666241251743. [PMID: 38711289 DOI: 10.1177/08850666241251743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Purpose: Secondary opportunistic coinfections are a significant contributor to morbidity and mortality in intensive care unit (ICU) patients, but can be difficult to identify. Presently, new blood RNA biomarkers were tested in ICU patients to diagnose viral, bacterial, and biofilm coinfections. Methods: COVID-19 ICU patients had whole blood drawn in RNA preservative and stored at -80°C. Controls and subclinical infections were also studied. Droplet digital polymerase chain reaction (ddPCR) quantified 6 RNA biomarkers of host neutrophil activation to bacterial (DEFA1), biofilm (alkaline phosphatase [ALPL], IL8RB/CXCR2), and viral infections (IFI27, RSAD2). Viral titer in blood was measured by ddPCR for SARS-CoV2 (SCV2). Results: RNA biomarkers were elevated in ICU patients relative to controls. DEFA1 and ALPL RNA were significantly higher in severe versus incidental/moderate cases. SOFA score was correlated with white blood cell count (0.42), platelet count (-0.41), creatinine (0.38), and lactate dehydrogenase (0.31). ALPL RNA (0.59) showed the best correlation with SOFA score. IFI27 (0.52) and RSAD2 (0.38) were positively correlated with SCV2 viral titer. Overall, 57.8% of COVID-19 patients had a positive RNA biomarker for bacterial or biofilm infection. Conclusions: RNA biomarkers of host neutrophil activation indicate the presence of bacterial and biofilm coinfections in most COVID-19 patients. Recognizing coinfections may help to guide the treatment of ICU patients.
Collapse
Affiliation(s)
- Philip Dela Cruz
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Richard Wargowsky
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Alberto Gonzalez-Almada
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Erick Perez Sifontes
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Eduard Shaykhinurov
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Kevin Jaatinen
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Tisha Jepson
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
- True Bearing Diagnostics, Washington, DC, USA
| | - John E Lafleur
- Department of Emergency Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - David Yamane
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - John Perkins
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Mary Pasquale
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Brian Giang
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Matthew McHarg
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Zach Falk
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
| | - Timothy A McCaffrey
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, DC, USA
- True Bearing Diagnostics, Washington, DC, USA
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University Medical Center, Washington, DC, USA
| |
Collapse
|
2
|
Savino F, Dini M, Clemente A, Calvi C, Pau A, Galliano I, Gambarino S, Bergallo M. Nasopharyngeal and Peripheral Blood Type II Interferon Signature Evaluation in Infants during Respiratory Syncytial Virus Infection. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:259. [PMID: 38399546 PMCID: PMC10890591 DOI: 10.3390/medicina60020259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Background and Objectives: In this study, we applied one-step real time rt-PCR technology type II INF signature to blood and nasopharyngeal (NPS) swabs of acute early recovery children < 1 years hospitalized for bronchiolitis with laboratory-confirmed RSV infection. Materials and Methods: A prospective observational case-control study was conducted in 2021-2022. The study took place in Children Hospital "Regina Margherita", Torino Italy. The study included 66 infants, of which 30 patients were hospitalized for bronchiolitis due to RSV infection and 36 age-matched controls. Inclusion criteria included a positive RSV test for infants with bronchiolitis. We collected peripheral blood and nasopharyngeal swabs for relative quantification of type II Interferon signature by One-Step Multiplex PCR real time. Results: IFN levels were downregulated in the peripheral blood of bronchiolitis patients; these data were not confirmed in the nasopharyngeal swab. There was no correlation between NPS and the type II IFN score in peripheral blood. Conclusions: our study shows for the first time that type II IFN score was significant reduced in peripheral blood of infants with bronchiolitis by RSV compared to age-matched healthy controls; in the NPS swab this resulted downregulation was not statistically significant and the type II IFN score in the NPS swab can be used as marker of resolution of infection or improvement of clinical conditions.
Collapse
Affiliation(s)
- Francesco Savino
- Early Infancy Special Care Unit, Regina Margherita Children Hospital, A.O.U. Città della Salute e della Scienza di Torino, 10126 Torino, Italy;
| | - Maddalena Dini
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
| | - Anna Clemente
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
| | - Cristina Calvi
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Anna Pau
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
| | - Ilaria Galliano
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Stefano Gambarino
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
| | - Massimiliano Bergallo
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| |
Collapse
|
3
|
Oruganti S, Rodrigues PRS, White D, Watkins WJ, Shapey S, Barrow A, Al Samsam R, Ali S, Gajraj M, Skone R, Jardine M, Evans J, Struik S, Song JE, Abood L, Paquete B, Foulkes S, Saunders B, Strang A, Kotecha SJ, Phillips B, Evans A, Buchanan I, Bowes S, Ali B, Gore M, Thomas-Turner R, Andrews R, Zaher S, Sharma S, Chakraborty M, Parkinson E, Liberatore F, Woolley T, Edkins S, Davies LC, Moet L, McLaren JE, Watson GL, O'Donnell V, Hood K, Ghazal P. Immune and metabolic markers for identifying and investigating severe Coronavirus disease and Sepsis in children and young people (pSeP/COVID ChYP study): protocol for a prospective cohort study. BMJ Open 2023; 13:e067002. [PMID: 36972964 PMCID: PMC10069273 DOI: 10.1136/bmjopen-2022-067002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
INTRODUCTION Early recognition and appropriate management of paediatric sepsis are known to improve outcomes. A previous system's biology investigation of the systemic immune response in neonates to sepsis identified immune and metabolic markers that showed high accuracy for detecting bacterial infection. Further gene expression markers have also been reported previously in the paediatric age group for discriminating sepsis from control cases. More recently, specific gene signatures were identified to discriminate between COVID-19 and its associated inflammatory sequelae. Through the current prospective cohort study, we aim to evaluate immune and metabolic blood markers which discriminate between sepses (including COVID-19) from other acute illnesses in critically unwell children and young persons, up to 18 years of age. METHODS AND ANALYSIS We describe a prospective cohort study for comparing the immune and metabolic whole-blood markers in patients with sepsis, COVID-19 and other illnesses. Clinical phenotyping and blood culture test results will provide a reference standard to evaluate the performance of blood markers from the research sample analysis. Serial sampling of whole blood (50 μL each) will be collected from children admitted to intensive care and with an acute illness to follow time dependent changes in biomarkers. An integrated lipidomics and RNASeq transcriptomics analyses will be conducted to evaluate immune-metabolic networks that discriminate sepsis and COVID-19 from other acute illnesses. This study received approval for deferred consent. ETHICS AND DISSEMINATION The study has received research ethics committee approval from the Yorkshire and Humber Leeds West Research Ethics Committee 2 (reference 20/YH/0214; IRAS reference 250612). Submission of study results for publication will involve making available all anonymised primary and processed data on public repository sites. TRIAL REGISTRATION NUMBER NCT04904523.
Collapse
Affiliation(s)
- Sivakumar Oruganti
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | - Daniel White
- School of Medicine, Cardiff University, Cardiff, UK
| | - William John Watkins
- Cochrane Institute of Primary Care and Public Health, Cardiff University, Cardiff, UK
| | - Selyf Shapey
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Anna Barrow
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Rim Al Samsam
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Sara Ali
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Malcolm Gajraj
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Richard Skone
- Department of Paediatric Intensive Care, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Michelle Jardine
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Jennifer Evans
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Siske Struik
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Jong Eun Song
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | - Barbara Paquete
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Sian Foulkes
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Benjamin Saunders
- Infectious Diseases services for Wales, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | | | - Bethan Phillips
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Awen Evans
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Iona Buchanan
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Susan Bowes
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Begum Ali
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Maya Gore
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Rhian Thomas-Turner
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | | | - Summia Zaher
- Department of Obstetrics and Gynaecology, University Hospital of Wales, Cardiff, UK
| | - Simran Sharma
- Infection and Immunity, Cardiff University, Cardiff, UK
- Women's Unit, Cardiff and Vale NHS Trust, Cardiff, UK
| | | | | | | | | | - Sarah Edkins
- School of Medicine, Cardiff University, Cardiff, UK
| | | | - Linda Moet
- School of Medicine, Cardiff University, Cardiff, UK
| | | | | | - Valerie O'Donnell
- Centre for Trials Research, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Kerry Hood
- Centre for Trials Research, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | | |
Collapse
|
4
|
Villamayor L, López-García D, Rivero V, Martínez-Sobrido L, Nogales A, DeDiego ML. The IFN-stimulated gene IFI27 counteracts innate immune responses after viral infections by interfering with RIG-I signaling. Front Microbiol 2023; 14:1176177. [PMID: 37187533 PMCID: PMC10175689 DOI: 10.3389/fmicb.2023.1176177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
The recognition of viral nucleic acids by host pattern recognition receptors (PRRs) is critical for initiating innate immune responses against viral infections. These innate immune responses are mediated by the induction of interferons (IFNs), IFN-stimulated genes (ISGs) and pro-inflammatory cytokines. However, regulatory mechanisms are critical to avoid excessive or long-lasting innate immune responses that may cause detrimental hyperinflammation. Here, we identified a novel regulatory function of the ISG, IFN alpha inducible protein 27 (IFI27) in counteracting the innate immune responses triggered by cytoplasmic RNA recognition and binding. Our model systems included three unrelated viral infections caused by Influenza A virus (IAV), Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), and Sendai virus (SeV), and transfection with an analog of double-stranded (ds) RNA. Furthermore, we found that IFI27 has a positive effect on IAV and SARS-CoV-2 replication, most likely due to its ability to counteract host-induced antiviral responses, including in vivo. We also show that IFI27 interacts with nucleic acids and PRR retinoic acid-inducible gene I (RIG-I), being the interaction of IFI27 with RIG-I most likely mediated through RNA binding. Interestingly, our results indicate that interaction of IFI27 with RIG-I impairs RIG-I activation, providing a molecular mechanism for the effect of IFI27 on modulating innate immune responses. Our study identifies a molecular mechanism that may explain the effect of IFI27 in counterbalancing innate immune responses to RNA viral infections and preventing excessive innate immune responses. Therefore, this study will have important implications in drug design to control viral infections and viral-induced pathology.
Collapse
Affiliation(s)
- Laura Villamayor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Darío López-García
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Vanessa Rivero
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | | | - Aitor Nogales
- Center for Animal Health Research, CISA-INIA-CSIC, Madrid, Spain
| | - Marta L. DeDiego
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- *Correspondence: Marta L. DeDiego,
| |
Collapse
|
5
|
Feng Q, Lin S, Liu H, Yang B, Han L, Han X, Xu L, Xie Z. Meta-Analysis of Whole Blood Transcriptome Datasets Characterizes the Immune Response of Respiratory Syncytial Virus Infection in Children. Front Cell Infect Microbiol 2022; 12:878430. [PMID: 35493728 PMCID: PMC9043598 DOI: 10.3389/fcimb.2022.878430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common and critical viral pathogen causing acute lower respiratory tract infection in infants and young children and has a huge disease burden worldwide. At present, there are many studies on RSV transcriptomics exploring the mechanism of disease, but different studies show different gene expression patterns and results due to different sample collection platforms and data analysis strategies. A meta-analysis was performed on eight whole blood transcriptome datasets containing 436 children with acute RSV infection and 241 healthy children. A total of 319 differentially expressed genes (DEGs) (P value <0.0001) were identified in a meta-analysis using a random effect model. Functional enrichment analysis showed that several pathways related to immunity were significantly altered, including the “chemokine signaling pathway”, “natural killer cell mediated cytotoxicity” and “cytokine–cytokine receptor interaction”. Immune cell type analysis showed that the proportion of neutrophils in most RSV-infected children was higher than that in healthy children. These immune characteristics may help to provide new insights into RSV infection in children.
Collapse
Affiliation(s)
- Qianyu Feng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Shujin Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fujian, China
| | - Huifang Liu
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong, China
| | - Bin Yang
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong, China
| | - Lifen Han
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fujian, China
- *Correspondence: Lili Xu, ; Xiao Han, ; Lifen Han,
| | - Xiao Han
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fujian, China
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
- *Correspondence: Lili Xu, ; Xiao Han, ; Lifen Han,
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Lili Xu, ; Xiao Han, ; Lifen Han,
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
6
|
Kanemasa H, Ishimura M, Eguchi K, Tanaka T, Nanishi E, Shiraishi A, Goto M, Motomura Y, Ohga S. The immunoregulatory function of peripheral blood CD71 + erythroid cells in systemic-onset juvenile idiopathic arthritis. Sci Rep 2021; 11:14396. [PMID: 34257378 PMCID: PMC8277864 DOI: 10.1038/s41598-021-93831-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022] Open
Abstract
CD71+ erythroid cells (CECs) are recognized to have an immunoregulatory function via direct cell–cell interaction and soluble mediators. Circulating CECs appear in newborns or patients with hemolytic and cardiopulmonary disorders. To assess the biological role of CECs in systemic inflammation, we studied the gene expression and function in systemic-onset juvenile idiopathic arthritis (SoJIA). Peripheral blood mononuclear cells of SoJIA patients expressed upregulated erythropoiesis-related genes. It represented the largest expansion of CECs during active phase SoJIA among other inflammatory diseases. Despite the opposing roles of erythropoietin and hepcidin in erythropoiesis, both serum levels were in concert with the amounts of SoJIA-driven CECs. Circulating CECs counts in inflammatory diseases were positively correlated with the levels of C-reactive protein, IL-6, IL-18, or soluble TNF receptors. Co-culture with active SoJIA-driven CECs suppressed secretions of IL-1β, IL-6, and IL-8 from healthy donor monocytes. The top upregulated gene in SoJIA-driven CECs was ARG2 compared with CECs from cord blood controls, although cytokine production from monocytes was suppressed by co-culture, even with an arginase inhibitor. CECs are driven to the periphery during the acute phase of SoJIA at higher levels than other inflammatory diseases. Circulating CECs may control excessive inflammation via the immunoregulatory pathways, partly involving arginase-2.
Collapse
Affiliation(s)
- Hikaru Kanemasa
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masataka Ishimura
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Katsuhide Eguchi
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tamami Tanaka
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Etsuro Nanishi
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akira Shiraishi
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Motohiro Goto
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitomo Motomura
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shouichi Ohga
- Departments of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| |
Collapse
|
7
|
Fettrelet T, Gigon L, Karaulov A, Yousefi S, Simon HU. The Enigma of Eosinophil Degranulation. Int J Mol Sci 2021; 22:ijms22137091. [PMID: 34209362 PMCID: PMC8268949 DOI: 10.3390/ijms22137091] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 12/18/2022] Open
Abstract
Eosinophils are specialized white blood cells, which are involved in the pathology of diverse allergic and nonallergic inflammatory diseases. Eosinophils are traditionally known as cytotoxic effector cells but have been suggested to additionally play a role in immunomodulation and maintenance of homeostasis. The exact role of these granule-containing leukocytes in health and diseases is still a matter of debate. Degranulation is one of the key effector functions of eosinophils in response to diverse stimuli. The different degranulation patterns occurring in eosinophils (piecemeal degranulation, exocytosis and cytolysis) have been extensively studied in the last few years. However, the exact mechanism of the diverse degranulation types remains unknown and is still under investigation. In this review, we focus on recent findings and highlight the diversity of stimulation and methods used to evaluate eosinophil degranulation.
Collapse
Affiliation(s)
- Timothée Fettrelet
- Institute of Pharmacology, University of Bern, Inselspital, INO-F, CH-3010 Bern, Switzerland; (T.F.); (L.G.); (S.Y.)
- Department of Biochemistry, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Lea Gigon
- Institute of Pharmacology, University of Bern, Inselspital, INO-F, CH-3010 Bern, Switzerland; (T.F.); (L.G.); (S.Y.)
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergology, Sechenov University, 119991 Moscow, Russia;
| | - Shida Yousefi
- Institute of Pharmacology, University of Bern, Inselspital, INO-F, CH-3010 Bern, Switzerland; (T.F.); (L.G.); (S.Y.)
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Inselspital, INO-F, CH-3010 Bern, Switzerland; (T.F.); (L.G.); (S.Y.)
- Department of Clinical Immunology and Allergology, Sechenov University, 119991 Moscow, Russia;
- Laboratory of Molecular Immunology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420012 Kazan, Russia
- Institute of Biochemistry, Medical School Brandenburg, D-16816 Neuruppin, Germany
- Correspondence: ; Tel.: +41-31-632-3281
| |
Collapse
|
8
|
Yin GQ, Zeng HX, Li ZL, Chen C, Zhong JY, Xiao MS, Zeng Q, Jiang WH, Wu PQ, Zeng JM, Hu XY, Chen HH, Ruo-Hu, Zhao HJ, Gao L, Liu C, Cai SX. Differential proteomic analysis of children infected with respiratory syncytial virus. Braz J Med Biol Res 2021; 54:e9850. [PMID: 33656056 PMCID: PMC7917709 DOI: 10.1590/1414-431x20209850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/16/2020] [Indexed: 01/09/2023] Open
Abstract
Respiratory syncytial virus (RSV) infection is the main cause of lower respiratory tract infection in children. However, there is no effective treatment for RSV infection. Here, we aimed to identify potential biomarkers to aid in the treatment of RSV infection. Children in the acute and convalescence phases of RSV infection were recruited and proteomic analysis was performed to identify differentially expressed proteins (DEPs). Subsequently, promising candidate proteins were determined by functional enrichment and protein-protein interaction network analysis, and underwent further validation by western blot both in clinical and mouse model samples. Among the 79 DEPs identified in RSV patient samples, 4 proteins (BPGM, TPI1, PRDX2, and CFL1) were confirmed to be significantly upregulated during RSV infection. Functional analysis showed that BPGM and TPI1 were mainly involved in glycolysis, indicating an association between RSV infection and the glycolysis metabolic pathway. Our findings provide insights into the proteomic profile during RSV infection and indicated that BPGM, TPI1, PRDX2, and CFL1 may be potential therapeutic biomarkers or targets for the treatment of RSV infection.
Collapse
Affiliation(s)
- Gen-Quan Yin
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hui-Xuan Zeng
- Department of General Practice Medicine, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, China
| | - Zi-Long Li
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, Shandong, China
| | - Chen Chen
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jia-Yong Zhong
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mi-Si Xiao
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qiang Zeng
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wen-Hui Jiang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Pei-Qiong Wu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jie-Min Zeng
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-Yin Hu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huan-Hui Chen
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ruo-Hu
- College of Computer Science, Guangdong Polytechnic Normal University, Guangzhou, Guangdong, China
| | - Hai-Jin Zhao
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lin Gao
- Guangdong Food and Drug Vocational College, Guangzhou, Guangdong, China
| | - Cong Liu
- Department of Cardiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Shao-Xi Cai
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
9
|
Identification of pathogenic genes and transcription factors in respiratory syncytial virus. BMC Pediatr 2021; 21:27. [PMID: 33419394 PMCID: PMC7796524 DOI: 10.1186/s12887-020-02480-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a major cause of acute lower respiratory infections in children, especially bronchiolitis. Our study aimed to identify the key genes and upstream transcription factors in RSV. METHODS To screen for RSV pathogenic genes, an integrated analysis was performed using the RSV microarray dataset in GEO. Functional annotation and potential pathways for differentially expressed genes (DEGs) were further explored by GO and KEGG enrichment analysis. We constructed the RSV-specific transcriptional regulatory network to identify key transcription factors for DEGs in RSV. RESULTS From three GEO datasets, we identified 1059 DEGs (493 up-regulated and 566 down-regulated genes, FDR < 0.05 and |Combined.ES| > 0.8) between RSV patients and normal controls. GO and KEGG analysis revealed that 'response to virus' (FDR = 7.13E-15), 'mitochondrion' (FDR = 1.39E-14) and 'Asthma' (FDR = 1.28E-06) were significantly enriched pathways for DEGs. The expression of IFI27, IFI44, IFITM3, FCER1A, and ISG15 were shown to be involved in the pathogenesis of RSV. CONCLUSIONS We concluded that IFI27, IFI44, IFITM3, FCER1A, and ISG15 may play a role in RSV. Our finding may contribute to the development of new potential biomarkers, reveal the underlying pathogenesis and also identify novel therapeutic targets for RSV.
Collapse
|
10
|
Dapat C, Kumaki S, Sakurai H, Nishimura H, Labayo HKM, Okamoto M, Saito M, Oshitani H. Gene signature of children with severe respiratory syncytial virus infection. Pediatr Res 2021; 89:1664-1672. [PMID: 33510411 PMCID: PMC8249238 DOI: 10.1038/s41390-020-01347-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/15/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND The limited treatment options for children with severe respiratory syncytial virus (RSV) infection highlights the need for a comprehensive understanding of the host cellular response during infection. We aimed to identify host genes that are associated with severe RSV disease and to identify drugs that can be repurposed for the treatment of severe RSV infection. METHODS We examined clinical data and blood samples from 37 hospitalized children (29 mild and 8 severe) with RSV infection. We tested RNA from blood samples using next-generation sequencing to profile global mRNA expression and identify cellular processes. RESULTS Retractions, decreased breath sounds, and tachypnea were associated with disease severity. We observed upregulation of genes related to neutrophil, inflammatory response, blood coagulation, and downregulation of genes related to T cell response in children with severe RSV. Using network-based approach, 43 drugs were identified that are predicted to interact with the gene products of these differentially expressed genes. CONCLUSIONS These results suggest that the changes in the expression pattern in the innate and adaptive immune responses may be associated with RSV clinical severity. Compounds that target these cellular processes can be repositioned as candidate drugs in the treatment of severe RSV. IMPACT Neutrophil, inflammation, and blood coagulation genes are upregulated in children with severe RSV infection. Expression of T cell response genes are suppressed in cases of severe RSV. Genes identified in this study can contribute in understanding the pathogenesis of RSV disease severity. Drugs that target cellular processes associated with severe RSV can be repositioned as potential therapeutic options.
Collapse
Affiliation(s)
- Clyde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Satoru Kumaki
- grid.415495.8Department of Pediatrics, Sendai Medical Center, 11-12 Miyagino 2-chome, Miyagino-ku, Sendai, 983-8520 Japan
| | - Hiroki Sakurai
- grid.415988.90000 0004 0471 4457Department of General Pediatrics, Miyagi Children’s Hospital, 3-17 Ochiai 4-chome, Aoba-ku, Sendai, 989-3126 Japan
| | - Hidekazu Nishimura
- grid.415495.8Virus Research Center, Sendai Medical Center, 11-12 Miyagino 2-chome, Miyagino-ku, Sendai, 983-8520 Japan
| | - Hannah Karen Mina Labayo
- grid.69566.3a0000 0001 2248 6943Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Michiko Okamoto
- grid.69566.3a0000 0001 2248 6943Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Mayuko Saito
- grid.69566.3a0000 0001 2248 6943Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Hitoshi Oshitani
- grid.69566.3a0000 0001 2248 6943Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| |
Collapse
|
11
|
Rinchai D, Altman MC, Konza O, Hässler S, Martina F, Toufiq M, Garand M, Kabeer BSA, Palucka K, Mejias A, Ramilo O, Bedognetti D, Mariotti‐Ferrandiz E, Klatzmann D, Chaussabel D. Definition of erythroid cell-positive blood transcriptome phenotypes associated with severe respiratory syncytial virus infection. Clin Transl Med 2020; 10:e244. [PMID: 33377660 PMCID: PMC7733317 DOI: 10.1002/ctm2.244] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/31/2022] Open
Abstract
Biomarkers to assess the risk of developing severe respiratory syncytial virus (RSV) infection are needed. We conducted a meta-analysis of 490 unique profiles from six public RSV blood transcriptome datasets. A repertoire of 382 well-characterized transcriptional modules was used to define dominant host responses to RSV infection. The consolidated RSV cohort was stratified according to four traits: "interferon response" (IFN), "neutrophil-driven inflammation" (Infl), "cell cycle" (CC), and "erythrocytes" (Ery). We identified eight prevalent blood transcriptome phenotypes, of which three Ery+ phenotypes comprised higher proportions of patients requiring intensive care. This finding confirms on a larger scale data from one of our earlier reports describing an association between an erythrocyte signature and RSV disease severity. Further contextual interpretation made it possible to associate this signature with immunosuppressive states (late stage cancer, pharmacological immunosuppression), and with a population of fetal glycophorin A+ erythroid precursors. Furthermore, we posit that this erythrocyte cell signature may be linked to a population of immunosuppressive erythroid cells previously described in the literature, and that overabundance of this cell population in RSV patients may underlie progression to severe disease. These findings outline potential priority areas for biomarker development and investigations into the immune biology of RSV infection. The approach that we developed and employed here should also permit to delineate prevalent blood transcriptome phenotypes in other settings.
Collapse
Affiliation(s)
| | - Matthew C. Altman
- Benaroya Research InstituteSeattleWashington
- University of WashingtonSeattleWashington
| | - Oceane Konza
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
| | - Signe Hässler
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
- Immunology‐Immunopathology‐Immunotherapy (i3)Sorbonne UniversitéINSERMParisFrance
| | - Federica Martina
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
| | | | | | | | | | - Asuncion Mejias
- Division of Infectious DiseasesNationwide Children's HospitalColumbusOhio
| | - Octavio Ramilo
- Division of Infectious DiseasesNationwide Children's HospitalColumbusOhio
| | - Davide Bedognetti
- Sidra MedicineDohaQatar
- Department of Internal Medicine and Medical SpecialtiesUniversity of GenoaGenoaItaly
| | | | - David Klatzmann
- Biotherapy (CIC‐BTi) and Inflammation‐Immunopathology‐Biotherapy Department (i2B)AP‐HP, Hôpital Pitié‐SalpêtrièreParisFrance
- Immunology‐Immunopathology‐Immunotherapy (i3)Sorbonne UniversitéINSERMParisFrance
| | | |
Collapse
|
12
|
Besteman SB, Callaghan A, Langedijk AC, Hennus MP, Meyaard L, Mokry M, Bont LJ, Calis JJA. Transcriptome of airway neutrophils reveals an interferon response in life-threatening respiratory syncytial virus infection. Clin Immunol 2020; 220:108593. [PMID: 32920212 DOI: 10.1016/j.clim.2020.108593] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND Neutrophils are the most abundant cell type infiltrating the airways during severe respiratory syncytial virus (RSV) infection. Their exact role in disease pathophysiology remains enigmatic. Therefore, we determined genome-wide RNA expression profiles of local and systemic neutrophils in RSV bronchiolitis to provide further insight into local neutrophil biology. METHODS We performed a single-center analysis, in 16 infants, admitted to the pediatric intensive care unit with severe RSV bronchiolitis. Neutrophils were isolated from blood and tracheobronchial aspirates (sputum). After low input RNA sequencing, differential expression of genes was determined followed by gene set analysis. RESULTS Paired transcriptomic analysis of airway versus blood neutrophils showed an inflammatory phenotype, characterized by NF-kB signaling and upregulated expression of IL-6 and interferon pathways. We observed distinct expression of neutrophil activation genes (TNFSF13B, FCER1G). DISCUSSION Our data indicate that airway neutrophils regulate their function at the transcriptional level in response to viral infection. It also suggests that local interferon drives the neutrophil response of severe RSV bronchiolitis.
Collapse
Affiliation(s)
- Sjanna B Besteman
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Amie Callaghan
- Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Annefleur C Langedijk
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Marije P Hennus
- Department of Paediatric Intensive Care, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Linde Meyaard
- Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Oncode Institute, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Michal Mokry
- Department of cardiology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Louis J Bont
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Jorg J A Calis
- Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Department of cardiology, University Medical Centre Utrecht, Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
| |
Collapse
|
13
|
A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus. Int J Mol Sci 2020; 21:ijms21051831. [PMID: 32155831 PMCID: PMC7084441 DOI: 10.3390/ijms21051831] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 12/30/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infection worldwide. The absence of a commercial vaccine and the limited success of current therapeutic strategies against RSV make further research necessary. We used a multi-cohort analysis approach to investigate host transcriptomic biomarkers and shed further light on the molecular mechanism underlying RSV-host interactions. We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. We identified > 1500 genes differentially expressed when comparing the transcriptomes of RSV-infected patients against healthy controls. Functional enrichment analysis showed several pathways significantly altered, including immunologic response mediated by RSV infection, pattern recognition receptors, cell cycle, and olfactory signaling. In addition, we identified a minimal 17-transcript host signature specific for RSV infection by comparing transcriptomic profiles against other respiratory viruses. These multi-genic signatures might help to investigate future drug targets against RSV infection.
Collapse
|
14
|
Jones AC, Anderson D, Galbraith S, Fantino E, Gutierrez Cardenas D, Read JF, Serralha M, Holt BJ, Strickland DH, Sly PD, Bosco A, Holt PG. Personalized Transcriptomics Reveals Heterogeneous Immunophenotypes in Children with Viral Bronchiolitis. Am J Respir Crit Care Med 2020; 199:1537-1549. [PMID: 30562046 DOI: 10.1164/rccm.201804-0715oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rationale: A subset of infants are hypersusceptible to severe/acute viral bronchiolitis (AVB), for reasons incompletely understood. Objectives: To characterize the cellular/molecular mechanisms underlying infant AVB in circulating cells/local airway tissues. Methods: Peripheral blood mononuclear cells and nasal scrapings were obtained from infants (<18 mo) and children (≥18 mo to 5 yr) during AVB and after convalescence. Immune response patterns were profiled by multiplex analysis of plasma cytokines, flow cytometry, and transcriptomics (RNA-Seq). Molecular profiling of group-level data used a combination of upstream regulator and coexpression network analysis, followed by individual subject-level data analysis using personalized N-of-1-pathways methodology. Measurements and Main Results: Group-level analyses demonstrated that infant peripheral blood mononuclear cell responses were dominated by monocyte-associated hyperupregulated type 1 IFN signaling/proinflammatory pathways (drivers: TNF [tumor necrosis factor], IL-6, TREM1 [triggering receptor expressed on myeloid cells 1], and IL-1B), versus a combination of inflammation (PTGER2 [prostaglandin E receptor 2] and IL-6) plus growth/repair/remodeling pathways (ERBB2 [erbb-b2 receptor tyrosine kinase 2], TGFB1 [transforming growth factor-β1], AREG [amphiregulin], and HGF [hepatocyte growth factor]) coupled with T-helper cell type 2 and natural killer cell signaling in children. Age-related differences were not attributable to differential steroid usage or variations in underlying viral pathogens. Nasal mucosal responses were comparable qualitatively in infants/children, dominated by IFN types 1-3, but the magnitude of upregulation was higher in infants (range, 6- to 48-fold) than children (5- to 17-fold). N-of-1-pathways analysis confirmed differential upregulation of innate immunity in infants and natural killer cell networks in children, and additionally demonstrated covert AVB response subphenotypes that were independent of chronologic age. Conclusions: Dysregulated expression of IFN-dependent pathways after respiratory viral infections is a defining immunophenotypic feature of AVB-susceptible infants and a subset of children. Susceptible subjects seem to represent a discrete subgroup who cluster based on (slow) kinetics of postnatal maturation of innate immune competence.
Collapse
Affiliation(s)
- Anya C Jones
- 1 Telethon Kids Institute and.,2 School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia; and
| | | | - Sally Galbraith
- 3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Emmanuelle Fantino
- 3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | | | - James F Read
- 1 Telethon Kids Institute and.,2 School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia; and
| | | | | | | | - Peter D Sly
- 3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Patrick G Holt
- 1 Telethon Kids Institute and.,3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
15
|
Yu J, Peterson DR, Baran AM, Bhattacharya S, Wylie TN, Falsey AR, Mariani TJ, Storch GA. Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection. J Infect Dis 2020; 219:1151-1161. [PMID: 30339221 DOI: 10.1093/infdis/jiy608] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Recently there has been a growing interest in the potential for host transcriptomic analysis to augment the diagnosis of infectious diseases. METHODS We compared nasal and blood samples for evaluation of the host transcriptomic response in children with acute respiratory syncytial virus (RSV) infection, symptomatic non-RSV respiratory virus infection, asymptomatic rhinovirus infection, and virus-negative asymptomatic controls. We used nested leave-one-pair-out cross-validation and supervised principal components analysis to define small sets of genes whose expression patterns accurately classified subjects. We validated gene classification scores using an external data set. RESULTS Despite lower quality of nasal RNA, the number of genes detected by microarray in each sample type was equivalent. Nasal gene expression signal derived mainly from epithelial cells but also included a variable leukocyte contribution. The number of genes with increased expression in virus-infected children was comparable in nasal and blood samples, while nasal samples also had decreased expression of many genes associated with ciliary function and assembly. Nasal gene expression signatures were as good or better for discriminating between symptomatic, asymptomatic, and uninfected children. CONCLSUSIONS Our results support the use of nasal samples to augment pathogen-based tests to diagnose viral respiratory infection.
Collapse
Affiliation(s)
- Jinsheng Yu
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Ann R Falsey
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
16
|
Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection. Sci Rep 2019; 9:13824. [PMID: 31554845 PMCID: PMC6761288 DOI: 10.1038/s41598-019-50217-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/09/2019] [Indexed: 01/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections and hospital visits during infancy and childhood. Although risk factors for RSV infection have been identified, the role of microbial species in the respiratory tract is only partially known. We aimed to understand the impact of interactions between the nasal microbiome and host transcriptome on the severity and clinical outcomes of RSV infection. We used 16 S rRNA sequencing to characterize the nasal microbiome of infants with RSV infection. We used RNA sequencing to interrogate the transcriptome of CD4+ T cells obtained from the same set of infants. After dimension reduction through principal component (PC) analysis, we performed an integrative analysis to identify significant co-variation between microbial clade and gene expression PCs. We then employed LIONESS (Linear Interpolation to Obtain Network Estimates for Single Samples) to estimate the clade-gene association patterns for each infant. Our network-based integrative analysis identified several clade-gene associations significantly related to the severity of RSV infection. The microbial taxa with the highest loadings in the implicated clade PCs included Moraxella, Corynebacterium, Streptococcus, Haemophilus influenzae, and Staphylococcus. Interestingly, many of the genes with the highest loadings in the implicated gene PCs are encoded in mitochondrial DNA, while others are involved in the host immune response. This study on microbiome-transcriptome interactions provides insights into how the host immune system mounts a response against RSV and specific infectious agents in nasal microbiota.
Collapse
|
17
|
Do LAH, Pellet J, van Doorn HR, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Tran Dac NA, Trinh HN, Nguyen TTH, Le Binh BT, Nguyen HMK, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, De Meulder B, Auffray C, Hofstra JJ, Farrar J, Bryant JE, de Jong M, Hibberd ML. Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection. J Infect Dis 2019; 217:134-146. [PMID: 29029245 PMCID: PMC5853303 DOI: 10.1093/infdis/jix519] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/25/2017] [Indexed: 12/29/2022] Open
Abstract
Background Most insights into the cascade of immune events after acute respiratory syncytial virus (RSV) infection have been obtained from animal experiments or in vitro models. Methods In this study, we investigated host gene expression profiles in nasopharyngeal (NP) swabs and whole blood samples during natural RSV and rhinovirus (hRV) infection (acute versus early recovery phase) in 83 hospitalized patients <2 years old with lower respiratory tract infections. Results Respiratory syncytial virus infection induced strong and persistent innate immune responses including interferon signaling and pathways related to chemokine/cytokine signaling in both compartments. Interferon-α/β, NOTCH1 signaling pathways and potential biomarkers HIST1H4E, IL7R, ISG15 in NP samples, or BCL6, HIST2H2AC, CCNA1 in blood are leading pathways and hub genes that were associated with both RSV load and severity. The observed RSV-induced gene expression patterns did not differ significantly in NP swab and blood specimens. In contrast, hRV infection did not as strongly induce expression of innate immunity pathways, and significant differences were observed between NP swab and blood specimens. Conclusions We conclude that RSV induced strong and persistent innate immune responses and that RSV severity may be related to development of T follicular helper cells and antiviral inflammatory sequelae derived from high activation of BCL6.
Collapse
Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Johann Pellet
- Murdoch Children's Research Institute, Melbourne, Australia
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | | | | | | | | | - Quoc Bao Vo
- Children Hospital 2, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | - Thanh Vu Vo
- Children Hospital 1, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Lu Viet Ho
- Children Hospital 2, Ho Chi Minh City, Vietnam
| | | | - Charles Auffray
- European Institute for Systems Biology and Medicine, Lyon, France
| | - Jorrit-Jan Hofstra
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Menno de Jong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom.,Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Martin L Hibberd
- Genome Institute of Singapore.,London School of Hygiene & Tropical Medicine, United Kingdom
| |
Collapse
|
18
|
A Brief History of Charcot-Leyden Crystal Protein/Galectin-10 Research. Molecules 2018; 23:molecules23112931. [PMID: 30424011 PMCID: PMC6278384 DOI: 10.3390/molecules23112931] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Eosinophils are present in tissues, such as the respiratory tract, spleen, lymph nodes and blood vessels. The significant presence of eosinophils in these tissues are associated with various diseases, including asthma, allergies, acute myeloid leukemia, etc. Charcot-Leyden crystal protein/galectin-10 is overexpressed in eosinophils and has also been identified in basophils and macrophages. In human body, this protein could spontaneously form Charcot-Leyden crystal in lymphocytes or in the lysates of lymphocytes. At present, the role of Charcot-Leyden crystal protein/galectin-10 in lymphocytes is not fully understood. This review summarizes research progress on Charcot-Leyden crystal protein/galectin-10, with emphasis on its history, cellular distributions, relations to diseases, structures and ligand binding specificity.
Collapse
|
19
|
Salas A, Pardo-Seco J, Cebey-López M, Gómez-Carballa A, Obando-Pacheco P, Rivero-Calle I, Currás-Tuala MJ, Amigo J, Gómez-Rial J, Martinón-Torres F. Whole Exome Sequencing reveals new candidate genes in host genomic susceptibility to Respiratory Syncytial Virus Disease. Sci Rep 2017; 7:15888. [PMID: 29162850 PMCID: PMC5698448 DOI: 10.1038/s41598-017-15752-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 11/01/2017] [Indexed: 01/09/2023] Open
Abstract
Respiratory syncytial virus (RSV) is an important cause of serious lower respiratory tract disease in infants. Several studies have shown evidence pointing to the genome of the host as an important factor determining susceptibility to respiratory disease caused by RSV. We sequenced the complete exomes of 54 patients infected by RSV that needed hospitalization due to development of severe bronchiolitis. The Iberian sample (IBS) from The 1000 Genomes Project (1000G) was used as control group; all the association results were pseudo-replicated using other 1000G-European controls and Spanish controls. The study points to SNP rs199665292 in the olfactory receptor (OR) gene OR13C5 as the best candidate variant (P-value = 1.16 × 10-12; OR = 5.56). Genetic variants at HLA genes (HLA-DQA1, HLA-DPB1), and in the mucin 4 gene (MUC4) also emerge as susceptibility candidates. By collapsing rare variants in genes and weighing by pathogenicity, we obtained confirmatory signals of association in the OR gene OR8U1/OR8U8, the taste receptor TAS2R19, and another mucin gene (MUC6). Overall, we identified new predisposition variants and genes related to RSV infection. Of special interest is the association of RSV to olfactory and taste receptors; this finding is in line with recent evidence pointing to their role in viral infectious diseases.
Collapse
Affiliation(s)
- Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela(USC), Galicia, Spain.
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain.
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain.
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela(USC), Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Miriam Cebey-López
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela(USC), Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Pablo Obando-Pacheco
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Irene Rivero-Calle
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - María-José Currás-Tuala
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela(USC), Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Jorge Amigo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela(USC), Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - José Gómez-Rial
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| |
Collapse
|
20
|
Russell CD, Unger SA, Walton M, Schwarze J. The Human Immune Response to Respiratory Syncytial Virus Infection. Clin Microbiol Rev 2017; 30:481-502. [PMID: 28179378 PMCID: PMC5355638 DOI: 10.1128/cmr.00090-16] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is an important etiological agent of respiratory infections, particularly in children. Much information regarding the immune response to RSV comes from animal models and in vitro studies. Here, we provide a comprehensive description of the human immune response to RSV infection, based on a systematic literature review of research on infected humans. There is an initial strong neutrophil response to RSV infection in humans, which is positively correlated with disease severity and mediated by interleukin-8 (IL-8). Dendritic cells migrate to the lungs as the primary antigen-presenting cell. An initial systemic T-cell lymphopenia is followed by a pulmonary CD8+ T-cell response, mediating viral clearance. Humoral immunity to reinfection is incomplete, but RSV IgG and IgA are protective. B-cell-stimulating factors derived from airway epithelium play a major role in protective antibody generation. Gamma interferon (IFN-γ) has a strongly protective role, and a Th2-biased response may be deleterious. Other cytokines (particularly IL-17A), chemokines (particularly CCL-5 and CCL-3), and local innate immune factors (including cathelicidins and IFN-λ) contribute to pathogenesis. In summary, neutrophilic inflammation is incriminated as a harmful response, whereas CD8+ T cells and IFN-γ have protective roles. These may represent important therapeutic targets to modulate the immunopathogenesis of RSV infection.
Collapse
Affiliation(s)
- Clark D Russell
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Stefan A Unger
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Marc Walton
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jürgen Schwarze
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
21
|
Abstract
To determine whether there is an airway IFN response in infants with acute bronchiolitis and to establish whether the rate of such a response is related to the severity of illness, the expression of some IFN-induced genes was measured in nasopharyngeal washes from 39 infants with acute bronchiolitis. The results indicate that in infants with a virus-associated acute bronchiolitis there is a strong activation of IFN system and that the severity of illness is inversely related to the level of expression of IFN-induced genes. This suggests that the IFN response plays an important role in determining virus–associated respiratory disease in early life.
Collapse
|
22
|
High M, Cho HY, Marzec J, Wiltshire T, Verhein KC, Caballero MT, Acosta PL, Ciencewicki J, McCaw ZR, Kobzik L, Miller-DeGraff L, Gladwell W, Peden DB, Serra ME, Shi M, Weinberg C, Suzuki O, Wang X, Bell DA, Polack FP, Kleeberger SR. Determinants of host susceptibility to murine respiratory syncytial virus (RSV) disease identify a role for the innate immunity scavenger receptor MARCO gene in human infants. EBioMedicine 2016; 11:73-84. [PMID: 27554839 PMCID: PMC5049919 DOI: 10.1016/j.ebiom.2016.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 08/02/2016] [Accepted: 08/05/2016] [Indexed: 11/29/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is the global leading cause of lower respiratory tract infection in infants. Nearly 30% of all infected infants develop severe disease including bronchiolitis, but susceptibility mechanisms remain unclear. Methods We infected a panel of 30 inbred strains of mice with RSV and measured changes in lung disease parameters 1 and 5 days post-infection and they were used in genome-wide association (GWA) studies to identify quantitative trait loci (QTL) and susceptibility gene candidates. Findings GWA identified QTLs for RSV disease phenotypes, and the innate immunity scavenger receptor Marco was a candidate susceptibility gene; targeted deletion of Marco worsened murine RSV disease. We characterized a human MARCO promoter SNP that caused loss of gene expression, increased in vitro cellular response to RSV infection, and associated with increased risk of disease severity in two independent populations of children infected with RSV. Interpretation Translational integration of a genetic animal model and in vitro human studies identified a role for MARCO in human RSV disease severity. Because no RSV vaccines are approved for clinical use, genetic studies have implications for diagnosing individuals who are at risk for severe RSV disease, and disease prevention strategies (e.g. RSV antibodies). In a panel of inbred strains of mice, RSV disease phenotypes were characterized that resemble those in human disease. We identified Marco as a susceptibility gene, and a human MARCO mutation increased risk of disease severity in children. These studies have implications for diagnosing individuals who are at risk for severe RSV disease and prevent disease.
RSV disease is the primary global cause for hospitalization one year after birth but the causes of differential RSV disease severity are not understood. We show that RSV disease phenotypes vary significantly between inbred strains of mice, and resemble those in human disease. We used genetic approaches to identify and validate the innate immunity gene Marco as a host susceptibility determinant for murine RSV disease. We then characterized a loss of function polymorphism in human MARCO that increases risk of severe RSV disease risk in infants. Results have important implications for identifying genetic risk factors for severe RSV disease.
Collapse
Affiliation(s)
- Monica High
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Hye-Youn Cho
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jacqui Marzec
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Tim Wiltshire
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Kirsten C Verhein
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - Patricio L Acosta
- Fundación INFANT, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Jonathan Ciencewicki
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Zackary R McCaw
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Lester Kobzik
- Department of Environmental Health, Harvard University School of Public Health, Boston, MA, USA
| | - Laura Miller-DeGraff
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Wes Gladwell
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - David B Peden
- Center for Environmental Medicine, Asthma and Lung Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Clarice Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Oscar Suzuki
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Xuting Wang
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Douglas A Bell
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Fernando P Polack
- Fundación INFANT, Buenos Aires, Argentina; Department of Pediatrics, Vanderbilt University, Nashville, TN, USA.
| | - Steven R Kleeberger
- Immunity, Inflammation, and Diseases Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
| |
Collapse
|
23
|
Hasegawa K, Dumas O, Hartert TV, Camargo CA. Advancing our understanding of infant bronchiolitis through phenotyping and endotyping: clinical and molecular approaches. Expert Rev Respir Med 2016; 10:891-9. [PMID: 27192374 DOI: 10.1080/17476348.2016.1190647] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Bronchiolitis is a major public health problem worldwide. However, no effective treatment strategies are available, other than supportive care. AREAS COVERED Although bronchiolitis has been considered a single disease diagnosed based on clinical characteristics, emerging evidence supports both clinical and pathobiological heterogeneity. The characterization of this heterogeneity supports the concept that bronchiolitis consists of multiple phenotypes or consistent grouping of characteristics. Expert commentary: Using unbiased statistical approaches, multidimentional clinical characteristics will derive bronchiolitis phenotypes. Furthermore, molecular and systems biology approaches will, by linking pathobiology to phenotype, identify endotypes. Large cohort studies of bronchiolitis with comprehensive clinical characterization and system-wide profiling of the '-omics' data (e.g., host genome, transcriptome, epigenome, viral genome, microbiome, metabolome) should enhance our ability to molecularly understand these phenotypes and lead to more targeted and personalized approaches to bronchiolitis treatment.
Collapse
Affiliation(s)
- Kohei Hasegawa
- a Department of Emergency Medicine , Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - Orianne Dumas
- b INSERM U1168, VIMA: Aging and Chronic Diseases, Epidemiological and Public Health Approaches, Univ. Versailles St-Quentin-en-Yvelines , Villejuif , France
| | - Tina V Hartert
- c Center for Asthma & Environmental Health Sciences Research, Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine , Vanderbilt University School of Medicine , Nashville , TN , USA
| | - Carlos A Camargo
- a Department of Emergency Medicine , Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| |
Collapse
|
24
|
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
| |
Collapse
|
25
|
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
| |
Collapse
|
26
|
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]
|
27
|
Grandin C, Lucas-Hourani M, Clavel M, Taborik F, Vabret A, Tangy F, Contamin H, Vidalain PO. Evidence for an intranasal immune response to human respiratory syncytial virus infection in cynomolgus macaques. J Gen Virol 2014; 96:782-792. [PMID: 25537374 DOI: 10.1099/vir.0.000039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
There is no large-scale therapy available against human respiratory syncytial virus (hRSV), a major pathogen responsible for acute respiratory diseases. Macaques represent an interesting animal model to evaluate potential treatments because of their genetic, anatomical and immunological proximity with humans. However, the parameters that influence hRSV growth and control in this model are still poorly understood. We have documented in the following study the influence of age as well as repeated infections on the virological, clinical and immunological parameters of this animal model. Following intranasal inoculation, hRSV replicated in the upper respiratory tract for less than 15 days with no clinical signs regardless of age. Interestingly, we observed the induction of a local immune response at the nasal mucosa as assessed by expression profiles of inflammatory and IFN-stimulated genes. Animals also developed specific antibodies and were immune to reinfection. Thus, we showed that even in infant macaques, intranasal hRSV infection induced both local and systemic immune responses to efficiently control the virus.
Collapse
Affiliation(s)
- Clément Grandin
- CNRS, UMR3569, Paris, France.,Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France.,Cynbiose SA, Marcy-l'Etoile, France
| | - Marianne Lucas-Hourani
- CNRS, UMR3569, Paris, France.,Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
| | | | | | - Astrid Vabret
- Université de Caen-Basse-Normandie, EA 4655-U2RM, Laboratoire de Virologie, CHU de Caen, France
| | - Frédéric Tangy
- CNRS, UMR3569, Paris, France.,Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
| | | | - Pierre-Olivier Vidalain
- CNRS, UMR3569, Paris, France.,Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Smith CL, Dickinson P, Forster T, Craigon M, Ross A, Khondoker MR, France R, Ivens A, Lynn DJ, Orme J, Jackson A, Lacaze P, Flanagan KL, Stenson BJ, Ghazal P. Identification of a human neonatal immune-metabolic network associated with bacterial infection. Nat Commun 2014; 5:4649. [PMID: 25120092 PMCID: PMC4143936 DOI: 10.1038/ncomms5649] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/09/2014] [Indexed: 12/26/2022] Open
Abstract
Understanding how human neonates respond to infection remains incomplete. Here, a system-level investigation of neonatal systemic responses to infection shows a surprisingly strong but unbalanced homeostatic immune response; developing an elevated set-point of myeloid regulatory signalling and sugar-lipid metabolism with concomitant inhibition of lymphoid responses. Innate immune-negative feedback opposes innate immune activation while suppression of T-cell co-stimulation is coincident with selective upregulation of CD85 co-inhibitory pathways. By deriving modules of co-expressed RNAs, we identify a limited set of networks associated with bacterial infection that exhibit high levels of inter-patient variability. Whereas, by integrating immune and metabolic pathways, we infer a patient-invariant 52-gene-classifier that predicts bacterial infection with high accuracy using a new independent patient population. This is further shown to have predictive value in identifying infection in suspected cases with blood culture-negative tests. Our results lay the foundation for future translation of host pathways in advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis. Infection remains a leading cause of morbidity and mortality in neonates worldwide. Here the authors report disproportionate immune stimulatory, co-inhibitory and metabolic pathway responses that specifically mark bacterial infection and can be used to predict sepsis in neonatal patients at the first clinical signs of infection.
Collapse
Affiliation(s)
- Claire L Smith
- 1] Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK [2] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [3]
| | - Paul Dickinson
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK [3]
| | - Thorsten Forster
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK
| | - Marie Craigon
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Alan Ross
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Mizanur R Khondoker
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2]
| | - Rebecca France
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Alasdair Ivens
- 1] Fios Genomics Ltd., ETTC, King's Buildings, Edinburgh EH9 3JL, UK [2]
| | - David J Lynn
- 1] Animal Bioscience Research Department, AGRIC, Teagasc, Grange, Dunsany, Co. Meath, Ireland [2]
| | - Judith Orme
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Allan Jackson
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Paul Lacaze
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Katie L Flanagan
- 1] MRC Research Laboratories, Atlantic Boulevard, PO Box 273, Fajara, Gambia [2]
| | - Benjamin J Stenson
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Peter Ghazal
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK
| |
Collapse
|
30
|
McErlean P, Berdnikovs S, Favoreto S, Shen J, Biyasheva A, Barbeau R, Eisley C, Barczak A, Ward T, Schleimer RP, Erle DJ, Boushey HA, Avila PC. Asthmatics with exacerbation during acute respiratory illness exhibit unique transcriptional signatures within the nasal mucosa. Genome Med 2014; 6:1. [PMID: 24433494 PMCID: PMC3971347 DOI: 10.1186/gm520] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/08/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Acute respiratory illness is the leading cause of asthma exacerbations yet the mechanisms underlying this association remain unclear. To address the deficiencies in our understanding of the molecular events characterizing acute respiratory illness-induced asthma exacerbations, we undertook a transcriptional profiling study of the nasal mucosa over the course of acute respiratory illness amongst individuals with a history of asthma, allergic rhinitis and no underlying respiratory disease. METHODS Transcriptional profiling experiments were performed using the Agilent Whole Human Genome 4X44K array platform. Time point-based microarray and principal component analyses were conducted to identify and distinguish acute respiratory illness-associated transcriptional profiles over the course of our study. Gene enrichment analysis was conducted to identify biological processes over-represented within each acute respiratory illness-associated profile, and gene expression was subsequently confirmed by quantitative polymerase chain reaction. RESULTS We found that acute respiratory illness is characterized by dynamic, time-specific transcriptional profiles whose magnitudes of expression are influenced by underlying respiratory disease and the mucosal repair signature evoked during acute respiratory illness. Most strikingly, we report that people with asthma who experience acute respiratory illness-induced exacerbations are characterized by a reduced but prolonged inflammatory immune response, inadequate activation of mucosal repair, and the expression of a newly described exacerbation-specific transcriptional signature. CONCLUSION Findings from our study represent a significant contribution towards clarifying the complex molecular interactions that typify acute respiratory illness-induced asthma exacerbations.
Collapse
Affiliation(s)
- Peter McErlean
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sergejs Berdnikovs
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Silvio Favoreto
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Junqing Shen
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Assel Biyasheva
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rebecca Barbeau
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
| | - Chris Eisley
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Barczak
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
| | - Theresa Ward
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Robert P Schleimer
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - David J Erle
- Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Homer A Boushey
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Pedro C Avila
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
31
|
Mejias A, Dimo B, Suarez NM, Garcia C, Suarez-Arrabal MC, Jartti T, Blankenship D, Jordan-Villegas A, Ardura MI, Xu Z, Banchereau J, Chaussabel D, Ramilo O. Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection. PLoS Med 2013; 10:e1001549. [PMID: 24265599 PMCID: PMC3825655 DOI: 10.1371/journal.pmed.1001549] [Citation(s) in RCA: 237] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 09/30/2013] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the leading cause of viral lower respiratory tract infection (LRTI) and hospitalization in infants. Mostly because of the incomplete understanding of the disease pathogenesis, there is no licensed vaccine, and treatment remains symptomatic. We analyzed whole blood transcriptional profiles to characterize the global host immune response to acute RSV LRTI in infants, to characterize its specificity compared with influenza and human rhinovirus (HRV) LRTI, and to identify biomarkers that can objectively assess RSV disease severity. METHODS AND FINDINGS This was a prospective observational study over six respiratory seasons including a cohort of infants hospitalized with RSV (n = 135), HRV (n = 30), and influenza (n = 16) LRTI, and healthy age- and sex-matched controls (n = 39). A specific RSV transcriptional profile was identified in whole blood (training cohort, n = 45 infants; Dallas, Texas, US) and validated in three different cohorts (test cohort, n = 46, Dallas, Texas, US; validation cohort A, n = 16, Turku, Finland; validation cohort B, n = 28, Columbus, Ohio, US) with high sensitivity (94% [95% CI 87%-98%]) and specificity (98% [95% CI 88%-99%]). It classified infants with RSV LRTI versus HRV or influenza LRTI with 95% accuracy. The immune dysregulation induced by RSV (overexpression of neutrophil, inflammation, and interferon genes, and suppression of T and B cell genes) persisted beyond the acute disease, and immune dysregulation was greatly impaired in younger infants (<6 mo). We identified a genomic score that significantly correlated with outcomes of care including a clinical disease severity score and, more importantly, length of hospitalization and duration of supplemental O2. CONCLUSIONS Blood RNA profiles of infants with RSV LRTI allow specific diagnosis, better understanding of disease pathogenesis, and assessment of disease severity. This study opens new avenues for biomarker discovery and identification of potential therapeutic or preventive targets, and demonstrates that large microarray datasets can be translated into a biologically meaningful context and applied to the clinical setting. Please see later in the article for the Editors' Summary.
Collapse
Affiliation(s)
- Asuncion Mejias
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail: (AM); (OR)
| | - Blerta Dimo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Nicolas M. Suarez
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Carla Garcia
- Division of Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - M. Carmen Suarez-Arrabal
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Tuomas Jartti
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Derek Blankenship
- Department of Statistics, Baylor Research Institute, Dallas, Texas, United States of America
| | - Alejandro Jordan-Villegas
- Division of Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Monica I. Ardura
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Zhaohui Xu
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
| | - Jacques Banchereau
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
| | - Damien Chaussabel
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
- Benaroya Research Institute, Seattle, Washington, United States of America
| | - Octavio Ramilo
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail: (AM); (OR)
| |
Collapse
|
32
|
Global gene expression profiling in infants with acute respiratory syncytial virus broncholitis demonstrates systemic activation of interferon signaling networks. Pediatr Infect Dis J 2013. [PMID: 23190772 DOI: 10.1097/inf.0b013e318278b4b3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a leading cause of pediatric lower respiratory tract infections and has a high impact on pediatric emergency department utilization. Variation in host response may influence the pathogenesis and disease severity. We evaluated global gene expression profiles to better understand the systemic host response to acute RSV bronchiolitis in infants and young children. METHODS Patients (age ≤ 24 months) who were clinically diagnosed with acute bronchiolitis and who had a positive rapid test for RSV assay were recruited from the Texas Children's Hospital emergency department. Global gene expression of peripheral whole blood cells were analyzed in 21 cases and 37 age-matched healthy controls. Transcripts exhibiting significant upregulation and downregulation as a result of RSV infection were identified and confirmed in a subset of samples using RNA sequencing. The potential pathways affected were analyzed. RESULTS Blood was obtained from patients with acute RSV bronchiolitis (mean age 6 months). Of these, 43% were admitted to the hospital, 52% were given intravenous fluids and 24% received oxygen. Highly significant expression differences were detected in a discovery cohort of White infants (N = 33) and validated in an independent group of African-American infants (N = 19). Individuals with mild disease (N = 15) could not be distinguished from subjects with clinically moderate disease (N = 5). Pathway enrichment analyses of the differentially expressed genes demonstrated extensive activation of the innate immune response, particularly the interferon signaling network. There was a significant downregulation of transcripts corresponding to antigen presentation.
Collapse
|
33
|
Tripp RA, Mejias A, Ramilo O. Host gene expression and respiratory syncytial virus infection. Curr Top Microbiol Immunol 2013; 372:193-209. [PMID: 24362691 DOI: 10.1007/978-3-642-38919-1_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in RNA interference (RNAi) and transcription studies have facilitated the application of systematic cell-based loss- or gain-of-function and cell response screening that enable genome-wide analysis of cell factors involved in viral replication and disease. Application of both experimental and computational biology approaches have led to crucial insights into virus infection, its life cycle, and host gene targets for disease intervention. A better understanding of the spatial and temporal host gene interactions during viral infection has enabled insights into mechanisms by which viral proteins co-opt host cell function, and host regulatory mechanisms that influence disease and treatment outcome. In this chapter, approaches to host gene discovery and transcriptome profiling for respiratory syncytial virus (RSV) are discussed in the context of biological relevance for disease intervention in the clinical setting and vaccine development.
Collapse
Affiliation(s)
- Ralph A Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA,
| | | | | |
Collapse
|
34
|
Plasticity and virus specificity of the airway epithelial cell immune response during respiratory virus infection. J Virol 2012; 86:5422-36. [PMID: 22398282 DOI: 10.1128/jvi.06757-11] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Airway epithelial cells (AECs) provide the first line of defense in the respiratory tract and are the main target of respiratory viruses. Here, using oligonucleotide and protein arrays, we analyze the infection of primary polarized human AEC cultures with influenza virus and respiratory syncytial virus (RSV), and we show that the immune response of AECs is quantitatively and qualitatively virus specific. Differentially expressed genes (DEGs) specifically induced by influenza virus and not by RSV included those encoding interferon B1 (IFN-B1), type III interferons (interleukin 28A [IL-28A], IL-28B, and IL-29), interleukins (IL-6, IL-1A, IL-1B, IL-23A, IL-17C, and IL-32), and chemokines (CCL2, CCL8, and CXCL5). Lack of type I interferon or STAT1 signaling decreased the expression and secretion of cytokines and chemokines by the airway epithelium. We also observed strong basolateral polarization of the secretion of cytokines and chemokines by human and murine AECs during infection. Importantly, the antiviral response of human AECs to influenza virus or to RSV correlated with the infection signature obtained from peripheral blood mononuclear cells (PBMCs) isolated from patients with acute influenza or RSV bronchiolitis, respectively. IFI27 (also known as ISG12) was identified as a biomarker of respiratory virus infection in both AECs and PBMCs. In addition, the extent of the transcriptional perturbation in PBMCs correlated with the clinical disease severity. Our results demonstrate that the human airway epithelium mounts virus-specific immune responses that are likely to determine the subsequent systemic immune responses and suggest that the absence of epithelial immune mediators after RSV infection may contribute to explaining the inadequacy of systemic immunity to the virus.
Collapse
|
35
|
Pennings JLA, Schuurhof A, Hodemaekers HM, Buisman A, de Rond LCGH, Widjojoatmodjo MN, Luytjes W, Kimpen JLL, Bont L, Janssen R. Systemic signature of the lung response to respiratory syncytial virus infection. PLoS One 2011; 6:e21461. [PMID: 21731757 PMCID: PMC3123345 DOI: 10.1371/journal.pone.0021461] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 06/02/2011] [Indexed: 02/03/2023] Open
Abstract
Respiratory Syncytial Virus is a frequent cause of severe bronchiolitis in children. To improve our understanding of systemic host responses to RSV, we compared BALB/c mouse gene expression responses at day 1, 2, and 5 during primary RSV infection in lung, bronchial lymph nodes, and blood. We identified a set of 53 interferon-associated and innate immunity genes that give correlated responses in all three murine tissues. Additionally, we identified blood gene signatures that are indicative of acute infection, secondary immune response, and vaccine-enhanced disease, respectively. Eosinophil-associated ribonucleases were characteristic for the vaccine-enhanced disease blood signature. These results indicate that it may be possible to distinguish protective and unfavorable patient lung responses via blood diagnostics.
Collapse
Affiliation(s)
- Jeroen L A Pennings
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Gene expression differences in lungs of mice during secondary immune responses to respiratory syncytial virus infection. J Virol 2010; 84:9584-94. [PMID: 20592085 DOI: 10.1128/jvi.00302-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vaccine-induced immunity has been shown to alter the course of a respiratory syncytial virus (RSV) infection both in murine models and in humans. To elucidate which mechanisms underlie the effect of vaccine-induced immunity on the course of RSV infection, transcription profiles in the lungs of RSV-infected mice were examined by microarray analysis. Three models were used: RSV reinfection as a model for natural immunity, RSV challenge after formalin-inactivated RSV vaccination as a model for vaccine-enhanced disease, and RSV challenge following vaccination with recombinant RSV virus lacking the G gene (DeltaG-RSV) as a model for vaccine-induced immunity. Gene transcription profiles, histopathology, and viral loads were analyzed at 1, 2, and 5 days after RSV challenge. On the first 2 days after challenge, all mice displayed an expression pattern in the lung similar of that found in primary infection, showing a strong innate immune response. On day 5 after RSV reinfection or after challenge following DeltaG-RSV vaccination, the innate immune response was waning. In contrast, in mice with vaccine-enhanced disease, the innate immune response 5 days after RSV challenge was still present even though viral replication was diminished. In addition, only in this group was Th2 gene expression induced. These findings support a hypothesis that vaccine-enhanced disease is mediated by prolonged innate immune responses and Th2 polarization in the absence of viral replication.
Collapse
|
37
|
Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev 2010; 22:611-33. [PMID: 19822891 DOI: 10.1128/cmr.00019-09] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.
Collapse
|
38
|
De Re V, Simula MP, Cannizzaro R, Pavan A, De Zorzi MA, Toffoli G, Canzonieri V. Galectin-10, eosinophils, and celiac disease. Ann N Y Acad Sci 2009; 1173:357-64. [PMID: 19758173 DOI: 10.1111/j.1749-6632.2009.04627.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Celiac disease (CD) is a chronic intestinal disease caused by intolerance to dietary wheat gluten in genetically susceptible individuals. There are a number of important open questions that impede the full explanation of the pathogenesis of this disease. We analyzed protein expression pattern in gut biopsies of CD subjects. Patients were selected and grouped according to histological inflammatory degree. Groups consisted of nine individuals with CD: three patients had a Marsh 0, three a Marsh I-II, and three a Marsh III. All CD patients showed a human leukocyte antigen DQ2/8 variant. Controls were three individuals with an excluded CD diagnosis. For the first time, galectin-10 expression was found related to the histological grade (P = 0.0092) and with the number of eosinophils in the lesion (P = 0.0040). Results suggest galectin-10 is a novel marker for evaluating CD tissue damage and eosinophils as a possible target for therapeutic approaches. Moreover, our data provide insights into alterations associated with CD tissue damage and pathogenesis.
Collapse
Affiliation(s)
- Valli De Re
- Experimental and Clinical Pharmacology Unit, Istituto Di Ricovero e Cura a Carattere Scientifico, Aviano, Italy.
| | | | | | | | | | | | | |
Collapse
|
39
|
Zaas AK, Chen M, Varkey J, Veldman T, Hero AO, Lucas J, Huang Y, Turner R, Gilbert A, Lambkin-Williams R, Øien NC, Nicholson B, Kingsmore S, Carin L, Woods CW, Ginsburg GS. Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 2009; 6:207-17. [PMID: 19664979 DOI: 10.1016/j.chom.2009.07.006] [Citation(s) in RCA: 291] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/27/2009] [Accepted: 07/22/2009] [Indexed: 01/26/2023]
Abstract
Acute respiratory infections (ARIs) are a common reason for seeking medical attention, and the threat of pandemic influenza will likely add to these numbers. Using human viral challenge studies with live rhinovirus, respiratory syncytial virus, and influenza A, we developed peripheral blood gene expression signatures that distinguish individuals with symptomatic ARIs from uninfected individuals with >95% accuracy. We validated this "acute respiratory viral" signature-encompassing genes with a known role in host defense against viral infections-across each viral challenge. We also validated the signature in an independently acquired data set for influenza A and classified infected individuals from healthy controls with 100% accuracy. In the same data set, we could also distinguish viral from bacterial ARIs (93% accuracy). These results demonstrate that ARIs induce changes in human peripheral blood gene expression that can be used to diagnose a viral etiology of respiratory infection and triage symptomatic individuals.
Collapse
Affiliation(s)
- Aimee K Zaas
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, NC 27710, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Polymorphisms of interferons and their receptors in the genetics of severe RSV-associated diseases. Arch Virol 2008; 153:2133-7. [PMID: 18953482 DOI: 10.1007/s00705-008-0232-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 10/06/2008] [Indexed: 01/25/2023]
Abstract
Because of their important role in the pathophysiology of severe RSV infection, IFNs represent an ideal group of candidate genes for determining RSV disease severity. We studied 14 polymorphisms within 7 genes involved in IFNs signalling. Our study populations consisted of 156 infants with severe RSV infection and 296 healthy control children. None of the genes showed association with severe RSV infection in children. Thus, despite the involvement of different IFNs in the pathophysiology of RSV infection, genetic variants in IFNG and related genes might not alter the risk for the development of severe RSV-associated diseases.
Collapse
|
41
|
Foell JL, Volkmer I, Giersberg C, Kornhuber M, Horneff G, Staege MS. Loss of detectability of Charcot-Leyden crystal protein transcripts in blood cells after treatment with dimethyl sulfoxide. J Immunol Methods 2008; 339:99-103. [PMID: 18789335 DOI: 10.1016/j.jim.2008.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 08/19/2008] [Accepted: 08/19/2008] [Indexed: 11/18/2022]
Abstract
Charcot-Leyden crystal protein (CLC) is a major secretory effector protein of eosinophils. In addition, CLC has been identified as marker for regulatory T-cells and differential expression of CLC has been described under diverse pathological conditions. By analysis of DNA microarray data from peripheral blood mononuclear cells (PBMC) we found differences for the expression of CLC between PBMC that had been cryopreserved or had been used for RNA isolation immediately after cell separation. Reverse transcriptase-polymerase chain reaction (RT-PCR) of separated cell populations indicated that contaminating granulocytes were the main source of CLC transcripts in PBMC. CLC was only detectable in fresh PBMC and not in cryopreserved material. Transcripts corresponding to CLC were also detectable by RT-PCR only in fresh PBMC and eosinophils. Loss of CLC transcripts in PBMC was induced by a short pulse with dimethyl sulfoxide (DMSO), indicating that the freezing medium was responsible for this phenomenon. We conclude that CLC transcripts are lost during cryopreservation in the presence of DMSO and can never be identified as differentially expressed in cryopreserved samples.
Collapse
Affiliation(s)
- Juergen L Foell
- Department of Pediatrics, Children's Cancer Research Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | | | | | | | | | | |
Collapse
|
42
|
Rosebeck S, Leaman DW. Mitochondrial localization and pro-apoptotic effects of the interferon-inducible protein ISG12a. Apoptosis 2008; 13:562-72. [PMID: 18330707 DOI: 10.1007/s10495-008-0190-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
ISG12a is one of the most highly induced genes following treatment of cells with type I interferons (IFNs). The encoded protein belongs to a family of poorly characterized, low molecular weight IFN-inducible proteins that includes 6-16 (G1P3), 1-8U (IFITM3), and 1-8D (IFITM2). Our studies demonstrate that the ISG12a protein associates with or inserts into the mitochondrial membrane. Transient expression of ISG12a led to decreased viable cell numbers and enhanced sensitivity to DNA-damage induced apoptosis, effects that were blocked by Bcl-2 co-expression or treatment with a pan-caspase inhibitor. ISG12a enhanced etoposide induced cytochrome c release, Bax activation and loss of mitochondrial membrane potential. siRNA-mediated inhibition of ectopic ISG12a protein expression prevented the sensitization to etoposide-induced apoptosis and also decreased the ability of IFN-beta pretreatment to sensitize cells to etoposide, thereby demonstrating a role for ISG12a in this process. These data suggest that ISG12a contributes to IFN-dependent perturbation of normal mitochondrial function, thus adding ISG12a to a growing list of IFN-induced proteins that impact cellular apoptosis.
Collapse
Affiliation(s)
- Shaun Rosebeck
- Department of Biological Sciences, The University of Toledo, Toledo, OH 43606, USA
| | | |
Collapse
|
43
|
Passtoors WM, Beekman M, Gunn D, Boer JM, Heijmans BT, Westendorp RGJ, Zwaan BJ, Slagboom PE. Genomic studies in ageing research: the need to integrate genetic and gene expression approaches. J Intern Med 2008; 263:153-66. [PMID: 18226093 DOI: 10.1111/j.1365-2796.2007.01904.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genome-wide and hypothesis-based approaches to the study of ageing and longevity have been dominated by genetic investigations. To identify essential mechanisms of a complex trait such as ageing in higher species, a holistic understanding of interacting pathways is required. More information on such interactions is expected to be obtained from global gene expression analysis if combined with genetic studies. Genetic sequence variation often provides a functional gene marker for the trait, whereas a gene expression profile may provide a quantitative biomarker representing complex cellular pathway interactions contributing to the trait. Thus far, gene expression studies have associated multiple pathways to ageing including mitochondrial electron transport and the oxidative stress response. However, most of the studies are underpowered to detect small age-changes. A systematic survey of gene expression changes as a function of age in human individuals and animal models is lacking. Well designed gene expression studies, especially at the level of biological processes, will provide hypotheses on gene-environmental interactions determining biological ageing rate. Cross-sectional studies monitoring the profile as a chronological marker of ageing must be integrated with prospective studies indicating which profiles represent biomarkers preceding and predicting physiological decline and mortality. New study designs such as the Leiden Longevity Study, including two generations of subjects from longevity families, aim to achieve these combined approaches.
Collapse
Affiliation(s)
- W M Passtoors
- Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.
| | | | | | | | | | | | | | | |
Collapse
|