51
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Johansson C, Kirsebom FCM. Neutrophils in respiratory viral infections. Mucosal Immunol 2021; 14:815-827. [PMID: 33758367 PMCID: PMC7985581 DOI: 10.1038/s41385-021-00397-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 02/04/2023]
Abstract
Viral respiratory infections are a common cause of severe disease, especially in infants, people who are immunocompromised, and in the elderly. Neutrophils, an important innate immune cell, infiltrate the lungs rapidly after an inflammatory insult. The most well-characterized effector mechanisms by which neutrophils contribute to host defense are largely extracellular and the involvement of neutrophils in protection from numerous bacterial and fungal infections is well established. However, the role of neutrophils in responses to viruses, which replicate intracellularly, has been less studied. It remains unclear whether and, by which underlying immunological mechanisms, neutrophils contribute to viral control or confer protection against an intracellular pathogen. Furthermore, neutrophils need to be tightly regulated to avoid bystander damage to host tissues. This is especially relevant in the lung where damage to delicate alveolar structures can compromise gas exchange with life-threatening consequences. It is inherently less clear how neutrophils can contribute to host immunity to viruses without causing immunopathology and/or exacerbating disease severity. In this review, we summarize and discuss the current understanding of how neutrophils in the lung direct immune responses to viruses, control viral replication and spread, and cause pathology during respiratory viral infections.
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Affiliation(s)
- Cecilia Johansson
- National Heart and Lung Institute, Imperial College London, London, UK.
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52
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Giacomelli Cao R, Christian L, Xu Z, Jaramillo L, Smith B, Karlsson EA, Schultz-Cherry S, Mejias A, Ramilo O. Early changes in interferon gene expression and antibody responses following influenza vaccination in pregnant women. J Infect Dis 2021; 225:341-351. [PMID: 34197595 DOI: 10.1093/infdis/jiab345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/29/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Influenza immunization during pregnancy provides protection to the mother and the infant. Studies in adults and children with inactivated influenza vaccine (IIV) have identified changes in immune gene expression that correlated with antibody responses. OBJECTIVE To define baseline blood transcriptional profiles and changes induced by IIV in pregnant women and to identify correlates with antibody responses. METHODS Pregnant women were immunized with IIV during the 2013-14 and 2014-15 seasons. Blood samples were collected on day (d) 0 (pre-vaccination), d1 and d7 post-vaccination for transcriptional profile analyses; and d0, d30, delivery and cord blood to measure antibody titers. RESULTS Transcriptional analysis demonstrated overexpression of interferon-stimulated genes (ISGs) on d1 and of plasma cell genes on d7. Pre-vaccination ISGs expression and ISGs over-expressed on d1 significantly correlated with increased H3N2, B Yamagata and B Victoria antibody titers. Plasma-cell gene expression on d7 correlated with increased B Yamagata and B Victoria antibody titers. Compared with women vaccinated during the previous influenza season, women who were not vaccinated the prior year showed more frequent significant correlations between ISGs and antibody titers. CONCLUSIONS Influenza vaccination in pregnant women resulted in enhanced expression of ISGs and plasma cell genes that correlated with antibody responses.
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Affiliation(s)
- Raquel Giacomelli Cao
- Center for Vaccines and Immunity, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Lisa Christian
- Institute for Behavioral Medical Research, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Psychiatry, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Zhaohui Xu
- Center for Vaccines and Immunity, Nationwide Children's Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
| | - Lisa Jaramillo
- Center for Vaccines and Immunity, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Bennett Smith
- Center for Vaccines and Immunity, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Erik A Karlsson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Current affiliation: Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, Nationwide Children's Hospital, Columbus, Ohio, USA
- Division of Infectious Diseases, Nationwide Children's Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
| | - Octavio Ramilo
- Center for Vaccines and Immunity, Nationwide Children's Hospital, Columbus, Ohio, USA
- Division of Infectious Diseases, Nationwide Children's Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
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53
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Heinonen S, Velazquez VM, Ye F, Mertz S, Acero-Bedoya S, Smith B, Bunsow E, Garcia-Mauriño C, Oliva S, Cohen DM, Moore-Clingenpeel M, Peeples ME, Ramilo O, Mejias A. Immune profiles provide insights into respiratory syncytial virus disease severity in young children. Sci Transl Med 2021; 12:12/540/eaaw0268. [PMID: 32321862 DOI: 10.1126/scitranslmed.aaw0268] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 11/21/2019] [Accepted: 03/05/2020] [Indexed: 12/29/2022]
Abstract
Respiratory syncytial virus (RSV) is associated with major morbidity in infants, although most cases result in mild disease. The pathogenesis of the disease is incompletely understood, especially the determining factors of disease severity. A better characterization of these factors may help with development of RSV vaccines and antivirals. Hence, identification of a "safe and protective" immunoprofile induced by natural RSV infection could be used as a as a surrogate of ideal vaccine-elicited responses in future clinical trials. In this study, we integrated blood transcriptional and cell immune profiling, RSV loads, and clinical data to identify factors associated with a mild disease phenotype in a cohort of 190 children <2 years of age. Children with mild disease (outpatients) showed higher RSV loads, greater induction of interferon (IFN) and plasma cell genes, and decreased expression of inflammation and neutrophil genes versus children with severe disease (inpatients). Additionally, only infants with severe disease had increased numbers of HLA-DRlow monocytes, not present in outpatients. Multivariable analyses confirmed that IFN overexpression was associated with decreased odds of hospitalization, whereas increased numbers of HLA-DRlow monocytes were associated with increased risk of hospitalization. These findings suggest that robust innate immune responses are associated with mild RSV infection in infants.
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Affiliation(s)
- Santtu Heinonen
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Victoria M Velazquez
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Fang Ye
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sara Mertz
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Santiago Acero-Bedoya
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Bennett Smith
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Eleonora Bunsow
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Cristina Garcia-Mauriño
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Silvia Oliva
- Division of Pediatric Emergency Medicine and Critical Care, Hospital Regional Universitario de Málaga, Málaga 29001, Spain.,Departamento de Farmacología y Pediatría, Facultad de Medicina, Universidad de Málaga, Málaga 29071, Spain
| | - Daniel M Cohen
- Division of Emergency Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Melissa Moore-Clingenpeel
- Biostatistics Core, The Research Institute at Nationwide Children's Hospital Columbus, OH 43205, USA
| | - Mark E Peeples
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Octavio Ramilo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA. .,Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA. .,Departamento de Farmacología y Pediatría, Facultad de Medicina, Universidad de Málaga, Málaga 29071, Spain.,Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH 43205, USA
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54
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Mejias A, Brenes-Chacon H, Garcia-Mauriño C, Moore-Clingenpeel M, Ramilo O. Clinical Disease Severity Scores and Viral Loads in Children With Respiratory Syncytial Virus Infection. Clin Infect Dis 2021; 72:e1160-e1162. [PMID: 33215632 DOI: 10.1093/cid/ciaa1752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Asuncion Mejias
- Center for Vaccines and Immunity Abigail Wexner Research Institute, Department of Pediatrics at Nationwide Children's Hospital, Columbus, OH, USA.,Division of nfectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA.,Departamento de Farmacologia y Pediatria, Facultad de Medicina, Universidad de Malaga, Malaga, Spain
| | - Helena Brenes-Chacon
- Center for Vaccines and Immunity Abigail Wexner Research Institute, Department of Pediatrics at Nationwide Children's Hospital, Columbus, OH, USA
| | - Cristina Garcia-Mauriño
- Center for Vaccines and Immunity Abigail Wexner Research Institute, Department of Pediatrics at Nationwide Children's Hospital, Columbus, OH, USA
| | - Melissa Moore-Clingenpeel
- Biostatistics Core, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Octavio Ramilo
- Center for Vaccines and Immunity Abigail Wexner Research Institute, Department of Pediatrics at Nationwide Children's Hospital, Columbus, OH, USA.,Division of nfectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
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55
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Rodriguez-Fernandez R, Mejias A, Ramilo O. Monoclonal Antibodies for Prevention of Respiratory Syncytial Virus Infection. Pediatr Infect Dis J 2021; 40:S35-S39. [PMID: 34042909 DOI: 10.1097/inf.0000000000003121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Respiratory syncytial virus (RSV) is the leading cause of hospitalizations in infants worldwide. Palivizumab, a humanized monoclonal antibody against the RSV F protein, is the only licensed agent for prevention of severe RSV infection in high-risk infants. Palivizumab is administered intramuscularly, every month during the RSV season, usually 5 doses are required. In recent years, the resolution of the structure of the RSV F protein, with identification of potent neutralizing epitopes, and new technologies for production of monoclonal antibodies (mAbs) have facilitated the development of new alternative strategies for the prevention of RSV infections. One promising approach is a new generation of mAbs directed to new neutralizing epitopes and with prolonged half life. These enhanced mAbs are expected to provide adequate protection during the complete RSV season with a single intramuscular (IM) dose. The long-term goal of this approach is to provide passive immunization for the prevention of RSV lower respiratory tract infection to all infants (preterm and full term) in the first months of life before their initial exposure to RSV.
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MESH Headings
- Antibodies, Monoclonal, Humanized/history
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Clinical Trials as Topic
- Epitopes/drug effects
- Half-Life
- History, 20th Century
- History, 21st Century
- Humans
- Immunization, Passive/methods
- Infant
- Infant, Newborn
- Respiratory Syncytial Virus Infections/prevention & control
- Respiratory Syncytial Virus, Human/drug effects
- Viral Fusion Proteins
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Affiliation(s)
- Rosa Rodriguez-Fernandez
- From the Center for Vaccines and Immunity, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
- Department of Pediatrics, Hospital Infantil Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón Madrid, Spain
| | - Asuncion Mejias
- From the Center for Vaccines and Immunity, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Octavio Ramilo
- From the Center for Vaccines and Immunity, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
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56
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Zheng H, Rao AM, Dermadi D, Toh J, Murphy Jones L, Donato M, Liu Y, Su Y, Dai CL, Kornilov SA, Karagiannis M, Marantos T, Hasin-Brumshtein Y, He YD, Giamarellos-Bourboulis EJ, Heath JR, Khatri P. Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses. Immunity 2021; 54:753-768.e5. [PMID: 33765435 PMCID: PMC7988739 DOI: 10.1016/j.immuni.2021.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.
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Affiliation(s)
- Hong Zheng
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Aditya M Rao
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Jiaying Toh
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Lara Murphy Jones
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA; Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Stanford University, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Yiran Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Cancer Biology program, Stanford University, CA 94305, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Cheng L Dai
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Minas Karagiannis
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | - Theodoros Marantos
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | | | | | | | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA.
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57
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Gómez-Carballa A, Barral-Arca R, Cebey-López M, Bello X, Pardo-Seco J, Martinón-Torres F, Salas A. Identification of a Minimal 3-Transcript Signature to Differentiate Viral from Bacterial Infection from Best Genome-Wide Host RNA Biomarkers: A Multi-Cohort Analysis. Int J Mol Sci 2021; 22:ijms22063148. [PMID: 33808774 PMCID: PMC8003556 DOI: 10.3390/ijms22063148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
The fight against the spread of antibiotic resistance is one of the most important challenges facing health systems worldwide. Given the limitations of current diagnostic methods, the development of fast and accurate tests for the diagnosis of viral and bacterial infections would improve patient management and treatment, as well as contribute to reducing antibiotic misuse in clinical settings. In this scenario, analysis of host transcriptomics constitutes a promising target to develop new diagnostic tests based on the host-specific response to infections. We carried out a multi-cohort meta-analysis of blood transcriptomic data available in public databases, including 11 different studies and 1209 samples from virus- (n = 695) and bacteria- (n = 514) infected patients. We applied a Parallel Regularized Regression Model Search (PReMS) on a set of previously reported genes that distinguished viral from bacterial infection to find a minimum gene expression bio-signature. This strategy allowed us to detect three genes, namely BAFT, ISG15 and DNMT1, that clearly differentiate groups of infection with high accuracy (training set: area under the curve (AUC) 0.86 (sensitivity: 0.81; specificity: 0.87); testing set: AUC 0.87 (sensitivity: 0.82; specificity: 0.86)). BAFT and ISG15 are involved in processes related to immune response, while DNMT1 is related to the preservation of methylation patterns, and its expression is modulated by pathogen infections. We successfully tested this three-transcript signature in the 11 independent studies, demonstrating its high performance under different scenarios. The main advantage of this three-gene signature is the low number of genes needed to differentiate both groups of patient categories.
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Affiliation(s)
- Alberto Gómez-Carballa
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Ruth Barral-Arca
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Miriam Cebey-López
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Xabier Bello
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Jacobo Pardo-Seco
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
| | - Antonio Salas
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15706 Galicia, Spain
- Correspondence:
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58
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Sharma A. Epidemiological transcriptomic data supports BCG protection in viral diseases including COVID-19. Gene 2021; 783:145574. [PMID: 33737124 PMCID: PMC7959679 DOI: 10.1016/j.gene.2021.145574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 01/03/2023]
Abstract
Epidemiological and clinical evidence suggests that Bacille Calmette-Guérin (BCG) vaccine induced trained immunity protects against non-specific infections. Multiple clinical trials are currently underway to assess effectiveness of the vaccine in the coronavirus disease 2019 (COVID-19). However, the durability and mechanism of BCG trained immunity remain unclear. Here, an integrative analysis of available epidemiological transcriptomic data related to BCG vaccination and respiratory tract viral infections as well as of reported transcriptomic alterations in COVID-19 is presented toward addressing this gap. Results suggest that the vaccine induces very long-lasting transcriptomic changes that mimic viral infections by, consistent with the present concept of trained immunity, upregulation of antiviral defense response, and oppose viral infections by, inconsistent with the concept, downregulation of myeloid cell activation. These durability and mechanistic insights argue against possible indiscriminate use of the vaccine and activated innate immune response associated safety concerns in COVID-19, in that order.
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Affiliation(s)
- Abhay Sharma
- CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110025 India.
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59
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Öner D, Drysdale SB, McPherson C, Lin GL, Janet S, Broad J, Pollard AJ, Aerssens J. Biomarkers for Disease Severity in Children Infected With Respiratory Syncytial Virus: A Systematic Literature Review. J Infect Dis 2021; 222:S648-S657. [PMID: 32794555 DOI: 10.1093/infdis/jiaa208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Clinical manifestations of respiratory syncytial virus (RSV) infection vary widely from mild, self-limiting illness to severe life-threatening disease. There are gaps in knowledge of biomarkers to objectively define severe disease and predict clinical outcomes. METHODS A systematic search was performed, 1945-March 2019 in databases Ovid Medline, Embase, Global health, Scopus, and Web of Science. Risk of bias was assessed using the Cochrane tool. RESULTS A total of 25 132 abstracts were screened and studies were assessed for quality, risk of bias, and extracted data; 111 studies met the inclusion criteria. RSV severity was correlated with antibody titers, reduced T and B cells, dysregulated innate immunity, neutrophil mobilization to the lungs and blood, decreased Th1 response, and Th2 weighted shift. Microbial exposures in respiratory tract may contribute to neutrophil mobilization to the lungs of the infants with severe RSV compared with mild RSV disease. CONCLUSIONS Although a wide range of biomarkers have been associated with RSV disease severity, robust validated biomarkers are lacking. This review illustrates the broad heterogeneity of study designs and high variability in the definition of severe RSV disease. Prospective studies are required to validate biomarkers. Additional research investigating epigenetics, metabolomics, and microbiome holds promise for novel biomarkers.
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Affiliation(s)
- Deniz Öner
- Infectious Diseases Translational Biomarkers, Janssen Pharmaceutica, Beerse, Belgium
| | - Simon B Drysdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom.,Paediatric Infectious Diseases Research Group, Institute of Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Calum McPherson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Gu-Lung Lin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Sophie Janet
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Jonathan Broad
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Jeroen Aerssens
- Infectious Diseases Translational Biomarkers, Janssen Pharmaceutica, Beerse, Belgium
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60
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Shilovskiy IP, Yumashev KV, Nikolsky AA, Vishnyakova LI, Khaitov MR. Molecular and Cellular Mechanisms of Respiratory Syncytial Viral Infection: Using Murine Models to Understand Human Pathology. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:290-306. [PMID: 33838630 PMCID: PMC7957450 DOI: 10.1134/s0006297921030068] [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] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/18/2020] [Accepted: 10/18/2020] [Indexed: 12/28/2022]
Abstract
Respiratory syncytial virus (RSV) causes severe pathology of the lower respiratory tract in infants, immunocompromised people, and elderly. Despite decades of research, there is no licensed vaccine against RSV, and many therapeutic drugs are still under development. Detailed understanding of molecular and cellular mechanisms of the RSV infection pathology can accelerate the development of efficacious treatment. Current studies on the RSV pathogenesis are based on the analysis of biopsies from the infected patients; however deeper understanding of molecular and cellular mechanisms of the RSV pathology could be achieved using animal models. Mice are the most often used model for RSV infection because they exhibit manifestations similar to those observed in humans (bronchial obstruction, mucous hypersecretion, and pulmonary inflammation mediated by lymphocytes, macrophages, and neutrophils). Additionally, the use of mice is economically feasible, and many molecular tools are available for studying RSV infection pathogenesis at the molecular and cellular levels. This review summarizes new data on the pathogenesis of RSV infection obtained in mouse models, which demonstrated the role of T cells in both the antiviral defense and the development of lung immunopathology. T cells not only eliminate the infected cells, but also produce significant amounts of the proinflammatory cytokines TNFα and IFNγ. Recently, a new subset of tissue-resident memory T cells (TRM) was identified that provide a strong antiviral defense without induction of lung immunopathology. These cells accumulate in the lungs after local rather than systemic administration of RSV antigens, which suggests new approaches to vaccination. The studies in mouse models have revealed a minor role of interferons in the anti-RSV protection, as RSV possesses mechanisms to escape the antiviral action of type I and III interferons, which may explain the low efficacy of interferon-containing drugs. Using knockout mice, a significant breakthrough has been achieved in understanding the role of many pro-inflammatory cytokines in lung immunopathology. It was found that in addition to TNFα and IFNγ, the cytokines IL-4, IL-5, IL-13, IL-17A, IL-33, and TSLP mediate the major manifestations of the RSV pathogenesis, such as bronchial obstruction, mucus hyperproduction, and lung infiltration by pro-inflammatory cells, while IL-6, IL-10, and IL-27 exhibit the anti-inflammatory effect. Despite significant differences between the mouse and human immune systems, mouse models have made a significant contribution to the understanding of molecular and cellular mechanisms of the pathology of human RSV infection.
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Affiliation(s)
- Igor P Shilovskiy
- National Research Center, Institute of Immunology, Federal Medico-Biological Agency, Moscow, 115522, Russia.
| | - Kirill V Yumashev
- National Research Center, Institute of Immunology, Federal Medico-Biological Agency, Moscow, 115522, Russia
| | - Alexandr A Nikolsky
- National Research Center, Institute of Immunology, Federal Medico-Biological Agency, Moscow, 115522, Russia
| | - Liudmila I Vishnyakova
- National Research Center, Institute of Immunology, Federal Medico-Biological Agency, Moscow, 115522, Russia
| | - Musa R Khaitov
- National Research Center, Institute of Immunology, Federal Medico-Biological Agency, Moscow, 115522, Russia
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61
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Wang L, Chu CY, McCall MN, Slaunwhite C, Holden-Wiltse J, Corbett A, Falsey AR, Topham DJ, Caserta MT, Mariani TJ, Walsh EE, Qiu X. Airway gene-expression classifiers for respiratory syncytial virus (RSV) disease severity in infants. BMC Med Genomics 2021; 14:57. [PMID: 33632195 PMCID: PMC7908785 DOI: 10.1186/s12920-021-00913-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A substantial number of infants infected with RSV develop severe symptoms requiring hospitalization. We currently lack accurate biomarkers that are associated with severe illness. METHOD We defined airway gene expression profiles based on RNA sequencing from nasal brush samples from 106 full-tem previously healthy RSV infected subjects during acute infection (day 1-10 of illness) and convalescence stage (day 28 of illness). All subjects were assigned a clinical illness severity score (GRSS). Using AIC-based model selection, we built a sparse linear correlate of GRSS based on 41 genes (NGSS1). We also built an alternate model based upon 13 genes associated with severe infection acutely but displaying stable expression over time (NGSS2). RESULTS NGSS1 is strongly correlated with the disease severity, demonstrating a naïve correlation (ρ) of ρ = 0.935 and cross-validated correlation of 0.813. As a binary classifier (mild versus severe), NGSS1 correctly classifies disease severity in 89.6% of the subjects following cross-validation. NGSS2 has slightly less, but comparable, accuracy with a cross-validated correlation of 0.741 and classification accuracy of 84.0%. CONCLUSION Airway gene expression patterns, obtained following a minimally-invasive procedure, have potential utility for development of clinically useful biomarkers that correlate with disease severity in primary RSV infection.
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Affiliation(s)
- Lu Wang
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Chin-Yi Chu
- Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | | | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Anthony Corbett
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Ann R Falsey
- Department of Medicine, University of Rochester School Medicine, Rochester, NY, USA
- Department of Medicine, Rochester General Hospital, Rochester, NY, USA
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester School Medicine, Rochester, NY, USA
| | - Mary T Caserta
- Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA.
| | - Edward E Walsh
- Department of Medicine, University of Rochester School Medicine, Rochester, NY, USA.
- Department of Medicine, Rochester General Hospital, Rochester, NY, USA.
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA.
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Rinchai D, Roelands J, Toufiq M, Hendrickx W, Altman MC, Bedognetti D, Chaussabel D. BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R. Bioinformatics 2021; 37:2382-2389. [PMID: 33624743 PMCID: PMC8388021 DOI: 10.1093/bioinformatics/btab121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/14/2021] [Accepted: 02/23/2021] [Indexed: 11/28/2022] Open
Abstract
Motivation We previously described the construction and characterization of fixed reusable blood transcriptional module repertoires. More recently we released a third iteration (‘BloodGen3’ module repertoire) that comprises 382 functionally annotated modules and encompasses 14 168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here an R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability and implementation The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | | | - Matthew C Altman
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA.,Systems Immunology, Benaroya Research Institute, Seattle, Washington, USA
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Dysregulated transcriptional responses to SARS-CoV-2 in the periphery. Nat Commun 2021; 12:1079. [PMID: 33597532 PMCID: PMC7889643 DOI: 10.1038/s41467-021-21289-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/15/2021] [Indexed: 01/31/2023] Open
Abstract
SARS-CoV-2 infection has been shown to trigger a wide spectrum of immune responses and clinical manifestations in human hosts. Here, we sought to elucidate novel aspects of the host response to SARS-CoV-2 infection through RNA sequencing of peripheral blood samples from 46 subjects with COVID-19 and directly comparing them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. Early SARS-CoV-2 infection triggers a powerful transcriptomic response in peripheral blood with conserved components that are heavily interferon-driven but also marked by indicators of early B-cell activation and antibody production. Interferon responses during SARS-CoV-2 infection demonstrate unique patterns of dysregulated expression compared to other infectious and healthy states. Heterogeneous activation of coagulation and fibrinolytic pathways are present in early COVID-19, as are IL1 and JAK/STAT signaling pathways, which persist into late disease. Classifiers based on differentially expressed genes accurately distinguished SARS-CoV-2 infection from other acute illnesses (auROC 0.95 [95% CI 0.92-0.98]). The transcriptome in peripheral blood reveals both diverse and conserved components of the immune response in COVID-19 and provides for potential biomarker-based approaches to diagnosis.
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Anderson J, Do LAH, Wurzel D, Quan Toh Z, Mulholland K, Pellicci DG, Licciardi PV. Severe respiratory syncytial virus disease in preterm infants: a case of innate immaturity. Thorax 2021; 76:942-950. [PMID: 33574121 DOI: 10.1136/thoraxjnl-2020-216291] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/12/2021] [Accepted: 01/27/2021] [Indexed: 11/03/2022]
Abstract
Respiratory syncytial virus (RSV) is the most common viral pathogen associated with acute lower respiratory tract infection (LRTI) in children under 5 years of age. Severe RSV disease is associated with the development of chronic respiratory complications such as recurrent wheezing and asthma. A common risk factor for developing severe RSV disease is premature gestation and this is largely due to an immature innate immune system. This increases susceptibility to RSV since the innate immune system is less able to protect against pathogens at a time when adaptive immunity has not fully developed. This review focuses on comparing different aspects of innate immunity between preterm and term infants to better understand why preterm infants are more susceptible to severe RSV disease. Identifying early life innate immune biomarkers associated with the development of severe RSV disease, and understanding how these compare between preterm and term infants, remains a critically important question that would aid the development of interventions to reduce the burden of disease in this vulnerable population.
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Affiliation(s)
- Jeremy Anderson
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Lien Anh Ha Do
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Pediatrics, The University of Melbourne-Parkville Campus, Melbourne, Victoria, Australia
| | - Danielle Wurzel
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Pediatrics, The University of Melbourne-Parkville Campus, Melbourne, Victoria, Australia.,The Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
| | - Zheng Quan Toh
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Pediatrics, The University of Melbourne-Parkville Campus, Melbourne, Victoria, Australia
| | - Kim Mulholland
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Pediatrics, The University of Melbourne-Parkville Campus, Melbourne, Victoria, Australia.,Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Daniel G Pellicci
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Pediatrics, The University of Melbourne-Parkville Campus, Melbourne, Victoria, Australia
| | - Paul V Licciardi
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia .,Department of Pediatrics, The University of Melbourne-Parkville Campus, Melbourne, Victoria, Australia
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Brenes-Chacon H, Garcia-Mauriño C, Moore-Clingenpeel M, Mertz S, Ye F, Cohen DM, Ramilo O, Mejias A. Age-dependent Interactions Among Clinical Characteristics, Viral Loads and Disease Severity in Young Children With Respiratory Syncytial Virus Infection. Pediatr Infect Dis J 2021; 40:116-122. [PMID: 33433159 PMCID: PMC7808270 DOI: 10.1097/inf.0000000000002914] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Age-dependent differences in clinical presentation and viral loads in infants and young children with respiratory syncytial virus (RSV) infection, and their correlation with disease severity are poorly defined. METHODS Previously healthy children <2 years old with mild (outpatients) and severe (inpatients) RSV infection were enrolled and viral loads measured by polymerase chain reaction in nasopharyngeal swabs. Patients were stratified by age in 0-<3, 3-6 and >6-24 months, and multivariable analyses were performed to identify clinical and viral factors associated with severe disease. RESULTS From 2014 to 2018, we enrolled 534 children with RSV infection, 130 outpatients with mild RSV infection and 404 inpatients with severe RSV disease. Median duration of illness was 4 days for both groups, yet viral loads were higher in outpatients than in inpatients (P < 0.001). In bivariate analyses, wheezing was more frequent in outpatients of older age (>3 months) than in inpatients (P < 0.01), while fever was more common in inpatients than outpatients (P < 0.01) and its frequency increased with age. Adjusted analyses confirmed that increased work of breathing and fever were consistently associated with hospitalization irrespective of age, while wheezing in infants >3 months, and higher RSV loads in children >6-24 months were independently associated with reduced disease severity. CONCLUSIONS Age had a significant impact defining the interactions among viral loads, specific clinical manifestations and disease severity in children with RSV infection. These observations highlight the importance of patient stratification when evaluating interventions against RSV.
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Affiliation(s)
| | | | | | | | - Fang Ye
- Center for Vaccines and Immunity
| | | | - Octavio Ramilo
- Center for Vaccines and Immunity
- Division of Pediatric Infectious Diseases, Nationwide Children’s Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity
- Division of Pediatric Infectious Diseases, Nationwide Children’s Hospital and The Ohio State University College of Medicine, Columbus, OH, USA
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Mahle RE, Suchindran S, Henao R, Steinbrink JM, Burke TW, McClain MT, Ginsburg GS, Woods CW, Tsalik EL. Validation of a host gene expression test for bacterial/viral discrimination in immunocompromised hosts. Clin Infect Dis 2021; 73:605-613. [PMID: 33462581 DOI: 10.1093/cid/ciab043] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Host gene expression has emerged as a complementary strategy to pathogen detection tests for the discrimination of bacterial and viral infection. The impact of immunocompromise on host response tests remains unknown. We evaluated a host response test discriminating bacterial, viral, and non-infectious conditions in immunocompromised subjects. METHODS An 81-gene signature was measured using RT-PCR in subjects with immunocompromise (chemotherapy, solid organ transplant, immunomodulatory agents, AIDS) with bacterial infection, viral infection, or noninfectious illness. A regularized logistic regression model trained in immunocompetent subjects was used to estimate the likelihood of each class in immunocompromised subjects. RESULTS Accuracy in the 136-subject immunocompetent training cohort was 84.6% for bacterial vs. non-bacterial discrimination and 80.8% for viral vs. non-viral discrimination. Model validation in 134 immunocompromised subjects showed overall accuracy of 73.9% for bacterial infection (p=0.04 relative to immunocompetent subjects) and 75.4% for viral infection (p=0.30). A scheme reporting results by quartile improved test utility. The highest probability quartile ruled-in bacterial and viral infection with 91.4% and 84.0% specificity, respectively. The lowest probability quartile ruled-out infection with 90.1% and 96.4% sensitivity for bacterial and viral infection, respectively. Performance was independent of the type or number of immunocompromising conditions. CONCLUSION A host gene expression test discriminated bacterial, viral, and non-infectious etiologies at a lower overall accuracy in immunocompromised patients compared to immunocompetent patients, though this difference was only significant for bacterial infection classification. With modified interpretive criteria, a host response strategy may offer clinically useful diagnostic information for patients with immunocompromise.
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Affiliation(s)
- Rachael E Mahle
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Sunil Suchindran
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Electrical and Computer Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina, USA
| | - Julie M Steinbrink
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thomas W Burke
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah T McClain
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham VA Health Care System, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher W Woods
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham VA Health Care System, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Emergency Medicine Service, Durham VA Health Care System, Durham, North Carolina, USA
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Holgado MP, Raiden S, Sananez I, Seery V, De Lillo L, Maldonado LL, Kamenetzky L, Geffner J, Arruvito L. Fcγ Receptor IIa (FCGR2A) Polymorphism Is Associated With Severe Respiratory Syncytial Virus Disease in Argentinian Infants. Front Cell Infect Microbiol 2021; 10:607348. [PMID: 33392111 PMCID: PMC7775358 DOI: 10.3389/fcimb.2020.607348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/19/2020] [Indexed: 12/02/2022] Open
Abstract
Background Most patients with respiratory syncytial virus (RSV) infection requiring hospitalization have no risk factors for severe disease. Genetic variation in the receptor for the Fc portion of IgG (FcγR) determines their affinity for IgG subclasses driving innate and adaptive antiviral immunity. We investigated the relationship between FcγRIIa-H131R polymorphism and RSV disease. Methods Blood samples were collected from 182 infants ≤24-month-old (50 uninfected, 114 RSV-infected with moderate course and 18 suffering severe disease). FcγRIIa-H131R SNP genotypic frequencies (HH, HR, RR) and anti-RSV IgG1, IgG2 and IgG3 levels were studied. Results Genotypic frequencies for FcγRIIa-H131R SNP were comparable between uninfected and RSV-infected infants. In contrast, we found a significant higher frequency of HH genotype in severe RSV-infected children compared to moderate patients. Among severe group, HH infants presented more factors associated to severity than HR or RR patients did. Furthermore, compared to moderate RSV-infected infants, severe patients showed higher levels of anti-RSV IgG1 and IgG3. Conclusions We found an association between an FcγRIIa (H131) polymorphism and severe RSV disease, which points towards a critical role for interactions between FcγRs and immune complexes in RSV pathogenesis. This genetic factor could also predict the worse outcome and identify those infants at risk during hospitalization.
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Affiliation(s)
- María Pía Holgado
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Silvina Raiden
- Hospital General de Niños "Pedro de Elizalde", Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Sananez
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Vanesa Seery
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Leonardo De Lillo
- Hospital General de Niños "Pedro de Elizalde", Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucas L Maldonado
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Kamenetzky
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Lourdes Arruvito
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
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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.
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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
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Tahamtan A, Besteman S, Samadizadeh S, Rastegar M, Bont L, Salimi V. Neutrophils in respiratory syncytial virus infection: From harmful effects to therapeutic opportunities. Br J Pharmacol 2020; 178:515-530. [PMID: 33169387 DOI: 10.1111/bph.15318] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is an important infectious agent in infants and young children. In most cases, RSV infection only causes mild disease, but in some, it requires invasive ventilation. Although antiviral drugs are obvious candidates to treat viral illness, and some have shown antiviral effects in humans, antivirals such as GS-5806, ALX-0171 and ALS-8176 have not yet met their expectations. Since the inappropriate or dysregulated immune response against RSV leads to harmful immune pathology, a robust immune cascade is probably underway by the time patients reach the hospital. RSV infection is associated with a strong neutrophil influx into the airway. It not clear if these cells contribute to antiviral defence or to lung pathology. This article discusses the protective and harmful roles of neutrophils during RSV infection and provides an overview of mechanisms by which neutrophil function could be targeted to prevent tissue injury and preserve homeostasis.
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Affiliation(s)
- Alireza Tahamtan
- Infectious Diseases Research Centre, Golestan University of Medical Sciences, Gorgan, Iran.,Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sjanna Besteman
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.,Center for Translation Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Saeed Samadizadeh
- Infectious Diseases Research Centre, Golestan University of Medical Sciences, Gorgan, Iran.,Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mostafa Rastegar
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Louis Bont
- Department of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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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.
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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
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71
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McClain MT, Constantine FJ, Nicholson BP, Nichols M, Burke TW, Henao R, Jones DC, Hudson LL, Jaggers LB, Veldman T, Mazur A, Park LP, Suchindran S, Tsalik EL, Ginsburg GS, Woods CW. A blood-based host gene expression assay for early detection of respiratory viral infection: an index-cluster prospective cohort study. THE LANCET. INFECTIOUS DISEASES 2020; 21:396-404. [PMID: 32979932 PMCID: PMC7515566 DOI: 10.1016/s1473-3099(20)30486-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023]
Abstract
Background Early and accurate identification of individuals with viral infections is crucial for clinical management and public health interventions. We aimed to assess the ability of transcriptomic biomarkers to identify naturally acquired respiratory viral infection before typical symptoms are present. Methods In this index-cluster study, we prospectively recruited a cohort of undergraduate students (aged 18–25 years) at Duke University (Durham, NC, USA) over a period of 5 academic years. To identify index cases, we monitored students for the entire academic year, for the presence and severity of eight symptoms of respiratory tract infection using a daily web-based survey, with symptoms rated on a scale of 0–4. Index cases were defined as individuals who reported a 6-point increase in cumulative daily symptom score. Suspected index cases were visited by study staff to confirm the presence of reported symptoms of illness and to collect biospecimen samples. We then identified clusters of close contacts of index cases (ie, individuals who lived in close proximity to index cases, close friends, and partners) who were presumed to be at increased risk of developing symptomatic respiratory tract infection while under observation. We monitored each close contact for 5 days for symptoms and viral shedding and measured transcriptomic responses at each timepoint each day using a blood-based 36-gene RT-PCR assay. Findings Between Sept 1, 2009, and April 10, 2015, we enrolled 1465 participants. Of 264 index cases with respiratory tract infection symptoms, 150 (57%) had a viral cause confirmed by RT-PCR. Of their 555 close contacts, 106 (19%) developed symptomatic respiratory tract infection with a proven viral cause during the observation window, of whom 60 (57%) had the same virus as their associated index case. Nine viruses were detected in total. The transcriptomic assay accurately predicted viral infection at the time of maximum symptom severity (mean area under the receiver operating characteristic curve [AUROC] 0·94 [95% CI 0·92–0·96]), as well as at 1 day (0·87 [95% CI 0·84–0·90]), 2 days (0·85 [0·82–0·88]), and 3 days (0·74 [0·71–0·77]) before peak illness, when symptoms were minimal or absent and 22 (62%) of 35 individuals, 25 (69%) of 36 individuals, and 24 (82%) of 29 individuals, respectively, had no detectable viral shedding. Interpretation Transcriptional biomarkers accurately predict and diagnose infection across diverse viral causes and stages of disease and thus might prove useful for guiding the administration of early effective therapy, quarantine decisions, and other clinical and public health interventions in the setting of endemic and pandemic infectious diseases. Funding US Defense Advanced Research Projects Agency.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA.
| | - Florica J Constantine
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Lori L Hudson
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - L Brett Jaggers
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mazur
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lawrence P Park
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Sunil Suchindran
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
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72
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Cebey-López M, Salas A. Recognising the asymptomatic enemy. THE LANCET. INFECTIOUS DISEASES 2020; 21:305-306. [PMID: 32979931 PMCID: PMC7515607 DOI: 10.1016/s1473-3099(20)30587-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Miriam Cebey-López
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Galicia 15706, Spain.
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain; GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
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73
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Challenges for the Newborn Immune Response to Respiratory Virus Infection and Vaccination. Vaccines (Basel) 2020; 8:vaccines8040558. [PMID: 32987691 PMCID: PMC7712002 DOI: 10.3390/vaccines8040558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
The initial months of life reflect an extremely challenging time for newborns as a naïve immune system is bombarded with a large array of pathogens, commensals, and other foreign entities. In many instances, the immune response of young infants is dampened or altered, resulting in increased susceptibility and disease following infection. This is the result of both qualitative and quantitative changes in the response of multiple cell types across the immune system. Here we provide a review of the challenges associated with the newborn response to respiratory viral pathogens as well as the hurdles and advances for vaccine-mediated protection.
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74
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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.
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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.
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75
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Auletta JJ, Adamson PC, Agin JE, Kearns P, Kennedy S, Kieran MW, Ludwinski DM, Knox LJ, McKay K, Rhiner P, Thiele CJ, Cripe TP. Pediatric cancer research: Surviving COVID-19. Pediatr Blood Cancer 2020; 67:e28435. [PMID: 32558190 PMCID: PMC7323039 DOI: 10.1002/pbc.28435] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/26/2022]
Abstract
A diverse panel of pediatric cancer advocates and experts, whose collective experience spans the continuum of international academic medicine, industry, government research, and cancer advocacy, recently discussed challenges for pediatric cancer research in the context of coronavirus disease 2019 (COVID-19). Specifically, this special report addresses the following focus areas: (a) the critical role that translational research has played in transforming pediatric cancer outcomes; (b) the current and potential future impact of COVID-19 on pediatric cancer research; (c) target areas of COVID-19 research that may have application in immunity, oncogenesis, and therapeutic discovery; and (d) future considerations and directions in maintaining pediatric cancer research during and after COVID-19.
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Affiliation(s)
- Jeffery J. Auletta
- Division of Pediatric Hematology/Oncology/BMTNationwide Children's HospitalColumbusOhio
- Divison of Infectious DiseasesNationwide Children's HospitalColumbusOhio
- Department of PediatricsThe Ohio State University College of MedicineColumbusOhio
- The Ohio State University Comprehensive Cancer CenterColumbusOhio
| | - Peter C. Adamson
- Oncology Development & Pediatric InnovationSanofiCambridgeMassachusetts
| | | | - Pamela Kearns
- European Society of Paediatric OncologyBrusselsBelgium
- Cancer Research UK Clinical Trials UnitNational Institute for Health Research (NIHR) Birmingham Biomedical Research CentreInstitute of Cancer and Genomic SciencesBirminghamUK
| | | | | | | | | | | | | | - Carol J. Thiele
- Pediatric Oncology BranchCenter for Cancer ResearchNational Cancer InstituteBethesdaMaryland
| | - Timothy P. Cripe
- Division of Pediatric Hematology/Oncology/BMTNationwide Children's HospitalColumbusOhio
- Department of PediatricsThe Ohio State University College of MedicineColumbusOhio
- The Ohio State University Comprehensive Cancer CenterColumbusOhio
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76
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Sundararaman A, Ray M, Ravindra PV, Halami PM. Role of probiotics to combat viral infections with emphasis on COVID-19. Appl Microbiol Biotechnol 2020; 104:8089-8104. [PMID: 32813065 PMCID: PMC7434852 DOI: 10.1007/s00253-020-10832-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
Interspecies transmissions of viruses between animals and humans may result in unpredictable pathogenic potential and new transmissible diseases. This mechanism has recently been exemplified by the discovery of new pathogenic viruses, such as the novel severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) pandemic, Middle-East respiratory syndrome-coronavirus epidemic in Saudi Arabia, and the deadly outbreak of Ebola in West Africa. The. SARS-CoV-2 causes coronavirus disease-19 (COVID-19), which is having a massive global impact in terms of economic disruption, and, above all, human health. The disease is characterized by dry cough, fever, fatigue, myalgia, and dyspnea. Other symptoms include headache, sore throat, rhinorrhea, and gastrointestinal disorders. Pneumonia appears to be the most common and severe manifestation of the infection. Currently, there is no vaccine or specific drug for COVID-19. Further, the development of new antiviral requires a considerable length of time and effort for drug design and validation. Therefore, repurposing the use of natural compounds can provide alternatives and can support therapy against COVID-19. In this review, we comprehensively discuss the prophylactic and supportive therapeutic role of probiotics for the management of COVID-19. In addition, the unique role of probiotics to modulate the gut microbe and assert gut homeostasis and production of interferon as an antiviral mechanism is described. Further, the regulatory role of probiotics on gut-lung axis and mucosal immune system for the potential antiviral mechanisms is reviewed and discussed.Key points• Gut microbiota role in antiviral diseases• Factors influencing the antiviral mechanism• Probiotics and Covid-19.
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Affiliation(s)
- Aravind Sundararaman
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India
| | - Mousumi Ray
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India
| | - P V Ravindra
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India
| | - Prakash M Halami
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India.
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77
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Fujiogi M, Camargo CA, Bernot JP, Freishtat RJ, Harmon B, Mansbach JM, Castro-Nallar E, Perez-Losada M, Hasegawa K. In infants with severe bronchiolitis: dual-transcriptomic profiling of nasopharyngeal microbiome and host response. Pediatr Res 2020; 88:144-146. [PMID: 31905367 PMCID: PMC7335686 DOI: 10.1038/s41390-019-0742-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/11/2019] [Accepted: 12/15/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Michimasa Fujiogi
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - James P. Bernot
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC,Division of Emergency Medicine, Children’s National Hospital, Washington, DC,Departments of Pediatrics and Integrative Systems Biology and Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Brennan Harmon
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC
| | - Jonathan M. Mansbach
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Eduardo Castro-Nallar
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Marcos Perez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC,Department of Pediatrics, George Washington University School of Medicine and Health Sciences and the Division of Emergency Medicine, Children’s National Hospital, Washington, DC,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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Baker S, Blohmke CJ, Maes M, Johnston PI, Darton TC. The Current Status of Enteric Fever Diagnostics and Implications for Disease Control. Clin Infect Dis 2020; 71:S64-S70. [PMID: 32725220 PMCID: PMC7388712 DOI: 10.1093/cid/ciaa503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enteric (typhoid) fever remains a problem in low- and middle-income countries that lack the infrastructure to maintain sanitation and where inadequate diagnostic methods have restricted our ability to identify and control the disease more effectively. As we move into a period of potential disease elimination through the introduction of typhoid conjugate vaccine (TCV), we again need to reconsider the role of typhoid diagnostics in how they can aid in facilitating disease control. Recent technological advances, including serology, transcriptomics, and metabolomics, have provided new insights into how we can detect signatures of invasive Salmonella organisms interacting with the host during infection. Many of these new techniques exhibit potential that could be further explored with the aim of creating a new enteric fever diagnostic to work in conjunction with TCV. We need a sustained effort within the enteric fever field to accelerate, validate, and ultimately introduce 1 (or more) of these methods to facilitate the disease control initiative. The window of opportunity is still open, but we need to recognize the need for communication with other research areas and commercial organizations to assist in the progression of these diagnostic approaches. The elimination of enteric fever is now becoming a real possibility, but new diagnostics need to be part of the equation and factored into future calculations for disease control.
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Affiliation(s)
- Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Peter I Johnston
- Florey Institute for Host-Pathogen Interactions, Department for Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
| | - Thomas C Darton
- Florey Institute for Host-Pathogen Interactions, Department for Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
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Nicolas De Lamballerie C, Pizzorno A, Dubois J, Padey B, Julien T, Traversier A, Carbonneau J, Orcel E, Lina B, Hamelin ME, Roche M, Textoris J, Boivin G, Legras-Lachuer C, Terrier O, Rosa-Calatrava M. Human Respiratory Syncytial Virus-Induced Immune Signature of Infection Revealed by Transcriptome Analysis of Clinical Pediatric Nasopharyngeal Swab Samples. J Infect Dis 2020; 223:1052-1061. [PMID: 32726438 DOI: 10.1093/infdis/jiaa468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/24/2020] [Indexed: 11/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) constitutes one the main causes of respiratory infection in neonates and infants worldwide. Transcriptome analysis of clinical samples using high-throughput technologies remains an important tool to better understand virus-host complex interactions in the real-life setting but also to identify new diagnosis/prognosis markers or therapeutics targets. A major challenge when exploiting clinical samples such as nasal swabs, washes, or bronchoalveolar lavages is the poor quantity and integrity of nucleic acids. In this study, we applied a tailored transcriptomics workflow to exploit nasal wash samples from children who tested positive for HRSV. Our analysis revealed a characteristic immune signature as a direct reflection of HRSV pathogenesis and highlighted putative biomarkers of interest such as IP-10, TMEM190, MCEMP1, and TIMM23.
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Affiliation(s)
- Claire Nicolas De Lamballerie
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Viroscan3D SAS, Lyon, France
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julie Carbonneau
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Marie-Eve Hamelin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Julien Textoris
- Pathophysiology of Injury-Induced Immunosuppression, Hospices Civils de Lyon, bioMérieux, Université Claude Bernard Lyon 1, Hôpital Edouard Herriot, Lyon, France
| | - Guy Boivin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | - Catherine Legras-Lachuer
- Viroscan3D SAS, Lyon, France.,Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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McClain MT, Constantine FJ, Henao R, Liu Y, Tsalik EL, Burke TW, Steinbrink JM, Petzold E, Nicholson BP, Rolfe R, Kraft BD, Kelly MS, Sempowski GD, Denny TN, Ginsburg GS, Woods CW. Dysregulated transcriptional responses to SARS-CoV-2 in the periphery support novel diagnostic approaches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.07.20.20155507. [PMID: 32743603 PMCID: PMC7386527 DOI: 10.1101/2020.07.20.20155507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to elucidate novel aspects of the host response to SARS-CoV-2 we performed RNA sequencing on peripheral blood samples across 77 timepoints from 46 subjects with COVID-19 and compared them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. Early SARS-CoV-2 infection triggers a conserved transcriptomic response in peripheral blood that is heavily interferon-driven but also marked by indicators of early B-cell activation and antibody production. Interferon responses during SARS-CoV-2 infection demonstrate unique patterns of dysregulated expression compared to other infectious and healthy states. Heterogeneous activation of coagulation and fibrinolytic pathways are present in early COVID-19, as are IL1 and JAK/STAT signaling pathways, that persist into late disease. Classifiers based on differentially expressed genes accurately distinguished SARS-CoV-2 infection from other acute illnesses (auROC 0.95). The transcriptome in peripheral blood reveals unique aspects of the immune response in COVID-19 and provides for novel biomarker-based approaches to diagnosis.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
- Durham Veterans Affairs Medical Center, Durham, NC
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
| | | | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Yiling Liu
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
- Durham Veterans Affairs Medical Center, Durham, NC
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Julie M Steinbrink
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | | | - Robert Rolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
| | - Bryan D Kraft
- Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University Medical Center, Durham, NC
| | - Matthew S Kelly
- Division of Pediatric Infectious Diseases, Duke University Medical Center
| | | | | | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
- Durham Veterans Affairs Medical Center, Durham, NC
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC
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81
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Ouellette CP, Sánchez PJ, Xu Z, Blankenship D, Zeray F, Ronchi A, Shimamura M, Chaussabel D, Lee L, Owen KE, Shoup AG, Ramilo O, Mejias A. Blood genome expression profiles in infants with congenital cytomegalovirus infection. Nat Commun 2020; 11:3548. [PMID: 32669541 PMCID: PMC7363904 DOI: 10.1038/s41467-020-17178-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 06/10/2020] [Indexed: 01/10/2023] Open
Abstract
Congenital CMV infection (cCMVi) affects 0.5–1% of all live births worldwide, making it the leading cause of sensorineural hearing loss (SNHL) in childhood. The majority of infants with cCMVi have normal hearing at birth, but are at risk of developing late-onset SNHL. Currently, we lack reliable biomarkers to predict the development of SNHL in these infants. Here, we evaluate blood transcriptional profiles in 80 infants with cCMVi (49 symptomatic, 31 asymptomatic), enrolled in the first 3 weeks of life, and followed for 3 years to assess emergence of late-onset SNHL. The biosignatures of symptomatic and asymptomatic cCMVi are indistinguishable, suggesting that immune responses of infants with asymptomatic and symptomatic cCMVi are not different. Random forest analyses of initial samples in infants with cCMVi, irrespective of their clinical classification, identify a 16-gene classifier signature associated with the development of SNHL with 92% accuracy, suggesting its potential value as a biomarker. Congenital CMV infection can result in sensorineural hearing loss, but predicting this outcome is not yet possible. Here, the authors show that while blood gene expression profiles are not substantially different between symptomatic and asymptomatic infants with congenital CMV infection, a 16-gene signature is identified and able to predict late-onset hearing loss in these children.
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Affiliation(s)
- Christopher P Ouellette
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA
| | - Pablo J Sánchez
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA.,Division of Neonatology, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, Divisions of Neonatal-Perinatal Medicine and Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhaohui Xu
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Fiker Zeray
- Children's Medical Center Dallas, Dallas, TX, USA
| | - Andrea Ronchi
- Department of Pediatrics, Divisions of Neonatal-Perinatal Medicine and Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Neonatal intensive care unit, Fondazione IRCCS, Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | - Masako Shimamura
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Lizette Lee
- Department of Pediatrics, Divisions of Neonatal-Perinatal Medicine and Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Children's Medical Center Dallas, Dallas, TX, USA
| | - Kris E Owen
- Children's Medical Center Dallas, Dallas, TX, USA.,Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Angela G Shoup
- Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Parkland Health and Hospital System, Dallas, TX, USA
| | - Octavio Ramilo
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Asuncion Mejias
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA. .,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
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82
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Li Y, Liu H, Xu Q, Wu R, Zhang Y, Li N, He X, Yang M, Liang M, Ma X. OASL as a Diagnostic Marker for Influenza Infection Revealed by Integrative Bioinformatics Analysis With XGBoost. Front Bioeng Biotechnol 2020; 8:729. [PMID: 32714913 PMCID: PMC7343705 DOI: 10.3389/fbioe.2020.00729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022] Open
Abstract
Host response biomarkers offer a promising alternative diagnostic solution for identifying acute respiratory infection (ARI) cases involving influenza infection. However, most of the published panels involve multiple genes, which is problematic in clinical settings because polymerase chain reaction (PCR)-based technology is the most widely used genomic technology in these settings, and it can only be used to measure a small number of targets. This study aimed to identify a single-gene biomarker with a high diagnostic accuracy by using integrated bioinformatics analysis with XGBoost. The gene expression profiles in dataset GSE68310 were used to construct a co-expression network using weighted correlation network analysis (WGCNA). Fourteen hub genes related to influenza infection (blue module) that were common to both the co-expression network and the protein–protein interaction network were identified. Thereafter, a single hub gene was selected using XGBoost, with feature selection conducted using recursive feature elimination with cross-validation (RFECV). The identified biomarker was oligoadenylate synthetases-like (OASL). The robustness of this biomarker was further examined using three external datasets. OASL expression profiling triggered by various infections was different enough to discriminate between influenza and non-influenza ARI infections. Thus, this study presented a workflow to identify a single-gene classifier across multiple datasets. Moreover, OASL was revealed as a biomarker that could identify influenza patients from among those with flu-like ARI. OASL has great potential for improving influenza diagnosis accuracy in ARI patients in the clinical setting.
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Affiliation(s)
- Yang Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongjie Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Quan Xu
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Rui Wu
- Department of Pathology, Peking University Third Hospital, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yi Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Naizhe Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaozhou He
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengjie Yang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mifang Liang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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83
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Tsai CH, Wu AC, Chiang BL, Yang YH, Hung SP, Su MW, Chang YJ, Lee YL. CEACAM3 decreases asthma exacerbations and modulates respiratory syncytial virus latent infection in children. Thorax 2020; 75:725-734. [PMID: 32606071 DOI: 10.1136/thoraxjnl-2019-214132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/15/2020] [Accepted: 05/05/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is associated with childhood asthma. Nevertheless, not all children exposed to RSV develop asthma symptoms, possibly because genes modulate the effects of RSV on asthma exacerbations. OBJECTIVE The purpose of this study was to identify genes that modulate the effect of RSV latent infection on asthma exacerbations. METHODS We performed a meta-analysis to investigate differentially expressed genes (DEGs) of RSV infection from Gene Expression Omnibus datasets. Expression quantitative trait loci (eQTL) methods were applied to select single nucleotide polymorphisms (SNPs) that were associated with DEGs. Gene-based analysis was used to identify SNPs that were significantly associated with asthma exacerbations in the Taiwanese Consortium of Childhood Asthma Study (TCCAS), and validation was attempted in an independent cohort, the Childhood Asthma Management Program (CAMP). Gene-RSV interaction analyses were performed to investigate the association between the interaction of SNPs and RSV latent infection on asthma exacerbations. RESULTS A total of 352 significant DEGs were found by meta-analysis of RSV-related genes. We used 38 123 SNPs related to DEGs to investigate the genetic main effects on asthma exacerbations. We found that eight RSV-related genes (GADD45A, GYPB, MS4A3, NFE2, RNASE3, EPB41L3, CEACAM6 and CEACAM3) were significantly associated with asthma exacerbations in TCCAS and also validated in CAMP. In TCCAS, rs7251960 (CEACAM3) significantly modulated the effect of RSV latent infection on asthma exacerbations (false-discovery rate <0.05). The rs7251960 variant was associated with CEACAM3 mRNA expression in lung tissue (p for trend=1.2×10-7). CEACAM3 mRNA was reduced in nasal mucosa from subjects with asthma exacerbations in two independent datasets. CONCLUSIONS rs7251960 is an eQTL for CEACAM3, and CEACAM3 mRNA expression is reduced in subjects experiencing asthma exacerbations. CEACAM3 may be a modulator of RSV latent infection on asthma exacerbations.
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Affiliation(s)
- Ching-Hui Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Ann Chen Wu
- Center for Healthcare Research in Pediatrics (CHeRP), PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Bor-Luen Chiang
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yao-Hsu Yang
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Shih-Pin Hung
- Department of Pediatrics, Cathay General Hospital, Taipei, Taiwan
| | - Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ya-Jen Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yungling L Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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84
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Gardinassi LG, Souza COS, Sales-Campos H, Fonseca SG. Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse. Front Immunol 2020; 11:1636. [PMID: 32670298 PMCID: PMC7332781 DOI: 10.3389/fimmu.2020.01636] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
The current pandemic of coronavirus disease 19 (COVID-19) has affected millions of individuals and caused thousands of deaths worldwide. The pathophysiology of the disease is complex and mostly unknown. Therefore, identifying the molecular mechanisms that promote progression of the disease is critical to overcome this pandemic. To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. Here, we provide novel perspectives on the pathophysiology of COVID-19 using robust functional approaches to analyze public transcriptome datasets. In addition, we compared the transcriptional signature of COVID-19 patients with individuals infected with SARS-CoV-1 and Influenza A (IAV) viruses. We identified a core transcriptional signature induced by the respiratory viruses in peripheral leukocytes, whereas the absence of significant type I interferon/antiviral responses characterized SARS-CoV-2 infection. We also identified the higher expression of genes involved in metabolic pathways including heme biosynthesis, oxidative phosphorylation and tryptophan metabolism. A BTM-driven meta-analysis of bronchoalveolar lavage fluid (BALF) from COVID-19 patients showed significant enrichment for neutrophils and chemokines, which were also significant in data from lung tissue of one deceased COVID-19 patient. Importantly, our results indicate higher expression of genes related to oxidative phosphorylation both in peripheral mononuclear leukocytes and BALF, suggesting a critical role for mitochondrial activity during SARS-CoV-2 infection. Collectively, these data point for immunopathological features and targets that can be therapeutically exploited to control COVID-19.
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Affiliation(s)
- Luiz G. Gardinassi
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Camila O. S. Souza
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Helioswilton Sales-Campos
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Simone G. Fonseca
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
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85
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Lempainen J, Korhonen LS, Kantojärvi K, Heinonen S, Toivonen L, Räty P, Ramilo O, Mejias A, Laine AP, Vuorinen T, Waris M, Karlsson L, Karlsson H, Paunio T, Peltola V. Associations Between IFI44L Gene Variants and Rates of Respiratory Tract Infections During Early Childhood. J Infect Dis 2020; 223:157-165. [DOI: 10.1093/infdis/jiaa341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Abstract
Background
Genetic heterogeneity in type I interferon (IFN)–related gene IFI44L may account for variable susceptibility to respiratory tract infections (RTIs) in children.
Methods
In 2 prospective, population-based birth cohorts, the STEPS Study and the FinnBrain Birth Cohort Study, IFI44L genotypes for rs273259 and rs1333969 were determined in relation to the development of RTIs until 1 or 2 years of age, respectively. At age 3 months, whole-blood transcriptional profiles were analyzed and nasal samples were tested for respiratory viruses in a subset of children.
Results
In the STEPS Study (n = 1135), IFI44L minor/minor gene variants were associated with lower rates of acute otitis media episodes (adjusted incidence rate ratio, 0.77 [95% confidence interval, .61–.96] for rs273259 and 0.74 [.55–.99] for rs1333969) and courses of antibiotics for RTIs (0.76 [.62–.95] and 0.73 [.56–.97], respectively. In the FinnBrain cohort (n = 971), IFI44L variants were associated with lower rates of RTIs and courses of antibiotics for RTIs. In respiratory virus–positive 3-month-old children, IFI44L gene variants were associated with decreased expression levels of IFI44L and several other IFN-related genes.
Conclusions
Variant forms of IFI44L gene were protective against early-childhood RTIs or acute otitis media, and they attenuated IFN pathway activation by respiratory viruses.
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Affiliation(s)
- Johanna Lempainen
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Laura S Korhonen
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Katri Kantojärvi
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Finnish Institute for Health and Welfare, Genomics and Biobank Unit, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Santtu Heinonen
- New Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Laura Toivonen
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Panu Räty
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Octavio Ramilo
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Antti-Pekka Laine
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Institute of Biomedicine, University of Turku and Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Matti Waris
- Institute of Biomedicine, University of Turku and Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Linnea Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Child Psychiatry, University of Turku and Turku University Hospital, Turku, Finland
| | - Hasse Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Psychiatry, University of Turku and Turku University Hospital, Turku, Finland
| | - Tiina Paunio
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Finnish Institute for Health and Welfare, Genomics and Biobank Unit, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, University of Turku and Turku University Hospital, Turku, Finland
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86
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Siefker DT, Vu L, You D, McBride A, Taylor R, Jones TL, DeVincenzo J, Cormier SA. Respiratory Syncytial Virus Disease Severity Is Associated with Distinct CD8 + T-Cell Profiles. Am J Respir Crit Care Med 2020; 201:325-334. [PMID: 31644878 DOI: 10.1164/rccm.201903-0588oc] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Rationale: Respiratory syncytial virus (RSV) causes significant morbidity and mortality in infants worldwide. Although T-helper type 2 (Th2) cell pathology is implicated in severe disease, the mechanisms underlying the development of immunopathology are incompletely understood.Objectives: We aimed to identify local immune responses associated with severe RSV in infants. Our hypothesis was that disease severity would correlate with enhanced Th2 cellular responses.Methods: Nasal aspirates were collected from infants hospitalized with severe (admitted to the pediatric ICU) or moderate (maintained in the general ward) RSV disease at 5 to 9 days after enrollment. The immune response was investigated by evaluating T-lymphocyte cellularity, cytokine concentration, and viral load.Measurements and Main Results: Patients with severe disease had increased proportions of CD8 (cluster of differentiation 8)-positive T cells expressing IL-4 (Tc2) and reduced proportions of CD8+ T cells expressing IFNγ (Tc1). Nasal aspirates from patients with severe disease had reduced concentrations of IL-17. Patients with greater frequencies of Tc1, CD8+ T cells expressing IL-17 (Tc17), and CD4+ T cells expressing IL-17 (Th17) had shorter durations of hospitalization.Conclusions: Severe RSV disease was associated with distinct T-cell profiles. Tc1, Tc17, and Th17 were associated with shorter hospital stay and may play a protective role, whereas Tc2 cells may play a previously underappreciated role in pathology.
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Affiliation(s)
- David T Siefker
- Department of Biological Sciences, College of Science, and Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Luan Vu
- Department of Biological Sciences, College of Science, and Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Dahui You
- Department of Pediatrics, and.,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | | | | | - Tamekia L Jones
- Department of Pediatrics, and.,Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee; and.,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - John DeVincenzo
- Department of Pediatrics, and.,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Stephania A Cormier
- Department of Biological Sciences, College of Science, and Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
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87
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Early-Life Respiratory Syncytial Virus Infection, Trained Immunity and Subsequent Pulmonary Diseases. Viruses 2020; 12:v12050505. [PMID: 32375305 PMCID: PMC7290378 DOI: 10.3390/v12050505] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
Respiratory syncytial virus (RSV) is often the first clinically relevant pathogen encountered in life, with nearly all children infected by two years of age. Many studies have also linked early-life severe respiratory viral infection with more pathogenic immune responses later in life that lead to pulmonary diseases like childhood asthma. This phenomenon is thought to occur through long-term immune system alterations following early-life respiratory viral infection and may include local responses such as unresolved inflammation and/or direct structural or developmental modifications within the lung. Furthermore, systemic responses that could impact the bone marrow progenitors may be a significant cause of long-term alterations, through inflammatory mediators and shifts in metabolic profiles. Among these alterations may be changes in transcriptional and epigenetic programs that drive persistent modifications throughout life, leaving the immune system poised toward pathogenic responses upon secondary insult. This review will focus on early-life severe RSV infection and long-term alterations. Understanding these mechanisms will not only lead to better treatment options to limit initial RSV infection severity but also protect against the development of childhood asthma linked to severe respiratory viral infections.
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88
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Distinguishing Kawasaki Disease from Febrile Infectious Disease Using Gene Pair Signatures. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6539398. [PMID: 32420360 PMCID: PMC7201505 DOI: 10.1155/2020/6539398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022]
Abstract
Kawasaki disease (KD) is an acute systemic vasculitis of childhood with prolonged fever, and the diagnosis of KD is mainly based on clinical criteria, which is prone to misdiagnosis with other febrile infectious (FI) diseases. Currently, there remain no effective molecular markers for KD diagnosis. In this study, we aimed to use a relative-expression-based method k-TSP and resampling framework to identify robust gene pair signatures to distinguish KD from bacterial and virus febrile infectious diseases. Our study pool consisted of 808 childhood patients from several studies and assigned to three groups, namely, the discovery set (n = 224), validation set-1 (n = 197), and validation set-2 (n = 387). We had identified 60 biologically relevant gene pairs and developed a top-ranked gene pair classifier (TRGP) using the first seven signatures, with the area under the receiver-operating characteristic curves (AUROC) of 0.947 (95% CI, 0.918-0.976), a sensitivity of 0.936 (95% CI, 0.872-0.987), and a specificity of 0.774 (95% CI, 0.705-0.836) in the discovery set. In the validation set-1, the TRGP classifier distinguished KD from FI with AUROC of 0.955 (95% CI, 0.919-0.991), a sensitivity of 0.959 (95% CI, 0.925-0.986), and a specificity of 0.863 (95% CI, 0.764-0.961). In the validation set-2, the predictive performance of classification was with an AUROC of 0.796 (95% CI, 0.747-0.845), a sensitivity of 0.797 (95% CI, 0.720-0.864), and a specificity of 0.661 (95% CI, 0.606-0.717). Our study reveals that gene pair signatures are robust across diverse studies and can be utilized as objective biomarkers to distinguish KD from FI, helping to develop a fast, simple, and effective molecular approach to improve the diagnosis of KD.
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89
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Hu M, Bogoyevitch MA, Jans DA. Impact of Respiratory Syncytial Virus Infection on Host Functions: Implications for Antiviral Strategies. Physiol Rev 2020; 100:1527-1594. [PMID: 32216549 DOI: 10.1152/physrev.00030.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the leading causes of viral respiratory tract infection in infants, the elderly, and the immunocompromised worldwide, causing more deaths each year than influenza. Years of research into RSV since its discovery over 60 yr ago have elucidated detailed mechanisms of the host-pathogen interface. RSV infection elicits widespread transcriptomic and proteomic changes, which both mediate the host innate and adaptive immune responses to infection, and reflect RSV's ability to circumvent the host stress responses, including stress granule formation, endoplasmic reticulum stress, oxidative stress, and programmed cell death. The combination of these events can severely impact on human lungs, resulting in airway remodeling and pathophysiology. The RSV membrane envelope glycoproteins (fusion F and attachment G), matrix (M) and nonstructural (NS) 1 and 2 proteins play key roles in modulating host cell functions to promote the infectious cycle. This review presents a comprehensive overview of how RSV impacts the host response to infection and how detailed knowledge of the mechanisms thereof can inform the development of new approaches to develop RSV vaccines and therapeutics.
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Affiliation(s)
- MengJie Hu
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia; and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Marie A Bogoyevitch
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia; and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - David A Jans
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia; and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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90
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The journey to a respiratory syncytial virus vaccine. Ann Allergy Asthma Immunol 2020; 125:36-46. [PMID: 32217187 DOI: 10.1016/j.anai.2020.03.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The high burden associated with respiratory syncytial virus (RSV) has made the development of RSV vaccine(s) a global health high priority. This review summarizes the journey to an RSV vaccine, the different strategies and challenges associated with the development of preventive strategies for RSV, and the diverse products that are undergoing clinical testing. DATA SOURCES Studies on RSV biology, immunology, epidemiology, and monoclonal antibodies (mAbs) and vaccines were searched using MEDLINE. We also searched PATH.org and ClinicalTrials.gov for updated information regarding the status of RSV vaccines and mAbs undergoing clinical trials. STUDY SELECTIONS We selected relevant studies conducted in infants and young children, pregnant women, and elderly population for the prevention of RSV infection. RESULTS Identification of a safe and immunogenic vaccine has been an important but elusive initiative for more than 60 years for different reasons, including the legacy of formalin-inactivated vaccine, our limited understanding of the immune response to RSV and how it relates to clinical disease severity, or the need for different end points according to the different vaccine platforms. Nevertheless, there are currently 39 vaccines and mAbs under development and 19 undergoing clinical trials. CONCLUSION Over the past decade, there have been significant advances in our knowledge of RSV molecular and structural biology and in understanding the human immune response to RSV. Despite the barriers, there are several promising mAbs and RSV vaccines undergoing clinical trials that hope to offer protection to the most vulnerable populations.
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91
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De Jacobis IT, Vona R, Straface E, Gambardella L, Ceglie G, de Gennaro F, Pontini I, Vittucci AC, Carè A, Cittadini C, Villani A, Pietraforte D. Sex differences in blood pro-oxidant status and platelet activation in children admitted with respiratory syncytial virus bronchiolitis: a pilot study. Ital J Pediatr 2020; 46:29. [PMID: 32143677 PMCID: PMC7059674 DOI: 10.1186/s13052-020-0792-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/25/2020] [Indexed: 12/29/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis in the pediatric population worldwide and an important cause of death in developing countries. It has been demonstrated that the balance between oxidant and antioxidant systems is disrupted in children with bronchiolitis and that oxidative stress contributes to the pathogenesis of this disease. Platelets play an important role in antimicrobial host defenses and contribute to pulmonary vascular repair being either targets or source of reactive oxidizing species. The main purpose of this study was to assessing sex differences in clinical characteristics and platelets activation during RSV bronchiolitis in infancy. Methods In this retrospective study a total of 203 patients (112 boys and 91 girls) with bronchiolitis, aged 12 months or less, admitted to the Bambino Gesù Pediatric Hospital of Rome (Italy) in the period from January to December 2017, were enrolled. Moreover, in a select group of patients (15 boys and 12 girls) with diagnosis of moderate bronchiolitis from RSV, a pilot study on oxidative stress and platelet characteristics was carried out by electron paramagnetic resonance and flow cytometry respectively. Age-matched healthy control subjects (10 boys and 10 girls) were chosen as controls. Data were analyzed using Student’ T test, Chi Squared test and one-way ANOVA test. Results This study highlights the influence of sex in the clinical course of bronchiolitis. In particular we found: i) a higher incidence of bronchiolitis in boys than in girls (55% vs 45%); ii) higher C reactive protein values in girls than boys (1.11 mg/dL vs 0.92 mg/dL respectively; p < 0.05); iii) a different degree of thrombocytosis during hospitalization (mild in the girls and severe in the boys). Moreover, in selected patients we found that compared to girls with bronchiolitis, boys showed: i) higher percentage of activated platelets (8% vs 2% respectively; p < 0.05) and iii) higher number of platelets forming homotypic aggregates (2.36% vs 0.84% respectively, p < 0.05). Conclusion The present study affirm that the bronchiolitis is an infection in which sex seems to act as a modulating factor only in the clinical course, influencing also the choice of the therapy should be made.
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Affiliation(s)
- Isabella Tarissi De Jacobis
- Internal Care Department, General Pediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Rosa Vona
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Elisabetta Straface
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Lucrezia Gambardella
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Giulia Ceglie
- Internal Care Department, General Pediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesca de Gennaro
- Internal Care Department, General Pediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Ilenia Pontini
- Internal Care Department, General Pediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Anna Chiara Vittucci
- Department of Pediatrics, Pediatric Infectious Diseases Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Alessandra Carè
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Camilla Cittadini
- Biomarkers Unit, Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alberto Villani
- Internal Care Department, General Pediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, Rome, Italy
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92
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Barral-Arca R, Gómez-Carballa A, Cebey-López M, Bello X, Martinón-Torres F, Salas A. 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:E1831. [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] [MESH Headings] [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.
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Affiliation(s)
- Ruth Barral-Arca
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (X.B.)
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, 15706 Santiago de Compostela, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (X.B.)
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, 15706 Santiago de Compostela, Spain
| | - Miriam Cebey-López
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (X.B.)
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, 15706 Santiago de Compostela, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (X.B.)
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, 15706 Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, 15706 Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (X.B.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, 15706 Santiago de Compostela, Spain
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93
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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.
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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
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94
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Kirsebom F, Michalaki C, Agueda-Oyarzabal M, Johansson C. Neutrophils do not impact viral load or the peak of disease severity during RSV infection. Sci Rep 2020; 10:1110. [PMID: 31980667 PMCID: PMC6981203 DOI: 10.1038/s41598-020-57969-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 01/07/2020] [Indexed: 11/30/2022] Open
Abstract
Lung and airway neutrophils are a hallmark of severe disease in infants with respiratory syncytial virus (RSV)-induced lower respiratory tract infections. Despite their abundance in the lungs during RSV infection of both mice and man, the role of neutrophils in viral control and in immune pathology is not clear. Here, antibody mediated neutrophil depletion was used to investigate the degree to which neutrophils impact the lung immune environment, the control of viral replication and the peak severity of disease after RSV infection of mice. Neutrophil depletion did not substantially affect the levels of inflammatory mediators such as type I interferons, IL-6, TNF-α or IL-1β in response to RSV. In addition, the lack of neutrophils did not change the viral load during RSV infection. Neither neutrophil depletion nor the enhancement of lung neutrophils by administration of the chemoattractant CXCL1 during RSV infection affected disease severity as measured by weight loss. Therefore, in this model of RSV infection, lung neutrophils do not offer obvious benefits to the host in terms of increasing anti-viral inflammatory responses or restricting viral replication and neutrophils do not contribute to disease severity.
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Affiliation(s)
- Freja Kirsebom
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | | | - Cecilia Johansson
- National Heart and Lung Institute, Imperial College London, London, UK.
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95
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Garcia-Mauriño C, Moore-Clingenpeel M, Thomas J, Mertz S, Cohen DM, Ramilo O, Mejias A. Viral Load Dynamics and Clinical Disease Severity in Infants With Respiratory Syncytial Virus Infection. J Infect Dis 2020; 219:1207-1215. [PMID: 30418604 PMCID: PMC6452299 DOI: 10.1093/infdis/jiy655] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/08/2018] [Indexed: 01/05/2023] Open
Abstract
Background The association between respiratory syncytial virus (RSV) loads and clinical outcomes in children remains to be defined. In most studies, viral loads (VL) were evaluated in hospitalized children and at a single time-point. We investigated the relationship between VLs and disease severity in both outpatients and inpatients with RSV infection. Methods We enrolled previously healthy children with RSV infection. Disease severity was defined by level of care (outpatients vs ward vs pediatric intensive care unit [PICU]), and a clinical disease severity score (CDSS). Nasopharyngeal VLs by polymerase chain reaction and CDSS were measured at enrollment and daily in inpatients. VL decay according to disease severity was analyzed using linear mixed modeling. Results From February 2015 to March 2017, we enrolled 150 infants: 39 outpatients and 111 inpatients. VLs were higher in outpatients than in age-matched inpatients. Among inpatients, initial VLs were comparable in ward and PICU patients, and preceded the peak CDSS. However, after excluding infants treated with steroids, those hospitalized in the ward had higher VLs than infants requiring PICU care (P < .001). Dynamic analyses showed that VL decay was delayed in PICU patients, especially in those treated with steroids. Conclusions Higher VLs at presentation and a faster and consistent VL decline were both associated with less severe RSV disease in children. Summary Infants with less severe respiratory syncytial virus (RSV) disease had higher viral loads (VL) at presentation, and faster and consistent VL decline. Conversely, VL decay and overall viral exposure were prolonged and higher in infants severe RSV disease receiving steroids.
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Affiliation(s)
- Cristina Garcia-Mauriño
- Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
| | - Melissa Moore-Clingenpeel
- Biostatistics Core, The Research Institute at Nationwide Children's Hospital, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
| | - Jessica Thomas
- Department of Clinical Research, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
| | - Sara Mertz
- Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
| | - Daniel M Cohen
- Division of Emergency Medicine, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
| | - Octavio Ramilo
- Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus.,Division of Pediatric Infectious Diseases, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
| | - Asuncion Mejias
- Center for Vaccines and Immunity, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus.,Division of Pediatric Infectious Diseases, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
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96
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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.
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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
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97
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Gomez JL, Himes BE, Kaminski N. Molecular Diagnostics in Pulmonary Infections. PRECISION IN PULMONARY, CRITICAL CARE, AND SLEEP MEDICINE 2020. [PMCID: PMC7121992 DOI: 10.1007/978-3-030-31507-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Infection of the lung parenchyma, or pneumonia, accounts for over four million deaths per year worldwide (Ferkol and Schraufnagel, Ann Am Thorac Soc 11:404–406, 2014). The condition is common, but also over-diagnosed, in part due to relatively poor laboratory and radiographic diagnostics. Indeed, we continue to rely on antiquated tools such as sputum culture and chest X-ray – the former of which lacks speed and sensitivity, and the latter specificity (Albaum et al. Chest 110:343–50, 1996). The resulting presumptive diagnoses of pneumonia lead to excessive use of empiric broad spectrum antibiotics; indeed, by some estimates, 30–70% of antibiotic prescriptions for lower respiratory tract infection are inappropriate (Kraus, PLoS One 12(3): e0174584, 2017). This approach begets microbial resistance, exposes patients to medication side effects, and puts patients at risk of potentially life-threatening complications including Clostridium difficile colitis. To improve diagnostic certainty in patients with suspected pneumonia, we must begin to consider and implement emerging technologies for efficient and accurate characterization of host responses to infection and identification of pathogens. In this chapter, we will discuss precision diagnostics already in common practice and those poised to be, and how these tools may ultimately enable personalization in the diagnosis of pneumonia.
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Affiliation(s)
- Jose L. Gomez
- Assistant Professor Pulmonary, Critical Care and Sleep Medicine Section, Department of Medicine, Yale University School of Medicine, New Haven, CT USA
| | - Blanca E. Himes
- Assistant Professor of Informatics, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Naftali Kaminski
- Boehringer-Ingelheim Endowed, Professor of Internal Medicine, Chief of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT USA
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98
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Furuse Y, Tamaki R, Okamoto M, Saito-Obata M, Suzuki A, Saito M, Imamura T, Khandaker I, Dapat I, Ueno F, Alday PP, Tan AG, Inobaya MT, Segubre-Mercado E, Tallo V, Lupisan S, Oshitani H. Association Between Preceding Viral Respiratory Infection and Subsequent Respiratory Illnesses Among Children: A Prospective Cohort Study in the Philippines. J Infect Dis 2019; 219:197-205. [PMID: 30189092 PMCID: PMC6306022 DOI: 10.1093/infdis/jiy515] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/23/2018] [Indexed: 11/30/2022] Open
Abstract
Background Acute respiratory infection (ARI) is of great concern in public health. It remains unclear whether viral infections can affect the host’s susceptibility to subsequent ARIs. Methods A prospective cohort study on ARIs of children below 5 years old was conducted in the Philippines from 2014 to 2016. The respiratory symptoms were recorded daily, and nasopharyngeal swabs were collected at both household and health facilities. The specimens were tested for respiratory viruses. We then determined whether viral etiology was associated with the severity of the present ARI and whether previous viral infections was associated with subsequent ARIs. Results A total of 3851 children and 16337 ARI episodes were enrolled and recorded, respectively. Samples were collected from 24% of all ARI episodes; collection rate at the healthcare facilities was 95%. Enterovirus D68, rhinovirus species C, and respiratory syncytial virus were significantly associated with severe ARIs. The risk for subsequent ARIs was significantly enhanced after infections with adenovirus, influenza A virus, parainfluenza virus type 4, and rhinovirus species C. Conclusions This study revealed that viral etiology plays a significant role in the severity of the present ARI and that viral infection affects the host’s susceptibility to subsequent ARIs.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan.,Hakubi Center for Advanced Research, Kyoto University, Japan.,Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
| | - Raita Tamaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito-Obata
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.,RITM-Tohoku Collaborating Research Center on Emerging and Reemerging Infectious Diseases, Muntinlupa, Philippines
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadatsugu Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Irona Khandaker
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Isolde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumihiko Ueno
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Alvin Gue Tan
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | | | | | - Veronica Tallo
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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99
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van Erp EA, Feyaerts D, Duijst M, Mulder HL, Wicht O, Luytjes W, Ferwerda G, van Kasteren PB. Respiratory Syncytial Virus Infects Primary Neonatal and Adult Natural Killer Cells and Affects Their Antiviral Effector Function. J Infect Dis 2019; 219:723-733. [PMID: 30252097 PMCID: PMC6376914 DOI: 10.1093/infdis/jiy566] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/18/2018] [Indexed: 01/01/2023] Open
Abstract
Background Respiratory syncytial virus (RSV) is a major cause of severe acute lower respiratory tract infections in infants. Natural killer (NK) cells are important antiviral effector cells that likely encounter RSV in the presence of virus-specific (maternal) antibodies. As NK cells potentially contribute to immunopathology, we investigated whether RSV affects their antiviral effector functions. Methods We assessed the phenotype and functionality of primary neonatal and adult NK cells by flow cytometry after stimulation with RSV or RSV-antibody complexes. Results We demonstrate for the first time that RSV infects neonatal and adult NK cells in vitro. Preincubation of virus with subneutralizing concentrations of RSV-specific antibodies significantly increased the percentage of infected NK cells. Upon infection, NK cells were significantly more prone to produce interferon-γ, while secretion of the cytotoxicity molecule perforin was not enhanced. Conclusions Our findings suggest that (antibody-enhanced) RSV infection of NK cells induces a proinflammatory rather than a cytotoxic response, which may contribute to immunopathology. Considering that most RSV vaccines currently being developed aim at inducing (maternal) antibodies, these results highlight the importance of understanding the interactions between innate effector cells and virus-specific antibodies.
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Affiliation(s)
- Elisabeth A van Erp
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Dorien Feyaerts
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Maxime Duijst
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - H Lie Mulder
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - Oliver Wicht
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - Willem Luytjes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - Gerben Ferwerda
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Puck B van Kasteren
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
- Correspondence: P. B. van Kasteren, PhD, National Institute for Public Health and the Environment, Center for Infectious Diseases Control, Postbus 1, 3720 BA Bilthoven, The Netherlands ()
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100
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Rogers LRK, de Los Campos G, Mias GI. Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. Front Immunol 2019; 10:2616. [PMID: 31787983 PMCID: PMC6854009 DOI: 10.3389/fimmu.2019.02616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022] Open
Abstract
Influenza, a communicable disease, affects thousands of people worldwide. Young children, elderly, immunocompromised individuals and pregnant women are at higher risk for being infected by the influenza virus. Our study aims to highlight differentially expressed genes in influenza disease compared to influenza vaccination, including variability due to age and sex. To accomplish our goals, we conducted a meta-analysis using publicly available microarray expression data. Our inclusion criteria included subjects with influenza, subjects who received the influenza vaccine and healthy controls. We curated 18 microarray datasets for a total of 3,481 samples (1,277 controls, 297 influenza infection, 1,907 influenza vaccination). We pre-processed the raw microarray expression data in R using packages available to pre-process Affymetrix and Illumina microarray platforms. We used a Box-Cox power transformation of the data prior to our down-stream analysis to identify differentially expressed genes. Statistical analyses were based on linear mixed effects model with all study factors and successive likelihood ratio tests (LRT) to identify differentially-expressed genes. We filtered LRT results by disease (Bonferroni adjusted p < 0.05) and used a two-tailed 10% quantile cutoff to identify biologically significant genes. Furthermore, we assessed age and sex effects on the disease genes by filtering for genes with a statistically significant (Bonferroni adjusted p < 0.05) interaction between disease and age, and disease and sex. We identified 4,889 statistically significant genes when we filtered the LRT results by disease factor, and gene enrichment analysis (gene ontology and pathways) included innate immune response, viral process, defense response to virus, Hematopoietic cell lineage and NF-kappa B signaling pathway. Our quantile filtered gene lists comprised of 978 genes each associated with influenza infection and vaccination. We also identified 907 and 48 genes with statistically significant (Bonferroni adjusted p < 0.05) disease-age and disease-sex interactions, respectively. Our meta-analysis approach highlights key gene signatures and their associated pathways for both influenza infection and vaccination. We also were able to identify genes with an age and sex effect. This gives potential for improving current vaccines and exploring genes that are expressed equally across ages when considering universal vaccinations for influenza.
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Affiliation(s)
- Lavida R K Rogers
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Gustavo de Los Campos
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States.,Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
| | - George I Mias
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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