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Armignacco R, Carlier N, Jouinot A, Birtolo MF, de Murat D, Tubach F, Hausfater P, Simon T, Gorochov G, Pourcher V, Beurton A, Goulet H, Manivet P, Bertherat J, Assié G. Whole blood transcriptome signature predicts severe forms of COVID-19: Results from the COVIDeF cohort study. Funct Integr Genomics 2024; 24:107. [PMID: 38772950 PMCID: PMC11108918 DOI: 10.1007/s10142-024-01359-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
COVID-19 is associated with heterogeneous outcome. Early identification of a severe progression of the disease is essential to properly manage the patients and improve their outcome. Biomarkers reflecting an increased inflammatory response, as well as individual features including advanced age, male gender, and pre-existing comorbidities, are risk factors of severe COVID-19. Yet, these features show limited accuracy for outcome prediction. The aim was to evaluate the prognostic value of whole blood transcriptome at an early stage of the disease. Blood transcriptome of patients with mild pneumonia was profiled. Patients with subsequent severe COVID-19 were compared to those with favourable outcome, and a molecular predictor based on gene expression was built. Unsupervised classification discriminated patients who would later develop a COVID-19-related severe pneumonia. The corresponding gene expression signature reflected the immune response to the viral infection dominated by a prominent type I interferon, with IFI27 among the most over-expressed genes. A 48-genes transcriptome signature predicting the risk of severe COVID-19 was built on a training cohort, then validated on an external independent cohort, showing an accuracy of 81% for predicting severe outcome. These results identify an early transcriptome signature of severe COVID-19 pneumonia, with a possible relevance to improve COVID-19 patient management.
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Affiliation(s)
- Roberta Armignacco
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France.
| | - Nicolas Carlier
- Service de Pneumologie, AP-HP, Hôpital Cochin, 75014, Paris, France
| | - Anne Jouinot
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France
- Service d'Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, 75014, Paris, France
| | | | - Daniel de Murat
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie Et de Santé Publique, AP-HP, 1901, F-75013, Paris, France
| | - Pierre Hausfater
- Emergency Department, APHP-Sorbonne Université, Hôpital Pitié-Salpêtrière, GRC-14 BIOSFAST, CIMI, UMR 1135, Sorbonne Université, Paris, France
| | - Tabassome Simon
- Service de Pharmacologie, Plateforme de Recherche Clinique URC-CRC-CRB de L'Est Parisien, Assistance Publique-Hôpitaux de Paris, Hôpital Saint Antoine, Sorbonne Université, Paris, France
| | - Guy Gorochov
- Centre d'Immunologie Et Des Maladies Infectieuses (CIMI), Department of Immunology, Sorbonne Université, Inserm, Hôpital Pitié Salpêtrière, Groupe Hospitalo-Universitaire Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Valérie Pourcher
- Department of Infectious Diseases, Hôpital Pitié Salpêtrière, Groupe Hospitalo-Universitaire Assistance Publique - Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Alexandra Beurton
- Service de Médecine Intensive Réanimation EOLE - Département R3S - Sorbonne, Université - Hôpital Universitaire Pitié - Salpêtrière - Assistance Publique Hôpitaux de Paris - 83 Boulevard de L'Hôpital, 75013, Paris, France
- UMRS 1158 Inserm-Sorbonne Université "Neurophysiologie Respiratoire Expérimentale Et Clinique'' Intensive Care Unit, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Hélène Goulet
- Emergency Department, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Philippe Manivet
- INSERM UMR 1141 "NeuroDiderot", Université Paris Cité, FHU I2-D2, Paris, France
- AP-HP, DMU BioGem, Centre de Ressources Biologiques Biobank Lariboisière/Saint Louis (BB-0033-00064), Hôpital Lariboisière, Paris, France
| | - Jérôme Bertherat
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France
- Service d'Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, 75014, Paris, France
| | - Guillaume Assié
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France.
- Service d'Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, 75014, Paris, France.
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2
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Divolis G, Synolaki E, Doulou A, Gavriil A, Giannouli CC, Apostolidou A, Foster ML, Matzuk MM, Skendros P, Galani IE, Sideras P. Neutrophil-derived Activin-A moderates their pro-NETotic activity and attenuates collateral tissue damage caused by Influenza A virus infection. Front Immunol 2024; 15:1302489. [PMID: 38476229 PMCID: PMC10929267 DOI: 10.3389/fimmu.2024.1302489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/24/2024] [Indexed: 03/14/2024] Open
Abstract
Background Pre-neutrophils, while developing in the bone marrow, transcribe the Inhba gene and synthesize Activin-A protein, which they store and release at the earliest stage of their activation in the periphery. However, the role of neutrophil-derived Activin-A is not completely understood. Methods To address this issue, we developed a neutrophil-specific Activin-A-deficient animal model (S100a8-Cre/Inhba fl/fl mice) and analyzed the immune response to Influenza A virus (IAV) infection. More specifically, evaluation of body weight and lung mechanics, molecular and cellular analyses of bronchoalveolar lavage fluids, flow cytometry and cell sorting of lung cells, as well as histopathological analysis of lung tissues, were performed in PBS-treated and IAV-infected transgenic animals. Results We found that neutrophil-specific Activin-A deficiency led to exacerbated pulmonary inflammation and widespread hemorrhagic histopathology in the lungs of IAV-infected animals that was associated with an exuberant production of neutrophil extracellular traps (NETs). Moreover, deletion of the Activin-A receptor ALK4/ACVR1B in neutrophils exacerbated IAV-induced pathology as well, suggesting that neutrophils themselves are potential targets of Activin-A-mediated signaling. The pro-NETotic tendency of Activin-A-deficient neutrophils was further verified in the context of thioglycollate-induced peritonitis, a model characterized by robust peritoneal neutrophilia. Of importance, transcriptome analysis of Activin-A-deficient neutrophils revealed alterations consistent with a predisposition for NET release. Conclusion Collectively, our data demonstrate that Activin-A, secreted by neutrophils upon their activation in the periphery, acts as a feedback mechanism to moderate their pro-NETotic tendency and limit the collateral tissue damage caused by neutrophil excess activation during the inflammatory response.
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Affiliation(s)
- Georgios Divolis
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Evgenia Synolaki
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Athanasia Doulou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Ariana Gavriil
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Christina C. Giannouli
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Anastasia Apostolidou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | - Martin M. Matzuk
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, United States
| | - Panagiotis Skendros
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna-Evdokia Galani
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Paschalis Sideras
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
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3
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Novak T, Crawford JC, Hahn G, Hall MW, Thair SA, Newhams MM, Chou J, Mourani PM, Tarquinio KM, Markovitz B, Loftis LL, Weiss SL, Higgerson R, Schwarz AJ, Pinto NP, Thomas NJ, Gedeit RG, Sanders RC, Mahapatra S, Coates BM, Cvijanovich NZ, Ackerman KG, Tellez DW, McQuillen P, Kurachek SC, Shein SL, Lange C, Thomas PG, Randolph AG. Transcriptomic profiles of multiple organ dysfunction syndrome phenotypes in pediatric critical influenza. Front Immunol 2023; 14:1220028. [PMID: 37533854 PMCID: PMC10390830 DOI: 10.3389/fimmu.2023.1220028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Background Influenza virus is responsible for a large global burden of disease, especially in children. Multiple Organ Dysfunction Syndrome (MODS) is a life-threatening and fatal complication of severe influenza infection. Methods We measured RNA expression of 469 biologically plausible candidate genes in children admitted to North American pediatric intensive care units with severe influenza virus infection with and without MODS. Whole blood samples from 191 influenza-infected children (median age 6.4 years, IQR: 2.2, 11) were collected a median of 27 hours following admission; for 45 children a second blood sample was collected approximately seven days later. Extracted RNA was hybridized to NanoString mRNA probes, counts normalized, and analyzed using linear models controlling for age and bacterial co-infections (FDR q<0.05). Results Comparing pediatric samples collected near admission, children with Prolonged MODS for ≥7 days (n=38; 9 deaths) had significant upregulation of nine mRNA transcripts associated with neutrophil degranulation (RETN, TCN1, OLFM4, MMP8, LCN2, BPI, LTF, S100A12, GUSB) compared to those who recovered more rapidly from MODS (n=27). These neutrophil transcripts present in early samples predicted Prolonged MODS or death when compared to patients who recovered, however in paired longitudinal samples, they were not differentially expressed over time. Instead, five genes involved in protein metabolism and/or adaptive immunity signaling pathways (RPL3, MRPL3, HLA-DMB, EEF1G, CD8A) were associated with MODS recovery within a week. Conclusion Thus, early increased expression of neutrophil degranulation genes indicated worse clinical outcomes in children with influenza infection, consistent with reports in adult cohorts with influenza, sepsis, and acute respiratory distress syndrome.
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Affiliation(s)
- Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
| | - Jeremy Chase Crawford
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Georg Hahn
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Mark W. Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Simone A. Thair
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Margaret M. Newhams
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
| | - Janet Chou
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Peter M. Mourani
- Department of Pediatrics, Section of Critical Care Medicine, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR, United States
| | - Keiko M. Tarquinio
- Division of Critical Care Medicine, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Barry Markovitz
- Department of Anesthesiology Critical Care Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Laura L. Loftis
- Division of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Scott L. Weiss
- Nemours Children’s Hospital Delaware, Critical Care Medicine, Wilmington, DE, United States
| | - Renee Higgerson
- Pediatric Critical Care Medicine, St. David’s Children’s Hospital, Austin, TX, United States
| | - Adam J. Schwarz
- Department of Pediatrics, Children’s Hospital of Orange County, Orange, CA, United States
| | - Neethi P. Pinto
- Department of Anesthesiology and Critical Care Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Neal J. Thomas
- Department of Pediatrics, Penn State Health Children’s Hospital, Penn State University College of Medicine, Hershey, PA, United States
| | - Rainer G. Gedeit
- Pediatric Critical Care, Milwaukee Hospital-Children’s Wisconsin, Milwaukee, WI, United States
| | - Ronald C. Sanders
- Section of Pediatric Critical Care, Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR, United States
| | - Sidharth Mahapatra
- Pediatric Critical Care Medicine, Children’s Hospital & Medical Center Omaha, University of Nebraska Medical Center, Omaha, NE, United States
| | - Bria M. Coates
- Division of Critical Care Medicine, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Natalie Z. Cvijanovich
- Division of Critical Care Medicine, UCSF Benioff Children’s Hospital, Oakland, CA, United States
| | - Kate G. Ackerman
- Department of Pediatrics, University of Rochester/UR Medicine Golisano Children’s Hospital, Rochester, NY, United States
| | - David W. Tellez
- Pediatric Critical Care Medicine, Phoenix Children’s Hospital, Phoenix, AZ, United States
| | - Patrick McQuillen
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - Stephen C. Kurachek
- Department of Critical Care, Children’s Specialty Center, Children’s Minnesota, Minneapolis, MN, United States
| | - Steven L. Shein
- Division of Pediatric Critical Care Medicine, University Hospitals Rainbow Babies and Children’s Hospital, Cleveland, OH, United States
| | - Christoph Lange
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Paul G. Thomas
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Adrienne G. Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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4
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Shojaei M, Shamshirian A, Monkman J, Grice L, Tran M, Tan CW, Teo SM, Rodrigues Rossi G, McCulloch TR, Nalos M, Raei M, Razavi A, Ghasemian R, Gheibi M, Roozbeh F, Sly PD, Spann KM, Chew KY, Zhu Y, Xia Y, Wells TJ, Senegaglia AC, Kuniyoshi CL, Franck CL, dos Santos AFR, de Noronha L, Motamen S, Valadan R, Amjadi O, Gogna R, Madan E, Alizadeh-Navaei R, Lamperti L, Zuñiga F, Nova-Lamperti E, Labarca G, Knippenberg B, Herwanto V, Wang Y, Phu A, Chew T, Kwan T, Kim K, Teoh S, Pelaia TM, Kuan WS, Jee Y, Iredell J, O’Byrne K, Fraser JF, Davis MJ, Belz GT, Warkiani ME, Gallo CS, Souza-Fonseca-Guimaraes F, Nguyen Q, Mclean A, Kulasinghe A, Short KR, Tang B. IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational study. Front Immunol 2023; 13:1060438. [PMID: 36685600 PMCID: PMC9850159 DOI: 10.3389/fimmu.2022.1060438] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023] Open
Abstract
Purpose Robust biomarkers that predict disease outcomes amongst COVID-19 patients are necessary for both patient triage and resource prioritisation. Numerous candidate biomarkers have been proposed for COVID-19. However, at present, there is no consensus on the best diagnostic approach to predict outcomes in infected patients. Moreover, it is not clear whether such tools would apply to other potentially pandemic pathogens and therefore of use as stockpile for future pandemic preparedness. Methods We conducted a multi-cohort observational study to investigate the biology and the prognostic role of interferon alpha-inducible protein 27 (IFI27) in COVID-19 patients. Results We show that IFI27 is expressed in the respiratory tract of COVID-19 patients and elevated IFI27 expression in the lower respiratory tract is associated with the presence of a high viral load. We further demonstrate that the systemic host response, as measured by blood IFI27 expression, is associated with COVID-19 infection. For clinical outcome prediction (e.g., respiratory failure), IFI27 expression displays a high sensitivity (0.95) and specificity (0.83), outperforming other known predictors of COVID-19 outcomes. Furthermore, IFI27 is upregulated in the blood of infected patients in response to other respiratory viruses. For example, in the pandemic H1N1/09 influenza virus infection, IFI27-like genes were highly upregulated in the blood samples of severely infected patients. Conclusion These data suggest that prognostic biomarkers targeting the family of IFI27 genes could potentially supplement conventional diagnostic tools in future virus pandemics, independent of whether such pandemics are caused by a coronavirus, an influenza virus or another as yet-to-be discovered respiratory virus.
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Affiliation(s)
- Maryam Shojaei
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia,Department of Medicine, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Amir Shamshirian
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Grice
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia,School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Siok Min Teo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gustavo Rodrigues Rossi
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy R. McCulloch
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Marek Nalos
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Maedeh Raei
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Razavi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Roya Ghasemian
- Antimicrobial Resistance Research Centre, Department of Infectious Diseases, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mobina Gheibi
- Student Research Committee, School of Allied Medical Sciences, Mazandaran University of Medical Science, Sari, Iran
| | | | - Peter D. Sly
- Child Health Research Centre, The University of Queensland, South Brisbane, QLD, Australia
| | - Kirsten M. Spann
- Centre for Immunology and Infection Control, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yanshan Zhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yao Xia
- School of Science, Edith Cowan University; School of Biomedical Science, University of Western Australia, Perth, WA, Australia
| | - Timothy J. Wells
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Alexandra Cristina Senegaglia
- Complexo Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Brazil,Core for Cell Technology, School of Medicine, PontifìciaUniversidade Católica do Paraná, Curitiba, Brazil
| | - Carmen Lúcia Kuniyoshi
- Complexo Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Brazil,Core for Cell Technology, School of Medicine, PontifìciaUniversidade Católica do Paraná, Curitiba, Brazil
| | | | | | | | - Sepideh Motamen
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza Valadan
- Molecular and Cell Biology Research Centre, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran,Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Omolbanin Amjadi
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Rajan Gogna
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark,Novo Nordisk Foundation centre for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Esha Madan
- Campania Centre for the Unknown, Lisbon, Portugal
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Liliana Lamperti
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile
| | - Felipe Zuñiga
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Gonzalo Labarca
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile,Faculty of Medicine, Universidad de Concepcion, Concepcion, Chile
| | - Ben Knippenberg
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Velma Herwanto
- Faculty of Medicine, Universitas Tarumanagara, Jakarta, Indonesia
| | - Ya Wang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia,Department of Medicine, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia
| | - Amy Phu
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Westmead Clinical School, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Tracy Chew
- Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, NSW, Australia
| | - Timothy Kwan
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Karan Kim
- Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Tiana M. Pelaia
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Win Sen Kuan
- Emergency Medicine Department, National University Hospital, National University Health System, Singapore, Singapore,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yvette Jee
- Emergency Medicine Department, National University Hospital, National University Health System, Singapore, Singapore
| | - Jon Iredell
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, NSW, Australia,Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Ken O’Byrne
- Queensland University of Technology, Centre for Genomics and PersonalisedHealth, School of Biomedical Sciences, Brisbane, QLD, Australia
| | - John F. Fraser
- Critical Care Research Group, The University of Queensland, Brisbane, QLD, Australia
| | - Melissa J. Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Gabrielle T. Belz
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Majid E. Warkiani
- Australia Centre for Health Technologies (CHT) & Institute for Biomedical Materials & Devices (IBMD), School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Carlos Salomon Gallo
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile,Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, The University of Queensland, Brisbane, QLD, Australia
| | | | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anthony Mclean
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia
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5
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Jhutty SS, Boehme JD, Jeron A, Volckmar J, Schultz K, Schreiber J, Schughart K, Zhou K, Steinheimer J, Stöcker H, Stegemann-Koniszewski S, Bruder D, Hernandez-Vargas EA. Predicting Influenza A Virus Infection in the Lung from Hematological Data with Machine Learning. mSystems 2022; 7:e0045922. [PMID: 36346236 PMCID: PMC9765554 DOI: 10.1128/msystems.00459-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The tracking of pathogen burden and host responses with minimally invasive methods during respiratory infections is central for monitoring disease development and guiding treatment decisions. Utilizing a standardized murine model of respiratory influenza A virus (IAV) infection, we developed and tested different supervised machine learning models to predict viral burden and immune response markers, i.e., cytokines and leukocytes in the lung, from hematological data. We performed independently in vivo infection experiments to acquire extensive data for training and testing of the models. We show here that lung viral load, neutrophil counts, cytokines (such as gamma interferon [IFN-γ] and interleukin 6 [IL-6]), and other lung infection markers can be predicted from hematological data. Furthermore, feature analysis of the models showed that blood granulocytes and platelets play a crucial role in prediction and are highly involved in the immune response against IAV. The proposed in silico tools pave the path toward improved tracking and monitoring of influenza virus infections and possibly other respiratory infections based on minimally invasively obtained hematological parameters. IMPORTANCE During the course of respiratory infections such as influenza, we do have a very limited view of immunological indicators to objectively and quantitatively evaluate the outcome of a host. Methods for monitoring immunological markers in a host's lungs are invasive and expensive, and some of them are not feasible to perform. Using machine learning algorithms, we show for the first time that minimally invasively acquired hematological parameters can be used to infer lung viral burden, leukocytes, and cytokines following influenza virus infection in mice. The potential of the framework proposed here consists of a new qualitative vision of the disease processes in the lung compartment as a noninvasive tool.
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Affiliation(s)
- Suneet Singh Jhutty
- Frankfurt Institute for Advanced Studiesgrid.417999.b, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | - Julia D. Boehme
- Immune Regulation Group, Helmholtz Centre for Infection Researchgrid.7490.a, Braunschweig, Germany
- Infection Immunology Group, Institute of Medical Microbiology, Infection Control and Prevention, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Andreas Jeron
- Immune Regulation Group, Helmholtz Centre for Infection Researchgrid.7490.a, Braunschweig, Germany
- Infection Immunology Group, Institute of Medical Microbiology, Infection Control and Prevention, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Julia Volckmar
- Immune Regulation Group, Helmholtz Centre for Infection Researchgrid.7490.a, Braunschweig, Germany
- Infection Immunology Group, Institute of Medical Microbiology, Infection Control and Prevention, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Kristin Schultz
- Immune Regulation Group, Helmholtz Centre for Infection Researchgrid.7490.a, Braunschweig, Germany
- Department of Infection Genetics, Helmholtz Centre for Infection Researchgrid.7490.a, Braunschweig, Germany
| | - Jens Schreiber
- Department of Pneumology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburggrid.5807.a, Magdeburg, Germany
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Researchgrid.7490.a, Braunschweig, Germany
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- University of Veterinary Medicine Hannover, Hannover, Germany
| | - Kai Zhou
- Frankfurt Institute for Advanced Studiesgrid.417999.b, Frankfurt am Main, Germany
| | - Jan Steinheimer
- Frankfurt Institute for Advanced Studiesgrid.417999.b, Frankfurt am Main, Germany
| | - Horst Stöcker
- Frankfurt Institute for Advanced Studiesgrid.417999.b, Frankfurt am Main, Germany
- Institut für Theoretische Physik, Goethe Universität Frankfurt, Frankfurt am Main, Germany
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Sabine Stegemann-Koniszewski
- Department of Pneumology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburggrid.5807.a, Magdeburg, Germany
| | - Dunja Bruder
- Immune Regulation Group, Helmholtz Centre for Infection Researchgrid.7490.a, Braunschweig, Germany
- Infection Immunology Group, Institute of Medical Microbiology, Infection Control and Prevention, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Esteban A. Hernandez-Vargas
- Frankfurt Institute for Advanced Studiesgrid.417999.b, Frankfurt am Main, Germany
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, USA
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6
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Chen L, Hua J, He X. Co-expression network analysis identifies potential candidate hub genes in severe influenza patients needing invasive mechanical ventilation. BMC Genomics 2022; 23:703. [PMID: 36243706 PMCID: PMC9569050 DOI: 10.1186/s12864-022-08915-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Influenza is a contagious disease that affects people of all ages and is linked to considerable mortality during epidemics and occasional outbreaks. Moreover, effective immunological biomarkers are needed for elucidating aetiology and preventing and treating severe influenza. Herein, we aimed to evaluate the key genes linked with the disease severity in influenza patients needing invasive mechanical ventilation (IMV). Three gene microarray data sets (GSE101702, GSE21802, and GSE111368) from blood samples of influenza patients were made available by the Gene Expression Omnibus (GEO) database. The GSE101702 and GSE21802 data sets were combined to create the training set. Hub indicators for IMV patients with severe influenza were determined using differential expression analysis and Weighted correlation network analysis (WGCNA) from the training set. The receiver operating characteristic curve (ROC) was also used to evaluate the hub genes from the test set's diagnostic accuracy. Different immune cells' infiltration levels in the expression profile and their correlation with hub gene markers were examined using single-sample gene set enrichment analysis (ssGSEA). RESULTS In the present study, we evaluated a total of 447 differential genes. WGCNA identified eight co-expression modules, with the red module having the strongest correlation with IMV patients. Differential genes were combined to obtain 3 hub genes (HLA-DPA1, HLA-DRB3, and CECR1). The identified genes were investigated as potential indicators for patients with severe influenza who required IMV using the least absolute shrinkage and selection operator (LASSO) approach. The ROC showed the diagnostic value of the three hub genes in determining the severity of influenza. Using ssGSEA, it has been revealed that the expression of key genes was negatively correlated with neutrophil activation and positively associated with adaptive cellular immune response. CONCLUSION We evaluated three novel hub genes that could be linked to the immunopathological mechanism of severe influenza patients who require IMV treatment and could be used as potential biomarkers for severe influenza prevention and treatment.
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Affiliation(s)
- Liang Chen
- Department of Infectious Diseases, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
| | - Jie Hua
- Department of Gastroenterology, Liyang People's Hospital, Liyang Branch Hospital of Jiangsu Province Hospital, Nanjing, China
| | - Xiaopu He
- Department of Geriatric Gastroenterology, The First Affiliated Hospital With Nanjing Medical University, No.300 Guangzhou Road, Nanjing city, 210029, Jiangsu Province, China.
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7
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Liu S, Huang Z, Fan R, Jia J, Deng X, Zou X, Li H, Cao B. Cycling and activated CD8 + T lymphocytes and their association with disease severity in influenza patients. BMC Immunol 2022; 23:40. [PMID: 36064355 PMCID: PMC9441835 DOI: 10.1186/s12865-022-00516-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND T cell lymphopenia was a significant characteristic of severe influenza infection and it was associated with the functional changes of T cells. It is necessary to clarify the T cells characteristics of kinetic changes and their correlation with disease severity. METHODS In a cohort of hospitalized influenza patients with varying degrees of severity, we characterized lymphocyte populations using flow cytometry. RESULTS The numbers of cycling (Ki67+) T cells at the acute phase of severe influenza were higher, especially in the memory (CD45RO+) T cell subsets. T cells from hospitalized influenza patients also had significantly higher levels of the exhausted marker PD-1. Cycling status of T cells was associated with T cell activation during the acute phase of influenza infection. The recruitment of cycling and activated (CD38+HLA-DR+) CD8+ T cells subset is delayed in severe influenza patients. CONCLUSIONS The increased numbers of cycling memory (Ki67+CD45RO+) T cells subsets and delayed kinetics of activated (CD38+HLA-DR+) CD8+ T cells, could serve as possible biological markers for disease severity.
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Affiliation(s)
- Shuai Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, Shandong, China
| | - Zhisheng Huang
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Ruyue Fan
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Ju Jia
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoyan Deng
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Zou
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Hui Li
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Bin Cao
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China. .,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China. .,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China.
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8
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Liu YE, Saul S, Rao AM, Robinson ML, Agudelo Rojas OL, Sanz AM, Verghese M, Solis D, Sibai M, Huang CH, Sahoo MK, Gelvez RM, Bueno N, Estupiñan Cardenas MI, Villar Centeno LA, Rojas Garrido EM, Rosso F, Donato M, Pinsky BA, Einav S, Khatri P. An 8-gene machine learning model improves clinical prediction of severe dengue progression. Genome Med 2022; 14:33. [PMID: 35346346 PMCID: PMC8959795 DOI: 10.1186/s13073-022-01034-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Each year 3-6 million people develop life-threatening severe dengue (SD). Clinical warning signs for SD manifest late in the disease course and are nonspecific, leading to missed cases and excess hospital burden. Better SD prognostics are urgently needed. METHODS We integrated 11 public datasets profiling the blood transcriptome of 365 dengue patients of all ages and from seven countries, encompassing biological, clinical, and technical heterogeneity. We performed an iterative multi-cohort analysis to identify differentially expressed genes (DEGs) between non-severe patients and SD progressors. Using only these DEGs, we trained an XGBoost machine learning model on public data to predict progression to SD. All model parameters were "locked" prior to validation in an independent, prospectively enrolled cohort of 377 dengue patients in Colombia. We measured expression of the DEGs in whole blood samples collected upon presentation, prior to SD progression. We then compared the accuracy of the locked XGBoost model and clinical warning signs in predicting SD. RESULTS We identified eight SD-associated DEGs in the public datasets and built an 8-gene XGBoost model that accurately predicted SD progression in the independent validation cohort with 86.4% (95% CI 68.2-100) sensitivity and 79.7% (95% CI 75.5-83.9) specificity. Given the 5.8% proportion of SD cases in this cohort, the 8-gene model had a positive and negative predictive value (PPV and NPV) of 20.9% (95% CI 16.7-25.6) and 99.0% (95% CI 97.7-100.0), respectively. Compared to clinical warning signs at presentation, which had 77.3% (95% CI 58.3-94.1) sensitivity and 39.7% (95% CI 34.7-44.9) specificity, the 8-gene model led to an 80% reduction in the number needed to predict (NNP) from 25.4 to 5.0. Importantly, the 8-gene model accurately predicted subsequent SD in the first three days post-fever onset and up to three days prior to SD progression. CONCLUSIONS The 8-gene XGBoost model, trained on heterogeneous public datasets, accurately predicted progression to SD in a large, independent, prospective cohort, including during the early febrile stage when SD prediction remains clinically difficult. The model has potential to be translated to a point-of-care prognostic assay to reduce dengue morbidity and mortality without overwhelming limited healthcare resources.
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Affiliation(s)
- Yiran E. Liu
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Cancer Biology Graduate Program, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
| | - Sirle Saul
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
| | - Aditya Manohar Rao
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Immunology Graduate Program, School of Medicine, Stanford University, CA Stanford, USA
| | - Makeda Lucretia Robinson
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | | | - Ana Maria Sanz
- grid.477264.4Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
| | - Michelle Verghese
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Daniel Solis
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Mamdouh Sibai
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Chun Hong Huang
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Malaya Kumar Sahoo
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Rosa Margarita Gelvez
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Bucaramanga, Colombia
| | - Nathalia Bueno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Bucaramanga, Colombia
| | | | | | | | - Fernando Rosso
- grid.477264.4Clinical Research Center, Fundación Valle del Lili, Cali, Colombia ,grid.477264.4Division of Infectious Diseases, Department of Internal Medicine, Fundación Valle del Lili, Cali, Colombia
| | - Michele Donato
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
| | - Benjamin A. Pinsky
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Shirit Einav
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Department of Microbiology and Immunology, School of Medicine, Stanford University, CA Stanford, USA
| | - Purvesh Khatri
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
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9
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Corry J, Kettenburg G, Upadhyay AA, Wallace M, Marti MM, Wonderlich ER, Bissel SJ, Goss K, Sturgeon TJ, Watkins SC, Reed DS, Bosinger SE, Barratt-Boyes SM. Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive influenza lethality in nonhuman primates. PLoS Pathog 2022; 18:e1010395. [PMID: 35271686 PMCID: PMC8939778 DOI: 10.1371/journal.ppat.1010395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/22/2022] [Accepted: 02/24/2022] [Indexed: 01/04/2023] Open
Abstract
Severe influenza kills tens of thousands of individuals each year, yet the mechanisms driving lethality in humans are poorly understood. Here we used a unique translational model of lethal H5N1 influenza in cynomolgus macaques that utilizes inhalation of small-particle virus aerosols to define mechanisms driving lethal disease. RNA sequencing of lung tissue revealed an intense interferon response within two days of infection that resulted in widespread expression of interferon-stimulated genes, including inflammatory cytokines and chemokines. Macaques with lethal disease had rapid and profound loss of alveolar macrophages (AMs) and infiltration of activated CCR2+ CX3CR1+ interstitial macrophages (IMs) and neutrophils into lungs. Parallel changes of AMs and neutrophils in bronchoalveolar lavage (BAL) correlated with virus load when compared to macaques with mild influenza. Both AMs and IMs in lethal influenza were M1-type inflammatory macrophages which expressed neutrophil chemotactic factors, while neutrophils expressed genes associated with activation and generation of neutrophil extracellular traps (NETs). NETs were prominent in lung and were found in alveolar spaces as well as lung parenchyma. Genes associated with pyroptosis but not apoptosis were increased in lung, and activated inflammatory caspases, IL-1β and cleaved gasdermin D (GSDMD) were present in bronchoalveolar lavage fluid and lung homogenates. Cleaved GSDMD was expressed by lung macrophages and alveolar epithelial cells which were present in large numbers in alveolar spaces, consistent with loss of epithelial integrity. Cleaved GSDMD colocalized with viral NP-expressing cells in alveoli, reflecting pyroptosis of infected cells. These novel findings reveal that a potent interferon and inflammatory cascade in lung associated with infiltration of inflammatory macrophages and neutrophils, elaboration of NETs and cell death by pyroptosis mediates lethal H5N1 influenza in nonhuman primates, and by extension humans. These innate pathways represent promising therapeutic targets to prevent severe influenza and potentially other primary viral pneumonias in humans. Influenza can cause acute lung injury and death, but the mechanisms resulting in lethal influenza in humans are not well understood. We used a novel model of lethal influenza in nonhuman primates caused by aerosol infection with highly pathogenic avian influenza virus that closely resembles human disease to define how the virus causes severe pneumonia. We found that a potent innate immune response starting with high-level production of interferons and inflammatory factors in the lung drives severe disease. Inflammatory cells including macrophages and neutrophils were recruited into lung because of this early response, which in turn led to release of neutrophil extracellular traps that blocked lung alveoli. In addition, a particularly inflammatory form of cell death known as pyroptosis occurred in lungs during lethal influenza. These new findings show that an intense interferon response leading to an inflammatory cascade of macrophages and neutrophils, release of neutrophil extracellular traps, and cell death by pyroptosis is responsible for acute lung injury in lethal influenza. These innate pathways could be targeted by drugs to prevent lung injury in critically ill influenza patients.
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Affiliation(s)
- Jacqueline Corry
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (JC); (SMBB)
| | - Gwenddolen Kettenburg
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amit A. Upadhyay
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Megan Wallace
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michelle M. Marti
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Elizabeth R. Wonderlich
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stephanie J. Bissel
- Division of Neuropathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kyndal Goss
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Timothy J. Sturgeon
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Douglas S. Reed
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Steven E. Bosinger
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Simon M. Barratt-Boyes
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (JC); (SMBB)
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10
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Kwan PKW, Cross GB, Naftalin CM, Ahidjo BA, Mok CK, Fanusi F, Permata Sari I, Chia SC, Kumar SK, Alagha R, Tham SM, Archuleta S, Sessions OM, Hibberd ML, Paton NI. A blood RNA transcriptome signature for COVID-19. BMC Med Genomics 2021; 14:155. [PMID: 34116667 PMCID: PMC8193593 DOI: 10.1186/s12920-021-01006-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background COVID-19 is a respiratory viral infection with unique features including a more chronic course and systemic disease manifestations including multiple organ involvement; and there are differences in disease severity between ethnic groups. The immunological basis for disease has not been fully characterised. Analysis of whole-blood RNA expression may provide valuable information on disease pathogenesis.
Methods We studied 45 patients with confirmed COVID-19 infection within 10 days from onset of illness and a control group of 19 asymptomatic healthy volunteers with no known exposure to COVID-19 in the previous 14 days. Relevant demographic and clinical information was collected and a blood sample was drawn from all participants for whole-blood RNA sequencing. We evaluated differentially-expressed genes in COVID-19 patients (log2 fold change ≥ 1 versus healthy controls; false-discovery rate < 0.05) and associated protein pathways and compared these to published whole-blood signatures for respiratory syncytial virus (RSV) and influenza. We developed a disease score reflecting the overall magnitude of expression of internally-validated genes and assessed the relationship between the disease score and clinical disease parameters. Results We found 135 differentially-expressed genes in the patients with COVID-19 (median age 35 years; 82% male; 36% Chinese, 53% South Asian ethnicity). Of the 117 induced genes, 14 were found in datasets from RSV and 40 from influenza; 95 genes were unique to COVID-19. Protein pathways were mostly generic responses to viral infections, including apoptosis by P53-associated pathway, but also included some unique pathways such as viral carcinogenesis. There were no major qualitative differences in pathways between ethnic groups. The composite gene-expression score was correlated with the time from onset of symptoms and nasal swab qPCR CT values (both p < 0.01) but was not related to participant age, gender, ethnicity or the presence or absence of chest X-ray abnormalities (all p > 0.05). Conclusions The whole-blood transcriptome of COVID-19 has overall similarity with other respiratory infections but there are some unique pathways that merit further exploration to determine clinical relevance. The approach to a disease score may be of value, but needs further validation in a population with a greater range of disease severity. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01006-w.
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Affiliation(s)
- Philip Kam Weng Kwan
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Gail B Cross
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Claire M Naftalin
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Bintou A Ahidjo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Chee Keng Mok
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Felic Fanusi
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Intan Permata Sari
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Siok Ching Chia
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Shoban Krishna Kumar
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Rawan Alagha
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Sai Meng Tham
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Sophia Archuleta
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - October M Sessions
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Martin L Hibberd
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas I Paton
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore. .,Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore. .,London School of Hygiene and Tropical Medicine, London, UK. .,Infectious Diseases Translational Research Programme, National University of Singapore, Singapore, Singapore. .,Infectious Diseases Translational Research Programme and Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 10, 1E Kent Ridge Road, Singapore, 119228, Singapore.
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11
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Sahoo D, Katkar GD, Khandelwal S, Behroozikhah M, Claire A, Castillo V, Tindle C, Fuller M, Taheri S, Rogers TF, Beutler N, Ramirez SI, Rawlings SA, Pretorius V, Smith DM, Burton DR, Alexander LEC, Duran J, Crotty S, Dan JM, Das S, Ghosh P. AI-guided discovery of the invariant host response to viral pandemics. EBioMedicine 2021; 68:103390. [PMID: 34127431 PMCID: PMC8193764 DOI: 10.1016/j.ebiom.2021.103390] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Coronavirus Disease 2019 (Covid-19) continues to challenge the limits of our knowledge and our healthcare system. Here we sought to define the host immune response, a.k.a, the "cytokine storm" that has been implicated in fatal COVID-19 using an AI-based approach. METHOD Over 45,000 transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a 'seed' gene; ACE2 was rationalized because it encodes the receptor that facilitates the entry of SARS-CoV-2 (the virus that causes COVID-19) into host cells. An AI-based approach was used to explore the utility of the signature in navigating the uncharted territory of Covid-19, setting therapeutic goals, and finding therapeutic solutions. FINDINGS The 166-gene signature was surprisingly conserved across all viral pandemics, including COVID-19, and a subset of 20-genes classified disease severity, inspiring the nomenclatures ViP and severe-ViP signatures, respectively. The ViP signatures pinpointed a paradoxical phenomenon wherein lung epithelial and myeloid cells mount an IL15 cytokine storm, and epithelial and NK cell senescence and apoptosis determine severity/fatality. Precise therapeutic goals could be formulated; these goals were met in high-dose SARS-CoV-2-challenged hamsters using either neutralizing antibodies that abrogate SARS-CoV-2•ACE2 engagement or a directly acting antiviral agent, EIDD-2801. IL15/IL15RA were elevated in the lungs of patients with fatal disease, and plasma levels of the cytokine prognosticated disease severity. INTERPRETATION The ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs. FUNDING This work was supported by the National Institutes for Health (NIH) [grants CA151673 and GM138385 (to DS) and AI141630 (to P.G), DK107585-05S1 (SD) and AI155696 (to P.G, D.S and S.D), U19-AI142742 (to S. C, CCHI Cooperative Centers for Human Immunology)]; Research Grants Program Office (RGPO) from the University of California Office of the President (UCOP) (R00RG2628 & R00RG2642 to P.G, D.S and S.D); the UC San Diego Sanford Stem Cell Clinical Center (to P.G, D.S and S.D); LJI Institutional Funds (to S.C); the VA San Diego Healthcare System Institutional funds (to L.C.A). GDK was supported through The American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists. ONE SENTENCE SUMMARY The host immune response in COVID-19.
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Affiliation(s)
- Debashis Sahoo
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0730, Leichtag Building 132, La Jolla, CA 92093-0831, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, USA; Moores Cancer Center, University of California San Diego, USA.
| | - Gajanan D Katkar
- Department of Cellular and Molecular Medicine, University of California San Diego, USA
| | - Soni Khandelwal
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0730, Leichtag Building 132, La Jolla, CA 92093-0831, USA
| | - Mahdi Behroozikhah
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, USA
| | - Amanraj Claire
- Department of Cellular and Molecular Medicine, University of California San Diego, USA
| | - Vanessa Castillo
- Department of Cellular and Molecular Medicine, University of California San Diego, USA
| | - Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California San Diego, USA
| | - MacKenzie Fuller
- Department of Cellular and Molecular Medicine, University of California San Diego, USA
| | - Sahar Taheri
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | | | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Laura E Crotty Alexander
- Pulmonary Critical Care Section, Veterans Affairs (VA) San Diego Healthcare System, La Jolla, California; Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Jason Duran
- Division of Cardiology, Department of Internal Medicine, UC San Diego Medical Center, La Jolla 92037
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, USA.
| | - Pradipta Ghosh
- Moores Cancer Center, University of California San Diego, USA; Department of Cellular and Molecular Medicine, University of California San Diego, USA; Medicine, University of California San Diego, USA.
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Sahoo D, Katkar GD, Khandelwal S, Behroozikhah M, Claire A, Castillo V, Tindle C, Fuller M, Taheri S, Rogers TF, Beutler N, Ramirez SI, Rawlings SA, Pretorius V, Smith DM, Burton DR, Alexander LEC, Duran J, Crotty S, Dan JM, Das S, Ghosh P. AI-guided discovery of the invariant host response to viral pandemics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 32995790 DOI: 10.1101/2020.09.21.305698] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We sought to define the host immune response, a.k.a, the "cytokine storm" that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a 'seed' gene; ACE2 was rationalized because it encodes the receptor that facilitates the entry of SARS-CoV-2 (the virus that causes COVID-19) into host cells. Surprisingly, this 166-gene signature was conserved in all vi ral p andemics, including COVID-19, and a subset of 20-genes classified disease severity, inspiring the nomenclatures ViP and severe-ViP signatures, respectively. The ViP signatures pinpointed a paradoxical phenomenon wherein lung epithelial and myeloid cells mount an IL15 cytokine storm, and epithelial and NK cell senescence and apoptosis determines severity/fatality. Precise therapeutic goals were formulated and subsequently validated in high-dose SARS-CoV-2-challenged hamsters using neutralizing antibodies that abrogate SARS-CoV-2•ACE2 engagement or a directly acting antiviral agent, EIDD-2801. IL15/IL15RA were elevated in the lungs of patients with fatal disease, and plasma levels of the cytokine tracked with disease severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs. One Sentence Summary The host immune response in COVID-19. PANEL RESEARCH IN CONTEXT Evidence before this study: The SARS-CoV-2 pandemic has inspired many groups to find innovative methodologies that can help us understand the host immune response to the virus; unchecked proportions of such immune response have been implicated in fatality. We searched GEO and ArrayExpress that provided many publicly available gene expression data that objectively measure the host immune response in diverse conditions. However, challenges remain in identifying a set of host response events that are common to every condition. There are no studies that provide a reproducible assessment of prognosticators of disease severity, the host response, and therapeutic goals. Consequently, therapeutic trials for COVID-19 have seen many more 'misses' than 'hits'. This work used multiple (> 45,000) gene expression datasets from GEO and ArrayExpress and analyzed them using an unbiased computational approach that relies upon fundamentals of gene expression patterns and mathematical precision when assessing them.Added value of this study: This work identifies a signature that is surprisingly conserved in all viral pandemics, including Covid-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed the nature and source of the 'cytokine storm' mounted by the host. They also helped formulate precise therapeutic goals and rationalized the repurposing of FDA-approved drugs.Implications of all the available evidence: The ViP signatures provide a quantitative and qualitative framework for assessing the immune response in viral pandemics when creating pre-clinical models; they serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs.
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Liu S, Huang Z, Deng X, Zou X, Li H, Mu S, Cao B. Identification of key candidate biomarkers for severe influenza infection by integrated bioinformatical analysis and initial clinical validation. J Cell Mol Med 2021; 25:1725-1738. [PMID: 33448094 PMCID: PMC7875920 DOI: 10.1111/jcmm.16275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
One of the key barriers for early identification and intervention of severe influenza cases is a lack of reliable immunologic indicators. In this study, we utilized differentially expressed genes screening incorporating weighted gene co‐expression network analysis in one eligible influenza GEO data set (GSE111368) to identify hub genes associated with clinical severity. A total of 10 genes (PBI, MMP8, TCN1, RETN, OLFM4, ELANE, LTF, LCN2, DEFA4 and HP) were identified. Gene set enrichment analysis (GSEA) for single hub gene revealed that these genes had a close association with antimicrobial response and neutrophils activity. To further evaluate these genes' ability for diagnosis/prognosis of disease developments, we adopted double validation with (a) another new independent data set (GSE101702); and (b) plasma samples collected from hospitalized influenza patients. We found that 10 hub genes presented highly correlation with disease severity. In particular, BPI and MMP8 encoding proteins in plasma achieved higher expression in severe and dead cases, which indicated an adverse disease development and suggested a frustrating prognosis. These findings provide new insight into severe influenza pathogenesis and identify two significant candidate genes that were superior to the conventional clinical indicators. These candidate genes or encoding proteins could be biomarker for clinical diagnosis and therapeutic targets for severe influenza infection.
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Affiliation(s)
- Shuai Liu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Zhisheng Huang
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiaoyan Deng
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Zou
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hui Li
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Shengrui Mu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Bin Cao
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China
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