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Title: Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury

Abstract

Systems biology offers considerable promise in uncovering novel pathways by which viruses and other microbial pathogens interact with host signaling and expression networks to mediate disease severity. In this study, we have developed an unbiased modeling approach to identify new pathways and network connections mediating acute lung injury, using severe acute respiratory syndrome coronavirus (SARS-CoV) as a model pathogen. We utilized a time course of matched virologic, pathological, and transcriptomic data within a novel methodological framework that can detect pathway enrichment among key highly connected network genes. This unbiased approach produced a high-priority list of 4 genes in one pathway out of over 3,500 genes that were differentially expressed following SARS-CoV infection. With these data, we predicted that the urokinase and other wound repair pathways would regulate lethal versus sublethal disease following SARS-CoV infection in mice. We validated the importance of the urokinase pathway for SARS-CoV disease severity using genetically defined knockout mice, proteomic correlates of pathway activation, and pathological disease severity. The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such asmore » SARS-CoV.« less

Authors:
 [1];  [2];  [2];  [1];  [3];  [3];  [4];  [4];  [4];  [4];  [5];  [6];  [3];  [3];  [4];  [4];  [4];  [3];  [7];  [2] more »;  [8] « less
  1. Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Epidemiology
  2. Oregon Health Sciences Univ., Portland, OR (United States). Dept. of Medical Informatics and Clinical Epidemiology. Division of Bioinformatics and Computational Biology
  3. Univ. of Washington, Seattle, WA (United States). School of Medicine. Dept. of Microbiology
  4. Oregon Health Sciences Univ., Portland, OR (United States). Oregon Clinical and Translational Research Inst.
  5. Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Genetics
  6. Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Microbiology and Immunology
  7. Univ. of Washington, Seattle, WA (United States). School of Medicine. Dept. of Microbiology; Univ. of Washington, Seattle, WA (United States). Washington National Primate Research Center
  8. Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Microbiology and Immunology; Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Epidemiology
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1626096
Grant/Contract Number:  
AC06-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 4; Journal Issue: 4; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology (ASM)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Microbiology

Citation Formats

Gralinski, Lisa E., Bankhead, Armand, Jeng, Sophia, Menachery, Vineet D., Proll, Sean, Belisle, Sarah E., Matzke, Melissa, Webb-Robertson, Bobbie-Jo M., Luna, Maria L., Shukla, Anil K., Ferris, Martin T., Bolles, Meagan, Chang, Jean, Aicher, Lauri, Waters, Katrina M., Smith, Richard D., Metz, Thomas O., Law, G. Lynn, Katze, Michael G., McWeeney, Shannon, and Baric, Ralph S. Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury. United States: N. p., 2013. Web. doi:10.1128/mbio.00271-13.
Gralinski, Lisa E., Bankhead, Armand, Jeng, Sophia, Menachery, Vineet D., Proll, Sean, Belisle, Sarah E., Matzke, Melissa, Webb-Robertson, Bobbie-Jo M., Luna, Maria L., Shukla, Anil K., Ferris, Martin T., Bolles, Meagan, Chang, Jean, Aicher, Lauri, Waters, Katrina M., Smith, Richard D., Metz, Thomas O., Law, G. Lynn, Katze, Michael G., McWeeney, Shannon, & Baric, Ralph S. Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury. United States. https://doi.org/10.1128/mbio.00271-13
Gralinski, Lisa E., Bankhead, Armand, Jeng, Sophia, Menachery, Vineet D., Proll, Sean, Belisle, Sarah E., Matzke, Melissa, Webb-Robertson, Bobbie-Jo M., Luna, Maria L., Shukla, Anil K., Ferris, Martin T., Bolles, Meagan, Chang, Jean, Aicher, Lauri, Waters, Katrina M., Smith, Richard D., Metz, Thomas O., Law, G. Lynn, Katze, Michael G., McWeeney, Shannon, and Baric, Ralph S. Tue . "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury". United States. https://doi.org/10.1128/mbio.00271-13. https://www.osti.gov/servlets/purl/1626096.
@article{osti_1626096,
title = {Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury},
author = {Gralinski, Lisa E. and Bankhead, Armand and Jeng, Sophia and Menachery, Vineet D. and Proll, Sean and Belisle, Sarah E. and Matzke, Melissa and Webb-Robertson, Bobbie-Jo M. and Luna, Maria L. and Shukla, Anil K. and Ferris, Martin T. and Bolles, Meagan and Chang, Jean and Aicher, Lauri and Waters, Katrina M. and Smith, Richard D. and Metz, Thomas O. and Law, G. Lynn and Katze, Michael G. and McWeeney, Shannon and Baric, Ralph S.},
abstractNote = {Systems biology offers considerable promise in uncovering novel pathways by which viruses and other microbial pathogens interact with host signaling and expression networks to mediate disease severity. In this study, we have developed an unbiased modeling approach to identify new pathways and network connections mediating acute lung injury, using severe acute respiratory syndrome coronavirus (SARS-CoV) as a model pathogen. We utilized a time course of matched virologic, pathological, and transcriptomic data within a novel methodological framework that can detect pathway enrichment among key highly connected network genes. This unbiased approach produced a high-priority list of 4 genes in one pathway out of over 3,500 genes that were differentially expressed following SARS-CoV infection. With these data, we predicted that the urokinase and other wound repair pathways would regulate lethal versus sublethal disease following SARS-CoV infection in mice. We validated the importance of the urokinase pathway for SARS-CoV disease severity using genetically defined knockout mice, proteomic correlates of pathway activation, and pathological disease severity. The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV.},
doi = {10.1128/mbio.00271-13},
journal = {mBio (Online)},
number = 4,
volume = 4,
place = {United States},
year = {Tue Aug 06 00:00:00 EDT 2013},
month = {Tue Aug 06 00:00:00 EDT 2013}
}

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dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvscl011/1661969

Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset
journal, August 2014


Sm010
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm010/1661981

Sm014
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm014/1661985

Sm020
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm020/1661990

Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia
journal, April 2020

  • Arachchillage, Deepa R. J.; Laffan, Mike
  • Journal of Thrombosis and Haemostasis, Vol. 18, Issue 5
  • DOI: 10.1111/jth.14820

Sm036
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm036/1661999

Sm038
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm038/1662000

Sm004
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm004/1661976

Molecular pathology of emerging coronavirus infections
journal, December 2014

  • Gralinski, Lisa E.; Baric, Ralph S.
  • The Journal of Pathology, Vol. 235, Issue 2
  • DOI: 10.1002/path.4454

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape
journal, January 2018

  • Menachery, Vineet D.; Schäfer, Alexandra; Burnum-Johnson, Kristin E.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 5
  • DOI: 10.1073/pnas.1706928115

Sm039
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm039/1662001

Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts
text, January 2014

  • S., Baric, Ralph; J., Eisfeld, Amie; J., Thomas, Matthew
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/5png-6y33

Attenuation and Restoration of Severe Acute Respiratory Syndrome Coronavirus Mutant Lacking 2'-O-Methyltransferase Activity
journal, January 2014

  • Menachery, V. D.; Yount, B. L.; Josset, L.
  • Journal of Virology, Vol. 88, Issue 8
  • DOI: 10.1128/jvi.03571-13

Sm008
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm008/1661979

Sm028
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm028/1661993

Sm033
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm033/1661996

Sm005
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm005/1661977

Sm001
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm001/1661974

Molecular pathology of emerging coronavirus infections
text, January 2014


Sm021
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm021/1661991

Conditioned Medium of Human Adipose Mesenchymal Stem Cells Increases Wound Closure and Protects Human Astrocytes Following Scratch Assay In Vitro
journal, September 2017

  • Baez-Jurado, Eliana; Hidalgo-Lanussa, Oscar; Guio-Vega, Gina
  • Molecular Neurobiology, Vol. 55, Issue 6
  • DOI: 10.1007/s12035-017-0771-4

Scl004
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvscl004/1661963

Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross
text, January 2015

  • Leonard, McMillan,; A., Churchill, Gary; R., Miller, Darla
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/z06v-7412

Sm013
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm013/1661984

Sm019
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm019/1661989

New Metrics for Evaluating Viral Respiratory Pathogenesis
text, January 2015

  • D., Menachery, Vineet; S., Baric, Ralph; T., Ferris, Martin
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/7qq9-f010

Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses
text, January 2017

  • Y., Feng, Joy; Yeojin, Park,; L., MacKman, Richard
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/ksj0-6e19

Sm029
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm029/1661994

A decade after SARS: strategies for controlling emerging coronaviruses
text, January 2013

  • Graham, Rachel L.; Donaldson, Eric F.; Baric, Ralph S.
  • Macmillan Publishers
  • DOI: 10.17615/ss8c-tg10

Scl010
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvscl010/1661968

Sm034
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm034/1661997

Sm009
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm009/1661980

New Metrics for Evaluating Viral Respiratory Pathogenesis
journal, June 2015


Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines
journal, July 2018

  • Menachery, Vineet D.; Gralinski, Lisa E.; Mitchell, Hugh D.
  • Journal of Virology, Vol. 92, Issue 17
  • DOI: 10.1128/jvi.00710-18

Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice
journal, June 2017

  • Gralinski, Lisa E.; Menachery, Vineet D.; Morgan, Andrew P.
  • G3 Genes|Genomes|Genetics, Vol. 7, Issue 6
  • DOI: 10.1534/g3.117.041434

A decade after SARS: strategies for controlling emerging coronaviruses
journal, November 2013

  • Graham, Rachel L.; Donaldson, Eric F.; Baric, Ralph S.
  • Nature Reviews Microbiology, Vol. 11, Issue 12
  • DOI: 10.1038/nrmicro3143

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape
text, January 2018

  • M., Webb-Robertson, Bobbie-Jo; D., Nicora, Carrie; O., Metz, Thomas
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/t9e6-8v94

A comprehensive collection of systems biology data characterizing the host response to viral infection
journal, October 2014

  • Aevermann, Brian D.; Pickett, Brett E.; Kumar, Sanjeev
  • Scientific Data, Vol. 1, Issue 1
  • DOI: 10.1038/sdata.2014.33

Sm018
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm018/1661988

Sm031
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm031/1661995

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus
journal, September 2016

  • McDermott, Jason E.; Mitchell, Hugh D.; Gralinski, Lisa E.
  • BMC Systems Biology, Vol. 10, Issue 1
  • DOI: 10.1186/s12918-016-0336-6

Pneumonia, Acute Respiratory Distress Syndrome, and Early Immune-Modulator Therapy
journal, February 2017

  • Lee, Kyung-Yil
  • International Journal of Molecular Sciences, Vol. 18, Issue 2
  • DOI: 10.3390/ijms18020388

Sm011
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm011/1661982

Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross
journal, October 2015


Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease
text, January 2018

  • R., Denison, Mark; Dustin, Siegel,; S., Ray, Adrian
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/9gnx-xm52

Sm007
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm007/1661978

Attenuation and Restoration of Severe Acute Respiratory Syndrome Coronavirus Mutant Lacking 2'-O-Methyltransferase Activity
text, January 2014

  • Agnihothram, Sudhakar; Katze, Michael G.; Josset, Laurence
  • American Society for Microbiology
  • DOI: 10.17615/8qve-1v06

Sm015
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm015/1661986

Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines
text, January 2018

  • T., McAnarney, Eileen; M., Waters, Katrina; E., Gralinski, Lisa
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/xghs-wp15

Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia
journal, April 2020

  • Tang, Ning; Li, Dengju; Wang, Xiong
  • Journal of Thrombosis and Haemostasis, Vol. 18, Issue 4
  • DOI: 10.1111/jth.14768

Sm023
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm023/1661992

Broad-spectrum coronavirus antiviral drug discovery
journal, February 2019


Sm035
dataset, January 2020

  • Waters, Katrina; Anderson, Lindsey; McDermott, Jason
  • Pacific Northwest National Laboratory 2; EMSL; PNNL
  • DOI: 10.25584/lhvsm035/1661998

Molecular pathology of emerging coronavirus infections
journal, December 2014

  • Gralinski, Lisa E.; Baric, Ralph S.
  • The Journal of Pathology, Vol. 235, Issue 2
  • DOI: 10.1002/path.4454

SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology
journal, March 2017

  • Morales, Lucía; Oliveros, Juan Carlos; Fernandez-Delgado, Raúl
  • Cell Host & Microbe, Vol. 21, Issue 3
  • DOI: 10.1016/j.chom.2017.01.015

Systems approaches to coronavirus pathogenesis
journal, June 2014


Systems analysis of West Nile virus infection
journal, June 2014


A decade after SARS: strategies for controlling emerging coronaviruses
journal, November 2013

  • Graham, Rachel L.; Donaldson, Eric F.; Baric, Ralph S.
  • Nature Reviews Microbiology, Vol. 11, Issue 12
  • DOI: 10.1038/nrmicro3143

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape
journal, January 2018

  • Menachery, Vineet D.; Schäfer, Alexandra; Burnum-Johnson, Kristin E.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 5
  • DOI: 10.1073/pnas.1706928115

Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses
journal, June 2017


Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis
journal, October 2018

  • Gralinski, Lisa E.; Sheahan, Timothy P.; Morrison, Thomas E.
  • mBio, Vol. 9, Issue 5
  • DOI: 10.1128/mbio.01753-18

Pulmonary vascular dysfunction in ARDS
journal, August 2014


Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross
journal, October 2015


The PDZ-Binding Motif of Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Is a Determinant of Viral Pathogenesis
journal, August 2014


An Epithelial Integrin Regulates the Amplitude of Protective Lung Interferon Responses against Multiple Respiratory Pathogens
journal, August 2016

  • Meliopoulos, Victoria A.; Van de Velde, Lee-Ann; Van de Velde, Nicholas C.
  • PLOS Pathogens, Vol. 12, Issue 8
  • DOI: 10.1371/journal.ppat.1005804

Host resilience to emerging coronaviruses
journal, July 2016


The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections
journal, September 2019

  • Mitchell, Hugh D.; Eisfeld, Amie J.; Stratton, Kelly G.
  • Frontiers in Cell and Developmental Biology, Vol. 7
  • DOI: 10.3389/fcell.2019.00200

Multi-omic network signatures of disease
journal, January 2014


SARS-CoV-2 Infection with Different Radiological Insights
journal, May 2020