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Tytuł:
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A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.
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Autorzy:
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Sego TJ; Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.; Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America.
Aponte-Serrano JO; Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.; Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America.
Ferrari Gianlupi J; Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.; Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America.
Heaps SR; Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.
Breithaupt K; Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.; Cognitive Science Program, Indiana University, Bloomington, Indiana, United States of America.
Brusch L; Center for Information Services and High Performance Computing (ZIH), Technische Universität, Dresden, Germany.
Crawshaw J; School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.
Osborne JM; School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.
Quardokus EM; Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.
Plemper RK; Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America.
Glazier JA; Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.; Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America.
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Źródło:
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PLoS computational biology [PLoS Comput Biol] 2020 Dec 21; Vol. 16 (12), pp. e1008451. Date of Electronic Publication: 2020 Dec 21 (Print Publication: 2020).
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Typ publikacji:
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Journal Article
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Język:
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English
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Imprint Name(s):
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Original Publication: San Francisco, CA : Public Library of Science, [2005]-
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MeSH Terms:
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Epithelium*/immunology
Epithelium*/virology
Models, Immunological*
Virus Diseases*/drug therapy
Virus Diseases*/immunology
Computational Biology/*methods
Antiviral Agents/therapeutic use ; COVID-19/immunology ; Computer Simulation ; Hepacivirus/immunology ; Hepatitis C/drug therapy ; Hepatitis C/immunology ; Humans ; SARS-CoV-2/immunology
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References:
-
Rev Immunogenet. 2000;2(3):374-86. (PMID: 11256746)
Thorax. 1993 Jul;48(7):765-9. (PMID: 8153928)
Methods Cell Biol. 2012;110:325-66. (PMID: 22482955)
J Virol. 2007 Jan;81(2):750-60. (PMID: 17035310)
Nature. 2016 Mar 17;531(7594):381-5. (PMID: 26934220)
J Biotechnol. 2007 Mar 10;128(4):875-94. (PMID: 17289202)
Ann Transl Med. 2020 Jun;8(11):693. (PMID: 32617313)
Biopharm Drug Dispos. 2016 Mar;37(2):75-92. (PMID: 26461173)
Microbiol Mol Biol Rev. 2018 Mar 28;82(2):. (PMID: 29592895)
J Immunol. 2010 Mar 15;184(6):2873-85. (PMID: 20154206)
Adv Drug Deliv Rev. 2009 Feb 27;61(2):86-100. (PMID: 19166889)
Science. 2020 Mar 13;367(6483):1260-1263. (PMID: 32075877)
Am Nat. 2005 Mar;165(3):364-73. (PMID: 15729666)
J Immunol. 2018 Aug 1;201(3):833-842. (PMID: 30038036)
Biophys J. 2005 Feb;88(2):851-66. (PMID: 15556983)
Travel Med Infect Dis. 2020 May - Jun;35:101647. (PMID: 32247927)
Biophys J. 2004 Jun;86(6):3359-72. (PMID: 15189840)
Nat Commun. 2019 May 13;10(1):2144. (PMID: 31086185)
Nat Immunol. 2004 Dec;5(12):1235-42. (PMID: 15516925)
Front Public Health. 2018 Mar 07;6:68. (PMID: 29594091)
J Virol. 2003 Aug;77(15):8181-6. (PMID: 12857886)
Am J Emerg Med. 2021 Jun;44:346-351. (PMID: 32327245)
Cell. 2020 Apr 16;181(2):281-292.e6. (PMID: 32155444)
Bioinformatics. 2009 Sep 15;25(18):2452-4. (PMID: 19578039)
Annu Rev Control. 2020;50:448-456. (PMID: 33020692)
Inf Sci (N Y). 2009 Apr 29;179(10):1379-1389. (PMID: 20161146)
Eur Radiol. 2020 Oct;30(10):5446-5454. (PMID: 32367418)
Gastroenterology. 2017 Dec;153(6):1647-1661.e9. (PMID: 28851562)
Infect Dis Model. 2018 Sep 20;3:176-191. (PMID: 30839905)
Crit Care. 2020 Apr 30;24(1):188. (PMID: 32354360)
Nucleic Acids Res. 2018 Oct 12;46(18):9321-9337. (PMID: 30184180)
PLoS One. 2010 Feb 18;5(2):e9249. (PMID: 20174629)
PLoS Comput Biol. 2013;9(3):e1002970. (PMID: 23516352)
Infect Immun. 1997 Aug;65(8):3286-92. (PMID: 9234788)
J Theor Biol. 2002 Sep 7;218(1):85-96. (PMID: 12297072)
Sci Adv. 2020 Nov 20;6(47):. (PMID: 33097472)
Biotechnol Bioeng. 1995 Jun 5;46(5):485-96. (PMID: 18623341)
Elife. 2021 Jul 20;10:. (PMID: 34282728)
Phys Rev Lett. 1992 Sep 28;69(13):2013-2016. (PMID: 10046374)
J Theor Biol. 2012 Nov 7;312:120-32. (PMID: 22814476)
Annu Rev Pathol. 2008;3:499-522. (PMID: 18039138)
PLoS One. 2016 Dec 20;11(12):e0168576. (PMID: 27997613)
J Theor Biol. 2005 Mar 21;233(2):221-36. (PMID: 15619362)
Immunol Rev. 2013 Sep;255(1):182-96. (PMID: 23947355)
J Pharm Sci. 2019 Jan;108(1):661-673. (PMID: 30399360)
J Theor Biol. 2006 Sep 21;242(2):464-77. (PMID: 16650441)
Immunity. 2010 Aug 27;33(2):266-78. (PMID: 20727790)
Emerg Infect Dis. 2020 Jun;26(6):1266-1273. (PMID: 32160149)
J Cell Biol. 2007 Oct 22;179(2):291-304. (PMID: 17954611)
Cell. 2006 Feb 24;124(4):783-801. (PMID: 16497588)
Wiley Interdiscip Rev Syst Biol Med. 2011 Jul-Aug;3(4):429-45. (PMID: 21197654)
Autoimmunity. 2011 Jun;44(4):282-93. (PMID: 21244331)
Phys Rev Lett. 2001 Oct 15;87(16):168102. (PMID: 11690248)
Antimicrob Agents Chemother. 2018 Feb 23;62(3):. (PMID: 29311073)
CPT Pharmacometrics Syst Pharmacol. 2020 Sep;9(9):509-514. (PMID: 32558354)
Front Immunol. 2012 Sep 05;3:268. (PMID: 22973270)
Front Immunol. 2014 Apr 16;5:171. (PMID: 24795718)
Virus Res. 2001 Sep;77(1):3-17. (PMID: 11451482)
Biochemistry. 2004 Jan 20;43(2):289-99. (PMID: 14717582)
bioRxiv. 2021 Nov 10;:. (PMID: 32511322)
Nat Rev Genet. 2020 Jun;21(6):339-354. (PMID: 32060427)
Curr Opin Syst Biol. 2018 Dec;12:46-52. (PMID: 31723715)
Nat Biotechnol. 2020 Aug;38(8):970-979. (PMID: 32591762)
Virus Evol. 2019 Jul 08;5(2):vez018. (PMID: 31304043)
Bioinformatics. 2014 May 1;30(9):1331-2. (PMID: 24443380)
Immunity. 2017 Apr 18;46(4):609-620. (PMID: 28389069)
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Grant Information:
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R01 AI141222 United States AI NIAID NIH HHS; R01 GM122424 United States GM NIGMS NIH HHS; R01 AI153400 United States AI NIAID NIH HHS; R01 AI071002 United States AI NIAID NIH HHS; R01 HD079327 United States HD NICHD NIH HHS; U24 EB028887 United States EB NIBIB NIH HHS
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Substance Nomenclature:
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0 (Antiviral Agents)
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Entry Date(s):
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Date Created: 20201221 Date Completed: 20210113 Latest Revision: 20240216
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Update Code:
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20240216
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PubMed Central ID:
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PMC7785254
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DOI:
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10.1371/journal.pcbi.1008451
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PMID:
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33347439
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Simulations of tissue-specific effects of primary acute viral infections like COVID-19 are essential for understanding disease outcomes and optimizing therapies. Such simulations need to support continuous updating in response to rapid advances in understanding of infection mechanisms, and parallel development of components by multiple groups. We present an open-source platform for multiscale spatiotemporal simulation of an epithelial tissue, viral infection, cellular immune response and tissue damage, specifically designed to be modular and extensible to support continuous updating and parallel development. The base simulation of a simplified patch of epithelial tissue and immune response exhibits distinct patterns of infection dynamics from widespread infection, to recurrence, to clearance. Slower viral internalization and faster immune-cell recruitment slow infection and promote containment. Because antiviral drugs can have side effects and show reduced clinical effectiveness when given later during infection, we studied the effects on progression of treatment potency and time-of-first treatment after infection. In simulations, even a low potency therapy with a drug which reduces the replication rate of viral RNA greatly decreases the total tissue damage and virus burden when given near the beginning of infection. Many combinations of dosage and treatment time lead to stochastic outcomes, with some simulation replicas showing clearance or control (treatment success), while others show rapid infection of all epithelial cells (treatment failure). Thus, while a high potency therapy usually is less effective when given later, treatments at late times are occasionally effective. We illustrate how to extend the platform to model specific virus types (e.g., hepatitis C) and add additional cellular mechanisms (tissue recovery and variable cell susceptibility to infection), using our software modules and publicly-available software repository.
Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: JAG is the owner/operator of Virtual Tissues for Health, LLC, which develops applications of multiscale tissue models in medical applications and is a shareholder in Gilead Life Sciences.
Update of: bioRxiv. 2020 May 07;:. (PMID: 32511367)
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