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Williams T, McCaw JM, Osborne JM. Spatial information allows inference of the prevalence of direct cell-to-cell viral infection. PLoS Comput Biol 2024; 20:e1012264. [PMID: 39042664 PMCID: PMC11296656 DOI: 10.1371/journal.pcbi.1012264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 08/02/2024] [Accepted: 06/19/2024] [Indexed: 07/25/2024] Open
Abstract
The role of direct cell-to-cell spread in viral infections-where virions spread between host and susceptible cells without needing to be secreted into the extracellular environment-has come to be understood as essential to the dynamics of medically significant viruses like hepatitis C and influenza. Recent work in both the experimental and mathematical modelling literature has attempted to quantify the prevalence of cell-to-cell infection compared to the conventional free virus route using a variety of methods and experimental data. However, estimates are subject to significant uncertainty and moreover rely on data collected by inhibiting one mode of infection by either chemical or physical factors, which may influence the other mode of infection to an extent which is difficult to quantify. In this work, we conduct a simulation-estimation study to probe the practical identifiability of the proportion of cell-to-cell infection, using two standard mathematical models and synthetic data that would likely be realistic to obtain in the laboratory. We show that this quantity cannot be estimated using non-spatial data alone, and that the collection of data which describes the spatial structure of the infection is necessary to infer the proportion of cell-to-cell infection. Our results provide guidance for the design of relevant experiments and mathematical tools for accurately inferring the prevalence of cell-to-cell infection in in vitro and in vivo contexts.
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Affiliation(s)
- Thomas Williams
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - James M. McCaw
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - James M. Osborne
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
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2
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Xu X, Nielsen BF, Sneppen K. Self-inhibiting percolation and viral spreading in epithelial tissue. eLife 2024; 13:RP94056. [PMID: 38941138 PMCID: PMC11213566 DOI: 10.7554/elife.94056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
SARS-CoV-2 induces delayed type-I/III interferon production, allowing it to escape the early innate immune response. The delay has been attributed to a deficiency in the ability of cells to sense viral replication upon infection, which in turn hampers activation of the antiviral state in bystander cells. Here, we introduce a cellular automaton model to investigate the spatiotemporal spreading of viral infection as a function of virus and host-dependent parameters. The model suggests that the considerable person-to-person heterogeneity in SARS-CoV-2 infections is a consequence of high sensitivity to slight variations in biological parameters near a critical threshold. It further suggests that within-host viral proliferation can be curtailed by the presence of remarkably few cells that are primed for IFN production. Thus, the observed heterogeneity in defense readiness of cells reflects a remarkably cost-efficient strategy for protection.
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Affiliation(s)
- Xiaochan Xu
- Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of CopenhagenCopenhagenDenmark
| | - Bjarke Frost Nielsen
- PandemiX Center, Department of Science and Environment, Roskilde UniversityRoskildeDenmark
- High Meadows Environmental Institute, Princeton UniversityPrincetonUnited States
| | - Kim Sneppen
- Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
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3
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Wang X, Baksh SS, Pratt RE, Dzau VJ, Hodgkinson CP. Modifying miRs for effective reprogramming of fibroblasts to cardiomyocytes. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102160. [PMID: 38495845 PMCID: PMC10943962 DOI: 10.1016/j.omtn.2024.102160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/22/2024] [Indexed: 03/19/2024]
Abstract
Reprogramming scar fibroblasts into cardiomyocytes has been proposed to reverse the damage associated with myocardial infarction. However, the limited improvement in cardiac function calls for enhanced strategies. We reported enhanced efficacy of our miR reprogramming cocktail miR combo (miR-1, miR-133a, miR-208a, and miR-499) via RNA-sensing receptor stimulation. We hypothesized that we could combine RNA-sensing receptor activation with fibroblast reprogramming by chemically modifying miR combo. To test the hypothesis, miR combo was modified to enhance interaction with the RNA-sensing receptor Rig1 via the addition of a 5'-triphosphate (5'ppp) group. Importantly, when compared with unmodified miR combo, 5'ppp-modified miR combo markedly improved reprogramming efficacy in vitro. Enhanced reprogramming efficacy correlated with a type-I interferon immune response with strong and selective secretion of interferon β (IFNβ). Antibody blocking studies and media replacement experiments indicated that 5'ppp-miR combo utilized IFNβ to enhance fibroblast reprogramming efficacy. In conclusion, miRs can acquire powerful additional roles through chemical modification that potentially increases their clinical applications.
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Affiliation(s)
- Xinghua Wang
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Syeda S. Baksh
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Richard E. Pratt
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Victor J. Dzau
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Conrad P. Hodgkinson
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
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4
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Olmos Liceaga D, Nunes SF, Saenz RA. Ex Vivo Experiments Shed Light on the Innate Immune Response from Influenza Virus. Bull Math Biol 2023; 85:115. [PMID: 37833614 DOI: 10.1007/s11538-023-01217-5] [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: 11/07/2022] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
The innate immune response is recognized as a key driver in controlling an influenza virus infection in a host. However, the mechanistic action of such innate response is not fully understood. Infection experiments on ex vivo explants from swine trachea represent an efficient alternative to animal experiments, as the explants conserved key characteristics of an organ from an animal. In the present work we compare three cellular automata models of influenza virus dynamics. The models are fitted to free virus and infected cells data from ex vivo swine trachea experiments. Our findings suggest that the presence of an immune response is necessary to explain the observed dynamics in ex vivo organ culture. Moreover, such immune response should include a refractory state for epithelial cells, and not just a reduced infection rate. Our results may shed light on how the immune system responds to an infection event.
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Affiliation(s)
- Daniel Olmos Liceaga
- Departamento de Matemáticas, Universidad de Sonora, Blvd. Rosales y Luis Encinas S/N, Col Centro, 83000, Hermosillo, SON, Mexico
| | - Sandro Filipe Nunes
- Cambridge Infectious Disease Consortium, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
- Animal Sciences and Technologies, Clinical Pharmacology and Safety Sciences, AstraZeneca Biopharmaceuticals R &D, Pepparedsleden 1, SE-43183, Mölndal, Sweden
| | - Roberto A Saenz
- Facultad de Ciencias, Universidad de Colima, Bernal Díaz del Castillo 340, Col Villas de San Sebastián, 28045, Colima, COL, Mexico.
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5
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Williams T, McCaw JM, Osborne JM. Choice of spatial discretisation influences the progression of viral infection within multicellular tissues. J Theor Biol 2023; 573:111592. [PMID: 37558160 DOI: 10.1016/j.jtbi.2023.111592] [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: 02/20/2023] [Revised: 06/16/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
There has been an increasing recognition of the utility of models of the spatial dynamics of viral spread within tissues. Multicellular models, where cells are represented as discrete regions of space coupled to a virus density surface, are a popular approach to capture these dynamics. Conventionally, such models are simulated by discretising the viral surface and depending on the rate of viral diffusion and other considerations, a finer or coarser discretisation may be used. The impact that this choice may have on the behaviour of the system has not been studied. Here we demonstrate that under realistic parameter regimes - where viral diffusion is small enough to support the formation of familiar ring-shaped infection plaques - the choice of spatial discretisation of the viral surface can qualitatively change key model outcomes including the time scale of infection. Importantly, we show that the choice between implementing viral spread as a cell-scale process, or as a high-resolution converged PDE can generate distinct model outcomes, which raises important conceptual questions about the strength of assumptions underpinning the spatial structure of the model. We investigate the mechanisms driving these discretisation artefacts, the impacts they may have on model predictions, and provide guidance on the design and implementation of spatial and especially multicellular models of viral dynamics. We obtain our results using the simplest TIV construct for the viral dynamics, and therefore anticipate that the important effects we describe will also influence model predictions in more complex models of virus-cell-immune system interactions. This analysis will aid in the construction of models for robust and biologically realistic modelling and inference.
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Affiliation(s)
- Thomas Williams
- School of Mathematics and Statistics, University of Melbourne, Australia
| | - James M McCaw
- School of Mathematics and Statistics, University of Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Australia
| | - James M Osborne
- School of Mathematics and Statistics, University of Melbourne, Australia.
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6
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Yip F, Lai B, Yang D. Role of Coxsackievirus B3-Induced Immune Responses in the Transition from Myocarditis to Dilated Cardiomyopathy and Heart Failure. Int J Mol Sci 2023; 24:ijms24097717. [PMID: 37175422 PMCID: PMC10178405 DOI: 10.3390/ijms24097717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is a cardiac disease marked by the stretching and thinning of the heart muscle and impaired left ventricular contractile function. While most patients do not develop significant cardiac diseases from myocarditis, disparate immune responses can affect pathological outcomes, including DCM progression. These altered immune responses, which may be caused by genetic variance, can prolong cytotoxicity, induce direct cleavage of host protein, or encourage atypical wound healing responses that result in tissue scarring and impaired mechanical and electrical heart function. However, it is unclear which alterations within host immune profiles are crucial to dictating the outcomes of myocarditis. Coxsackievirus B3 (CVB3) is a well-studied virus that has been identified as a causal agent of myocarditis in various models, along with other viruses such as adenovirus, parvovirus B19, and SARS-CoV-2. This paper takes CVB3 as a pathogenic example to review the recent advances in understanding virus-induced immune responses and differential gene expression that regulates iron, lipid, and glucose metabolic remodeling, the severity of cardiac tissue damage, and the development of DCM and heart failure.
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Affiliation(s)
- Fione Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Brian Lai
- The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Decheng Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
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7
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Aristotelous AC, Chen A, Forest MG. A hybrid discrete-continuum model of immune responses to SARS-CoV-2 infection in the lung alveolar region, with a focus on interferon induced innate response. J Theor Biol 2022; 555:111293. [PMID: 36208668 PMCID: PMC9533651 DOI: 10.1016/j.jtbi.2022.111293] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 01/14/2023]
Abstract
We develop a lattice-based, hybrid discrete-continuum modeling framework for SARS-CoV-2 exposure and infection in the human lung alveolar region, or parenchyma, the massive surface area for gas exchange. COVID-19 pneumonia is alveolar infection by the SARS-CoV-2 virus significant enough to compromise gas exchange. The modeling framework orchestrates the onset and progression of alveolar infection, spatially and temporally, beginning with a pre-immunity baseline, upon which we superimpose multiple mechanisms of immune protection conveyed by interferons and antibodies. The modeling framework is tunable to individual profiles, focusing here on degrees of innate immunity, and to the evolving infection-replication properties of SARS-CoV-2 variant strains. The model employs partial differential equations for virion, interferon, and antibody concentrations governed by diffusion in the thin fluid coating of alveolar cells, species and lattice interactions corresponding to sources and sinks for each species, and multiple immune protections signaled by interferons. The spatial domain is a two-dimensional, rectangular lattice of alveolar type I (non-infectable) and type II (infectable) cells with a stochastic, species-concentration-governed, switching dynamics of type II lattice sites from healthy to infected. Once infected, type II cells evolve through three phases: an eclipse phase during which RNA copies (virions) are assembled; a shedding phase during which virions and interferons are released; and then cell death. Model simulations yield the dynamic spread of, and immune protection against, alveolar infection and viral load from initial sites of exposure. We focus in this paper on model illustrations of the diversity of outcomes possible from alveolar infection, first absent of immune protection, and then with varying degrees of four known mechanisms of interferon-induced innate immune protection. We defer model illustrations of antibody protection to future studies. Results presented reinforce previous recognition that interferons produced solely by infected cells are insufficient to maintain a high efficacy level of immune protection, compelling additional mechanisms to clear alveolar infection, such as interferon production by immune cells and adaptive immunity (e.g., T cells). This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
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Affiliation(s)
- Andreas C. Aristotelous
- Department of Mathematics, The University of Akron, Akron, OH 44325-4002, United States of America,Corresponding author
| | - Alex Chen
- Department of Mathematics, California State University, Dominguez Hills, CA 90747, United States of America
| | - M. Gregory Forest
- Departments of Mathematics, Applied Physical Sciences, and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3250, United States of America
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Desikan R, Linderman SL, Davis C, Zarnitsyna VI, Ahmed H, Antia R. Vaccine models predict rules for updating vaccines against evolving pathogens such as SARS-CoV-2 and influenza in the context of pre-existing immunity. Front Immunol 2022; 13:985478. [PMID: 36263031 PMCID: PMC9574365 DOI: 10.3389/fimmu.2022.985478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, vaccines for SARS-CoV-2 and influenza viruses are updated if the new vaccine induces higher antibody-titers to circulating variants than current vaccines. This approach does not account for complex dynamics of how prior immunity skews recall responses to the updated vaccine. We: (i) use computational models to mechanistically dissect how prior immunity influences recall responses; (ii) explore how this affects the rules for evaluating and deploying updated vaccines; and (iii) apply this to SARS-CoV-2. Our analysis of existing data suggests that there is a strong benefit to updating the current SARS-CoV-2 vaccines to match the currently circulating variants. We propose a general two-dose strategy for determining if vaccines need updating as well as for vaccinating high-risk individuals. Finally, we directly validate our model by reanalysis of earlier human H5N1 influenza vaccine studies.
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Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Stevenage, Hertfordshire, United Kingdom
- *Correspondence: Rajat Desikan, ; Rustom Antia,
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | | | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, United States
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, United States
- *Correspondence: Rajat Desikan, ; Rustom Antia,
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Desikan R, Linderman SL, Davis C, Zarnitsyna V, Ahmed H, Antia R. Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.21.492928. [PMID: 35665010 PMCID: PMC9164442 DOI: 10.1101/2022.05.21.492928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
When should vaccines to evolving pathogens such as SARS-CoV-2 be updated? Our computational models address this focusing on updating SARS-CoV-2 vaccines to the currently circulating Omicron variant. Current studies typically compare the antibody titers to the new variant following a single dose of the original-vaccine versus the updated-vaccine in previously immunized individuals. These studies find that the updated-vaccine does not induce higher titers to the vaccine-variant compared with the original-vaccine, suggesting that updating may not be needed. Our models recapitulate this observation but suggest that vaccination with the updated-vaccine generates qualitatively different humoral immunity, a small fraction of which is specific for unique epitopes to the new variant. Our simulations suggest that these new variant-specific responses could dominate following subsequent vaccination or infection with either the currently circulating or future variants. We suggest a two-dose strategy for determining if the vaccine needs updating and for vaccinating high-risk individuals.
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Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Gunnels Wood Rd, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
- These authors contributed equally
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Veronika Zarnitsyna
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- These authors contributed equally
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10
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Endothelial Dysfunction through Oxidatively Generated Epigenetic Mark in Respiratory Viral Infections. Cells 2021; 10:cells10113067. [PMID: 34831290 PMCID: PMC8623825 DOI: 10.3390/cells10113067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
The bronchial vascular endothelial network plays important roles in pulmonary pathology during respiratory viral infections, including respiratory syncytial virus (RSV), influenza A(H1N1) and importantly SARS-Cov-2. All of these infections can be severe and even lethal in patients with underlying risk factors.A major obstacle in disease prevention is the lack of appropriate efficacious vaccine(s) due to continuous changes in the encoding capacity of the viral genome, exuberant responsiveness of the host immune system and lack of effective antiviral drugs. Current management of these severe respiratory viral infections is limited to supportive clinical care. The primary cause of morbidity and mortality is respiratory failure, partially due to endothelial pulmonary complications, including edema. The latter is induced by the loss of alveolar epithelium integrity and by pathological changes in the endothelial vascular network that regulates blood flow, blood fluidity, exchange of fluids, electrolytes, various macromolecules and responses to signals triggered by oxygenation, and controls trafficking of leukocyte immune cells. This overview outlines the latest understanding of the implications of pulmonary vascular endothelium involvement in respiratory distress syndrome secondary to viral infections. In addition, the roles of infection-induced cytokines, growth factors, and epigenetic reprogramming in endothelial permeability, as well as emerging treatment options to decrease disease burden, are discussed.
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11
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Ramos TI, Villacis-Aguirre CA, Santiago Vispo N, Santiago Padilla L, Pedroso Santana S, Parra NC, Alonso JRT. Forms and Methods for Interferon's Encapsulation. Pharmaceutics 2021; 13:1533. [PMID: 34683824 PMCID: PMC8538586 DOI: 10.3390/pharmaceutics13101533] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022] Open
Abstract
Interferons (IFNs) are cytokines involved in the immune response that act on innate and adaptive immunity. These proteins are natural cell-signaling glycoproteins expressed in response to viral infections, tumors, and biological inducers and constitute the first line of defense of vertebrates against infectious agents. They have been marketed for more than 30 years with considerable impact on the global therapeutic protein market thanks to their diversity in terms of biological activities. They have been used as single agents or with combination treatment regimens, demonstrating promising clinical results, resulting in 22 different formulations approved by regulatory agencies. The 163 clinical trials with currently active IFNs reinforce their importance as therapeutics for human health. However, their application has presented difficulties due to the molecules' size, sensitivity to degradation, and rapid elimination from the bloodstream. For some years now, work has been underway to obtain new drug delivery systems to provide adequate therapeutic concentrations for these cytokines, decrease their toxicity and prolong their half-life in the circulation. Although different research groups have presented various formulations that encapsulate IFNs, to date, there is no formulation approved for use in humans. The current review exhibits an updated summary of all encapsulation forms presented in the scientific literature for IFN-α, IFN-ß, and IFN-γ, from the year 1996 to the year 2021, considering parameters such as: encapsulating matrix, route of administration, target, advantages, and disadvantages of each formulation.
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Affiliation(s)
- Thelvia I. Ramos
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción P.O. Box 160-C, Chile; (T.I.R.); (C.A.V.-A.); (S.P.S.); (N.C.P.)
- Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas—ESPE, Sangolquí 171103, Ecuador
| | - Carlos A. Villacis-Aguirre
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción P.O. Box 160-C, Chile; (T.I.R.); (C.A.V.-A.); (S.P.S.); (N.C.P.)
| | - Nelson Santiago Vispo
- School of Biological Sciences and Engineering, Yachay Tech University, Hda. San José s/n y Proyecto Yachay, Urcuquí 100119, Ecuador;
| | | | - Seidy Pedroso Santana
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción P.O. Box 160-C, Chile; (T.I.R.); (C.A.V.-A.); (S.P.S.); (N.C.P.)
| | - Natalie C. Parra
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción P.O. Box 160-C, Chile; (T.I.R.); (C.A.V.-A.); (S.P.S.); (N.C.P.)
| | - Jorge Roberto Toledo Alonso
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción P.O. Box 160-C, Chile; (T.I.R.); (C.A.V.-A.); (S.P.S.); (N.C.P.)
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12
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Sego TJ, Aponte-Serrano JO, Gianlupi JF, Glazier JA. Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection. BMC Biol 2021; 19:196. [PMID: 34496857 PMCID: PMC8424622 DOI: 10.1186/s12915-021-01115-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The biophysics of an organism span multiple scales from subcellular to organismal and include processes characterized by spatial properties, such as the diffusion of molecules, cell migration, and flow of intravenous fluids. Mathematical biology seeks to explain biophysical processes in mathematical terms at, and across, all relevant spatial and temporal scales, through the generation of representative models. While non-spatial, ordinary differential equation (ODE) models are often used and readily calibrated to experimental data, they do not explicitly represent the spatial and stochastic features of a biological system, limiting their insights and applications. However, spatial models describing biological systems with spatial information are mathematically complex and computationally expensive, which limits the ability to calibrate and deploy them and highlights the need for simpler methods able to model the spatial features of biological systems. RESULTS In this work, we develop a formal method for deriving cell-based, spatial, multicellular models from ODE models of population dynamics in biological systems, and vice versa. We provide examples of generating spatiotemporal, multicellular models from ODE models of viral infection and immune response. In these models, the determinants of agreement of spatial and non-spatial models are the degree of spatial heterogeneity in viral production and rates of extracellular viral diffusion and decay. We show how ODE model parameters can implicitly represent spatial parameters, and cell-based spatial models can generate uncertain predictions through sensitivity to stochastic cellular events, which is not a feature of ODE models. Using our method, we can test ODE models in a multicellular, spatial context and translate information to and from non-spatial and spatial models, which help to employ spatiotemporal multicellular models using calibrated ODE model parameters. We additionally investigate objects and processes implicitly represented by ODE model terms and parameters and improve the reproducibility of spatial, stochastic models. CONCLUSION We developed and demonstrate a method for generating spatiotemporal, multicellular models from non-spatial population dynamics models of multicellular systems. We envision employing our method to generate new ODE model terms from spatiotemporal and multicellular models, recast popular ODE models on a cellular basis, and generate better models for critical applications where spatial and stochastic features affect outcomes.
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Affiliation(s)
- T J Sego
- Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, IN, USA.
| | - Josua O Aponte-Serrano
- Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, IN, USA
| | - Juliano F Gianlupi
- Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, IN, USA
| | - James A Glazier
- Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, IN, USA
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13
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Muller CP. Can integrated post-exposure vaccination against SARS-COV2 mitigate severe disease? THE LANCET REGIONAL HEALTH. EUROPE 2021; 5:100118. [PMID: 34027513 PMCID: PMC8127950 DOI: 10.1016/j.lanepe.2021.100118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Claude P. Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
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Perelson AS, Ke R. Mechanistic Modeling of SARS-CoV-2 and Other Infectious Diseases and the Effects of Therapeutics. Clin Pharmacol Ther 2021; 109:829-840. [PMID: 33410134 DOI: 10.1002/cpt.2160] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022]
Abstract
Modern viral kinetic modeling and its application to therapeutics is a field that attracted the attention of the medical, pharmaceutical, and modeling communities during the early days of the AIDS epidemic. Its successes led to applications of modeling methods not only to HIV but a plethora of other viruses, such as hepatitis C virus (HCV), hepatitis B virus and cytomegalovirus, which along with HIV cause chronic diseases, and viruses such as influenza, respiratory syncytial virus, West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which generally cause acute infections. Here we first review the historical development of mathematical models to understand HIV and HCV infections and the effects of treatment by fitting the models to clinical data. We then focus on recent efforts and contributions of applying these models towards understanding SARS-CoV-2 infection and highlight outstanding questions where modeling can provide crucial insights and help to optimize nonpharmaceutical and pharmaceutical interventions of the coronavirus disease 2019 (COVID-19) pandemic. The review is written from our personal perspective emphasizing the power of simple target cell limited models that provided important insights and then their evolution into more complex models that captured more of the virology and immunology. To quote Albert Einstein, "Everything should be made as simple as possible, but not simpler," and this idea underlies the modeling we describe below.
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Affiliation(s)
- Alan S Perelson
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Ruian Ke
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
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