1
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Dobrovolny HM. Mathematical Modeling of Virus-Mediated Syncytia Formation: Past Successes and Future Directions. Results Probl Cell Differ 2024; 71:345-370. [PMID: 37996686 DOI: 10.1007/978-3-031-37936-9_17] [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] [Indexed: 11/25/2023]
Abstract
Many viruses have the ability to cause cells to fuse into large multi-nucleated cells, known as syncytia. While the existence of syncytia has long been known and its importance in helping spread viral infection within a host has been understood, few mathematical models have incorporated syncytia formation or examined its role in viral dynamics. This review examines mathematical models that have incorporated virus-mediated cell fusion and the insights they have provided on how syncytia can change the time course of an infection. While the modeling efforts are limited, they show promise in helping us understand the consequences of syncytia formation if future modeling efforts can be coupled with appropriate experimental efforts to help validate the models.
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Affiliation(s)
- Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, USA.
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2
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Padmanabhan P, Dixit NM. Modelling how increased Cathepsin B/L and decreased TMPRSS2 usage for cell entry by the SARS-CoV-2 Omicron variant may affect the efficacy and synergy of TMPRSS2 and Cathepsin B/L inhibitors. J Theor Biol 2023; 572:111568. [PMID: 37393986 DOI: 10.1016/j.jtbi.2023.111568] [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: 02/13/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
The SARS-CoV-2 Omicron variant harbours many mutations in its spike protein compared to the original SARS-CoV-2 strain, which may alter its ability to enter cells, cell tropism, and response to interventions blocking virus entry. To elucidate these effects, we developed a mathematical model of SARS-CoV-2 entry into target cells and applied it to analyse recent in vitro data. SARS-CoV-2 can enter cells via two pathways, one using the host proteases Cathepsin B/L and the other using the host protease TMPRSS2. We found enhanced entry efficiency of the Omicron variant in cells where the original strain preferentially used Cathepsin B/L and reduced efficiency where it used TMPRSS2. The Omicron variant thus appears to have evolved to use the Cathepsin B/L pathway better but at the expense of its ability to use the TMPRSS2 pathway compared to the original strain. We estimated >4-fold enhanced efficiency of the Omicron variant in entry via the Cathepsin B/L pathway and >3-fold reduced efficiency via the TMPRSS2 pathway compared to the original or other strains in a cell type-dependent manner. Our model predicted that Cathepsin B/L inhibitors would be more efficacious and TMPRSS2 inhibitors less efficacious in blocking Omicron variant entry into cells than the original strain. Furthermore, model predictions suggested that drugs simultaneously targeting the two pathways would exhibit synergy. The maximum synergy and drug concentrations yielding it would differ for the Omicron variant compared to the original strain. Our findings provide insights into the cell entry mechanisms of the Omicron variant and have implications for intervention targeting these mechanisms.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane 4072, Australia.
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India; Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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3
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Han M, Cantaloube-Ferrieu V, Xie M, Armani-Tourret M, Woottum M, Pagès JC, Colin P, Lagane B, Benichou S. HIV-1 cell-to-cell spread overcomes the virus entry block of non-macrophage-tropic strains in macrophages. PLoS Pathog 2022; 18:e1010335. [PMID: 35622876 PMCID: PMC9182568 DOI: 10.1371/journal.ppat.1010335] [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: 02/04/2022] [Revised: 06/09/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022] Open
Abstract
Macrophages (MΦ) are increasingly recognized as HIV-1 target cells involved in the pathogenesis and persistence of infection. Paradoxically, in vitro infection assays suggest that virus isolates are mostly T-cell-tropic and rarely MΦ-tropic. The latter are assumed to emerge under CD4+ T-cell paucity in tissues such as the brain or at late stage when the CD4 T-cell count declines. However, assays to qualify HIV-1 tropism use cell-free viral particles and may not fully reflect the conditions of in vivo MΦ infection through cell-to-cell viral transfer. Here, we investigated the capacity of viruses expressing primary envelope glycoproteins (Envs) with CCR5 and/or CXCR4 usage from different stages of infection, including transmitted/founder Envs, to infect MΦ by a cell-free mode and through cell-to-cell transfer from infected CD4+ T cells. The results show that most viruses were unable to enter MΦ as cell-free particles, in agreement with the current view that non-M-tropic viruses inefficiently use CD4 and/or CCR5 or CXCR4 entry receptors on MΦ. In contrast, all viruses could be effectively cell-to-cell transferred to MΦ from infected CD4+ T cells. We further showed that viral transfer proceeded through Env-dependent cell-cell fusion of infected T cells with MΦ targets, leading to the formation of productively infected multinucleated giant cells. Compared to cell-free infection, infected T-cell/MΦ contacts showed enhanced interactions of R5 M- and non-M-tropic Envs with CD4 and CCR5, resulting in a reduced dependence on receptor expression levels on MΦ for viral entry. Altogether, our results show that virus cell-to-cell transfer overcomes the entry block of isolates initially defined as non-macrophage-tropic, indicating that HIV-1 has a more prevalent tropism for MΦ than initially suggested. This sheds light into the role of this route of virus cell-to-cell transfer to MΦ in CD4+ T cell rich tissues for HIV-1 transmission, dissemination and formation of tissue viral reservoirs.
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Affiliation(s)
- Mingyu Han
- Institut Cochin, Inserm U1016, Paris, France
- CNRS, UMR8104, Paris, France
- Université de Paris, Paris, France
| | | | - Maorong Xie
- Institut Cochin, Inserm U1016, Paris, France
- CNRS, UMR8104, Paris, France
- Université de Paris, Paris, France
| | | | - Marie Woottum
- Institut Cochin, Inserm U1016, Paris, France
- CNRS, UMR8104, Paris, France
- Université de Paris, Paris, France
| | - Jean-Christophe Pagès
- Institut RESTORE, Université de Toulouse, CNRS U-5070, EFS, ENVT, Inserm U1301, Toulouse, France
| | - Philippe Colin
- Infinity, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - Bernard Lagane
- Infinity, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
- * E-mail: (BL); (SB)
| | - Serge Benichou
- Institut Cochin, Inserm U1016, Paris, France
- CNRS, UMR8104, Paris, France
- Université de Paris, Paris, France
- * E-mail: (BL); (SB)
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4
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Pedersen JG, Egedal JH, Packard TA, Thavachelvam K, Xie G, van der Sluis RM, Greene WC, Roan NR, Jakobsen MR. Cell-Extrinsic Priming Increases Permissiveness of CD4+ T Cells to Human Immunodeficiency Virus Infection by Increasing C-C Chemokine Receptor Type 5 Co-receptor Expression and Cellular Activation Status. Front Microbiol 2021; 12:763030. [PMID: 34899645 PMCID: PMC8661899 DOI: 10.3389/fmicb.2021.763030] [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: 08/23/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
The chemokine receptor CCR5 is expressed on multiple cell types, including macrophages, dendritic cells, and T cells, and is the major co-receptor used during HIV transmission. Using a standard αCD3/CD28 in vitro stimulation protocol to render CD4+ T cells from PBMCs permissive to HIV infection, we discovered that the percentage of CCR5+ T cells was significantly elevated in CD4+ T cells when stimulated in the presence of peripheral blood mononuclear cells (PBMCs) as compared to when stimulated as purified CD4+ T cells. This indicated that environmental factors unique to the T-PBMCs condition affect surface expression of CCR5 on CD4+ T cells. Conditioned media from αCD3/CD28-stimulated PBMCs induced CCR5 expression in cultures of unstimulated cells. Cytokine profile analysis of these media suggests IL-12 as an inducer of CCR5 expression. Mass cytometric analysis showed that stimulated T-PBMCs exhibited a uniquely activated phenotype compared to T-Pure. In line with increased CCR5 expression and activation status in stimulated T-PBMCs, CD4+ T cells from these cultures were more susceptible to infection by CCR5-tropic HIV-1 as compared with T-Pure cells. These results suggest that in order to increase ex vivo infection rates of blood-derived CD4+ T cells, standard stimulation protocols used in HIV infection studies should implement T-PBMCs or purified CD4+ T cells should be supplemented with IL-12.
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Affiliation(s)
| | - Johanne H Egedal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Gladstone Institute of Virology, San Francisco, CA, United States
| | - Thomas A Packard
- Gladstone Institute of Virology, San Francisco, CA, United States
| | | | - Guorui Xie
- Gladstone Institute of Virology, San Francisco, CA, United States.,Department of Urology, University of California, San Francisco, San Francisco, CA, United States
| | - Renée Marije van der Sluis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - Warner C Greene
- Gladstone Institute of Virology, San Francisco, CA, United States
| | - Nadia R Roan
- Gladstone Institute of Virology, San Francisco, CA, United States.,Department of Urology, University of California, San Francisco, San Francisco, CA, United States
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5
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Garg AK, Mittal S, Padmanabhan P, Desikan R, Dixit NM. Increased B Cell Selection Stringency In Germinal Centers Can Explain Improved COVID-19 Vaccine Efficacies With Low Dose Prime or Delayed Boost. Front Immunol 2021; 12:776933. [PMID: 34917089 PMCID: PMC8669483 DOI: 10.3389/fimmu.2021.776933] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
The efficacy of COVID-19 vaccines appears to depend in complex ways on the vaccine dosage and the interval between the prime and boost doses. Unexpectedly, lower dose prime and longer prime-boost intervals have yielded higher efficacies in clinical trials. To elucidate the origins of these effects, we developed a stochastic simulation model of the germinal center (GC) reaction and predicted the antibody responses elicited by different vaccination protocols. The simulations predicted that a lower dose prime could increase the selection stringency in GCs due to reduced antigen availability, resulting in the selection of GC B cells with higher affinities for the target antigen. The boost could relax this selection stringency and allow the expansion of the higher affinity GC B cells selected, improving the overall response. With a longer dosing interval, the decay in the antigen with time following the prime could further increase the selection stringency, amplifying this effect. The effect remained in our simulations even when new GCs following the boost had to be seeded by memory B cells formed following the prime. These predictions offer a plausible explanation of the observed paradoxical effects of dosage and dosing interval on vaccine efficacy. Tuning the selection stringency in the GCs using prime-boost dosages and dosing intervals as handles may help improve vaccine efficacies.
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Affiliation(s)
- Amar K. Garg
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Soumya Mittal
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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6
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Desikan R, Antia R, Dixit NM. Physical 'strength' of the multi-protein chain connecting immune cells: Does the weakest link limit antibody affinity maturation?: The weakest link in the multi-protein chain facilitating antigen acquisition by B cells in germinal centres limits antibody affinity maturation. Bioessays 2021; 43:e2000159. [PMID: 33448042 DOI: 10.1002/bies.202000159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
Abstract
The affinities of antibodies (Abs) for their target antigens (Ags) gradually increase in vivo following an infection or vaccination, but reach saturation at values well below those realisable in vitro. This 'affinity ceiling' could in many cases restrict our ability to fight infections and compromise vaccines. What determines the affinity ceiling has been an unresolved question for decades. Here, we argue that it arises from the strength of the chain of protein complexes that is pulled by B cells during the process of Ag acquisition. The affinity ceiling is determined by the strength of the weakest link in the chain. We identify the weakest link and show that the resulting affinity ceiling can explain the Ab affinities realized in vivo, providing a conceptual understanding of Ab affinity maturation. We explore plausible evolutionary underpinnings of the affinity ceiling, examine supporting evidence and alternative hypotheses and discuss implications for vaccination strategies.
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Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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7
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Padmanabhan P, Desikan R, Dixit NM. Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection. PLoS Comput Biol 2020; 16:e1008461. [PMID: 33290397 PMCID: PMC7748278 DOI: 10.1371/journal.pcbi.1008461] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 12/18/2020] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
The entry of SARS-CoV-2 into target cells requires the activation of its surface spike protein, S, by host proteases. The host serine protease TMPRSS2 and cysteine proteases Cathepsin B/L can activate S, making two independent entry pathways accessible to SARS-CoV-2. Blocking the proteases prevents SARS-CoV-2 entry in vitro. This blockade may be achieved in vivo through 'repurposing' drugs, a potential treatment option for COVID-19 that is now in clinical trials. Here, we found, surprisingly, that drugs targeting the two pathways, although independent, could display strong synergy in blocking virus entry. We predicted this synergy first using a mathematical model of SARS-CoV-2 entry and dynamics in vitro. The model considered the two pathways explicitly, let the entry efficiency through a pathway depend on the corresponding protease expression level, which varied across cells, and let inhibitors compromise the efficiency in a dose-dependent manner. The synergy predicted was novel and arose from effects of the drugs at both the single cell and the cell population levels. Validating our predictions, available in vitro data on SARS-CoV-2 and SARS-CoV entry displayed this synergy. Further, analysing the data using our model, we estimated the relative usage of the two pathways and found it to vary widely across cell lines, suggesting that targeting both pathways in vivo may be important and synergistic given the broad tissue tropism of SARS-CoV-2. Our findings provide insights into SARS-CoV-2 entry into target cells and may help improve the deployability of drug combinations targeting host proteases required for the entry.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queesnsland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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8
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Nandy B, Saurabh S, Sahoo AK, Dixit NM, Maiti PK. The SPL7013 dendrimer destabilizes the HIV-1 gp120-CD4 complex. NANOSCALE 2015; 7:18628-18641. [PMID: 26495445 DOI: 10.1039/c5nr04632g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The poly (l-lysine)-based SPL7013 dendrimer with naphthalene disulphonate surface groups blocks the entry of HIV-1 into target cells and is in clinical trials for development as a topical microbicide. Its mechanism of action against R5 HIV-1, the HIV-1 variant implicated in transmission across individuals, remains poorly understood. Using docking and fully atomistic MD simulations, we find that SPL7013 binds tightly to R5 gp120 in the gp120-CD4 complex but weakly to gp120 alone. Further, the binding, although to multiple regions of gp120, does not occlude the CD4 binding site on gp120, suggesting that SPL7013 does not prevent the binding of R5 gp120 to CD4. Using MD simulations to compute binding energies of several docked structures, we find that SPL7013 binding to gp120 significantly weakens the gp120-CD4 complex. Finally, we use steered molecular dynamics (SMD) to study the kinetics of the dissociation of the gp120-CD4 complex in the absence of the dendrimer and with the dendrimer bound in each of the several stable configurations to gp120. We find that SPL7013 significantly lowers the force required to rupture the gp120-CD4 complex and accelerates its dissociation. Taken together, our findings suggest that SPL7013 compromises the stability of the R5 gp120-CD4 complex, potentially preventing the accrual of the requisite number of gp120-CD4 complexes across the virus-cell interface, thereby blocking virus entry.
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Affiliation(s)
- Bidisha Nandy
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India.
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9
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Regoes RR, Magnus C. The role of chance in primate lentiviral infectivity: from protomer to host organism. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 129:327-51. [PMID: 25595809 DOI: 10.1016/bs.pmbts.2014.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Infection is best described as a stochastic process. Whether a host becomes infected upon exposure has a strong random element. The same applies to cells exposed to virions. In this review, we show how the mathematical formalism for stochastic processes has been used to describe and understand the infection by the Human and Simian Immunodeficiency Virus on different levels. We survey quantitative studies on the establishment of infection in the host (the organismal level) and on the infection of target cells (the cellular and molecular level). We then discuss how a synthesis of the approaches across these levels could give rise to a predictive framework for assessing the efficacy of microbicides and vaccines.
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Affiliation(s)
- Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
| | - Carsten Magnus
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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10
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Mathematical model of multivalent virus-antibody complex formation in humans following acute and chronic HIV infections. J Math Biol 2014; 71:513-32. [PMID: 25190279 DOI: 10.1007/s00285-014-0826-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/29/2014] [Indexed: 10/24/2022]
Abstract
Antibodies that bind viral surface proteins can limit the spread of the infection through neutralizing and non-neutralizing functions. During both acute and chronic Human Immunodeficiency Virus infection, antibody-virion immune complexes are formed, but fail to ensure protection. In this study, we develop a mathematical model of multivalent antibody binding and use it to determine the dynamical interactions that lead to immune complexes formation and the role of complexes with increased numbers of bound antibodies in the pathogenesis of the disease. We compare our predictions with published temporal virus and immune complex data from acute infected patients. Finally, we derive quantitative and qualitative conditions needed for antibody-induced protection.
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11
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Dumas F, Preira P, Salomé L. Membrane organization of virus and target cell plays a role in HIV entry. Biochimie 2014; 107 Pt A:22-7. [PMID: 25193376 PMCID: PMC7126522 DOI: 10.1016/j.biochi.2014.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/22/2014] [Indexed: 01/08/2023]
Abstract
The initial steps of the Human Immunodeficiency Virus (HIV) replication cycle play a crucial role that arbitrates viral tropism and infection efficiency. Before the release of its genome into the host cell cytoplasm, viruses operate a complex sequence of events that take place at the plasma membrane of the target cell. The first step is the binding of the HIV protein envelope (Env) to the cellular receptor CD4. This triggers conformational changes of the gp120 viral protein that allow its interaction with a co-receptor that can be either CCR5 or CXCR4, defining the tropism of the virus entering the cell. This sequential interaction finally drives the fusion of the viral and host cell membrane or to the endocytosis of the viruses. Here, we discuss how the membrane composition and organization of both the virus and the target cell can affect these steps and thus influence the capability of the viruses to infect cells. An overview of lipid role in HIV infection is proposed. We discuss the influence of lipid composition on HIV early steps of infection. We discuss the role of membrane organization an dynamics in HIV entry.
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Affiliation(s)
- Fabrice Dumas
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France.
| | - Pascal Preira
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse, France
| | - Laurence Salomé
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse, France.
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12
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Sheik-Khalil E, Bray MA, Özkaya Şahin G, Scarlatti G, Jansson M, Carpenter AE, Fenyö EM. Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition. BMC Infect Dis 2014; 14:472. [PMID: 25176034 PMCID: PMC4261578 DOI: 10.1186/1471-2334-14-472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/18/2014] [Indexed: 12/04/2022] Open
Abstract
Background Standardized techniques to detect HIV-neutralizing antibody responses are of great importance in the search for an HIV vaccine. Methods Here, we present a high-throughput, high-content automated plaque reduction (APR) assay based on automated microscopy and image analysis that allows evaluation of neutralization and inhibition of cell-cell fusion within the same assay. Neutralization of virus particles is measured as a reduction in the number of fluorescent plaques, and inhibition of cell-cell fusion as a reduction in plaque area. Results We found neutralization strength to be a significant factor in the ability of virus to form syncytia. Further, we introduce the inhibitory concentration of plaque area reduction (ICpar) as an additional measure of antiviral activity, i.e. fusion inhibition. Conclusions We present an automated image based high-throughput, high-content HIV plaque reduction assay. This allows, for the first time, simultaneous evaluation of neutralization and inhibition of cell-cell fusion within the same assay, by quantifying the reduction in number of plaques and mean plaque area, respectively. Inhibition of cell-to-cell fusion requires higher quantities of inhibitory reagent than inhibition of virus neutralization. Electronic supplementary material The online version of this article (doi:10.1186/1471-2334-14-472) contains supplementary material, which is available to authorized users.
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13
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Savage AM, Li Y, Matolyak LE, Doncel GF, Turner SR, Gandour RD. Anti-HIV Activities of Precisely Defined, Semirigid, Carboxylated Alternating Copolymers. J Med Chem 2014; 57:6354-63. [DOI: 10.1021/jm401913w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alice M. Savage
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yi Li
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lindsay E. Matolyak
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Gustavo F. Doncel
- CONRAD, Eastern Virginia Medical School, 601 Colley Avenue, Norfolk, Virginia 23507, United States
| | - S. Richard Turner
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Richard D. Gandour
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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14
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Co-expression of foreign proteins tethered to HIV-1 envelope glycoprotein on the cell surface by introducing an intervening second membrane-spanning domain. PLoS One 2014; 9:e96790. [PMID: 24804933 PMCID: PMC4013048 DOI: 10.1371/journal.pone.0096790] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/11/2014] [Indexed: 11/19/2022] Open
Abstract
The envelope glycoprotein (Env) of human immunodeficiency virus type I (HIV-1) mediates membrane fusion. To analyze the mechanism of HIV-1 Env-mediated membrane fusion, it is desirable to determine the expression level of Env on the cell surface. However, the quantification of Env by immunological staining is often hampered by the diversity of HIV-1 Env and limited availability of universal antibodies that recognize different Envs with equal efficiency. To overcome this problem, here we linked a tag protein called HaloTag at the C-terminus of HIV-1 Env. To relocate HaloTag to the cell surface, we introduced a second membrane-spanning domain (MSD) between Env and HaloTag. The MSD of transmembrane protease serine 11D, a type II transmembrane protein, successfully relocated HaloTag to the cell surface. The surface level of Env can be estimated indirectly by staining HaloTag with a specific membrane-impermeable fluorescent ligand. This tagging did not compromise the fusogenicity of Env drastically. Furthermore, fusogenicity of Env was preserved even after the labeling with the ligands. We have also found that an additional foreign peptide or protein such as C34 or neutralizing single-chain variable fragment (scFv) can be linked to the C-terminus of the HaloTag protein. Using these constructs, we were able to determine the required length of C34 and critical residues of neutralizing scFv for blocking membrane fusion, respectively.
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15
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Stock P, Barin B, Hatano H, Rogers R, Roland M, Lee TH, Busch M, Deeks S. Reduction of HIV persistence following transplantation in HIV-infected kidney transplant recipients. Am J Transplant 2014; 14:1136-41. [PMID: 24698537 PMCID: PMC4012326 DOI: 10.1111/ajt.12699] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/14/2014] [Accepted: 02/03/2014] [Indexed: 01/25/2023]
Abstract
Chronic inflammation may contribute to human immunodeficiency virus (HIV) persistence through a number of potential pathways. We explored the impact of immunosuppressant therapy on peripheral blood measures of HIV persistence following kidney transplantation. Stored plasma and peripheral blood mononuclear cells prior to transplantation and at weeks 12, 26, 52 and 104 posttransplant were obtained from 91 transplant recipients. In a multivariate model, higher pretransplant plasma HIV RNA level (p < 0.0001) and a longer duration of follow-up posttransplant (p = 0.09) were associated with higher posttransplant plasma HIV RNA levels. A higher baseline HIV DNA (p < 0.0001) was significantly associated with higher HIV DNA levels posttransplant, while higher CD4+ T cell count (p = 0.001), sirolimus use (p = 0.04) and a longer duration of follow-up (p = 0.06) were associated with lower posttransplant HIV DNA levels. The association between sirolimus exposure and lower frequency of cells containing HIV DNA levels posttransplant suggest that the immune-modifying drugs may affect the level of HIV persistence during effect therapy. Future studies of sirolimus as a reservoir-modifying agent are warranted.
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Affiliation(s)
| | | | - H. Hatano
- University of California, San Francisco
| | | | | | - T.-H Lee
- Blood Systems Research Institute
| | - M. Busch
- Blood Systems Research Institute
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Abstract
Virions of the Human Immunodeficiency Virus (HIV) infect cells by first attaching with their surface spikes to the CD4 receptor on target cells. This leads to conformational changes in the viral spikes, enabling the virus to engage a coreceptor, commonly CCR5 or CXCR4, and consecutively to insert the fusion peptide into the cellular membrane. Finally, the viral and the cellular membranes fuse. The HIV spike is a trimer consisting of three identical heterodimers composed of the gp120 and gp41 envelope proteins. Each of the gp120 proteins in the trimer is capable of attaching to the CD4 receptor and the coreceptor, and each of the three gp41 units harbors a fusion domain. It is still under debate how many of the envelope subunits within a given trimer have to bind to the CD4 receptors and to the coreceptors, and how many gp41 protein fusion domains are required for fusion. These numbers are referred to as subunit stoichiometries. We present a mathematical framework for estimating these parameters individually by analyzing infectivity assays with pseudotyped viruses. We find that the number of spikes that are engaged in mediating cell entry and the distribution of the spike number play important roles for the estimation of the subunit stoichiometries. Our model framework also shows why it is important to subdivide the question of the number of functional subunits within one trimer into the three different subunit stoichiometries. In a second step, we extend our models to study whether the subunits within one trimer cooperate during receptor binding and fusion. As an example for how our models can be applied, we reanalyze a data set on subunit stoichiometries. We find that two envelope proteins have to engage with CD4-receptors and coreceptors and that two fusion proteins must be revealed within one trimer for viral entry. Our study is motivated by the mechanism of HIV entry but the experimental technique and the model framework can be extended to other viral systems as well.
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Padmanabhan P, Dixit NM. Mathematical model of viral kinetics in vitro estimates the number of E2-CD81 complexes necessary for hepatitis C virus entry. PLoS Comput Biol 2011; 7:e1002307. [PMID: 22174670 PMCID: PMC3234214 DOI: 10.1371/journal.pcbi.1002307] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 10/31/2011] [Indexed: 02/07/2023] Open
Abstract
Interaction between the hepatitis C virus (HCV) envelope protein E2 and the host receptor CD81 is essential for HCV entry into target cells. The number of E2-CD81 complexes necessary for HCV entry has remained difficult to estimate experimentally. Using the recently developed cell culture systems that allow persistent HCV infection in vitro, the dependence of HCV entry and kinetics on CD81 expression has been measured. We reasoned that analysis of the latter experiments using a mathematical model of viral kinetics may yield estimates of the number of E2-CD81 complexes necessary for HCV entry. Here, we constructed a mathematical model of HCV viral kinetics in vitro, in which we accounted explicitly for the dependence of HCV entry on CD81 expression. Model predictions of viral kinetics are in quantitative agreement with experimental observations. Specifically, our model predicts triphasic viral kinetics in vitro, where the first phase is characterized by cell proliferation, the second by the infection of susceptible cells and the third by the growth of cells refractory to infection. By fitting model predictions to the above data, we were able to estimate the threshold number of E2-CD81 complexes necessary for HCV entry into human hepatoma-derived cells. We found that depending on the E2-CD81 binding affinity, between 1 and 13 E2-CD81 complexes are necessary for HCV entry. With this estimate, our model captured data from independent experiments that employed different HCV clones and cells with distinct CD81 expression levels, indicating that the estimate is robust. Our study thus quantifies the molecular requirements of HCV entry and suggests guidelines for intervention strategies that target the E2-CD81 interaction. Further, our model presents a framework for quantitative analyses of cell culture studies now extensively employed to investigate HCV infection. The interaction between the hepatitis C virus (HCV) envelope protein E2 and the host cell surface receptor CD81 is critical for HCV entry into hepatocytes and presents a promising drug and vaccine target. Yet, the number of E2-CD81 complexes that must be formed between a virus and a target cell to enable viral entry remains unknown. Direct observation of the E2-CD81 complexes preceding viral entry has not been possible. We constructed a mathematical model of HCV viral kinetics in vitro and using it to analyze data from recent cell culture studies obtained estimates of the threshold number of E2-CD81 complexes necessary for HCV entry. We found that depending on the E2-CD81 binding affinity, between 1 and 13 complexes are necessary for HCV entry into human hepatoma-derived cells. Our study thus presents new, quantitative insights into the molecular requirements of HCV entry, which may serve as a guideline for intervention strategies targeting the E2-CD81 interaction. Further, our study shows that HCV viral kinetics in vitro can be described using a mathematical model, thus facilitating quantitative analyses of the wealth of data now emanating from cell culture studies of HCV infection.
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Affiliation(s)
- Pranesh Padmanabhan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
- Bioinformatics Centre, Indian Institute of Science, Bangalore, India
- * E-mail:
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