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Symmonds J, Gaufin T, Xu C, Raehtz KD, Ribeiro RM, Pandrea I, Apetrei C. Making a Monkey out of Human Immunodeficiency Virus/Simian Immunodeficiency Virus Pathogenesis: Immune Cell Depletion Experiments as a Tool to Understand the Immune Correlates of Protection and Pathogenicity in HIV Infection. Viruses 2024; 16:972. [PMID: 38932264 DOI: 10.3390/v16060972] [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] [Received: 03/27/2024] [Revised: 05/31/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Understanding the underlying mechanisms of HIV pathogenesis is critical for designing successful HIV vaccines and cure strategies. However, achieving this goal is complicated by the virus's direct interactions with immune cells, the induction of persistent reservoirs in the immune system cells, and multiple strategies developed by the virus for immune evasion. Meanwhile, HIV and SIV infections induce a pandysfunction of the immune cell populations, making it difficult to untangle the various concurrent mechanisms of HIV pathogenesis. Over the years, one of the most successful approaches for dissecting the immune correlates of protection in HIV/SIV infection has been the in vivo depletion of various immune cell populations and assessment of the impact of these depletions on the outcome of infection in non-human primate models. Here, we present a detailed analysis of the strategies and results of manipulating SIV pathogenesis through in vivo depletions of key immune cells populations. Although each of these methods has its limitations, they have all contributed to our understanding of key pathogenic pathways in HIV/SIV infection.
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Affiliation(s)
- Jen Symmonds
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Thaidra Gaufin
- Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA
| | - Cuiling Xu
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Kevin D Raehtz
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ivona Pandrea
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Cristian Apetrei
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Mainou E, Berendam SJ, Obregon-Perko V, Uffman EA, Phan CT, Shaw GM, Bar KJ, Kumar MR, Fray EJ, Siliciano JM, Siliciano RF, Silvestri G, Permar SR, Fouda GG, McCarthy J, Chahroudi A, Chan C, Conway JM. Comparative analysis of within-host dynamics of acute infection and viral rebound dynamics in postnatally SHIV-infected ART-treated infant rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595130. [PMID: 38826467 PMCID: PMC11142125 DOI: 10.1101/2024.05.21.595130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Viral dynamics of acute HIV infection and HIV rebound following suspension of antiretroviral therapy may be qualitatively similar but must differ given, for one, development of adaptive immune responses. Understanding the differences of acute HIV infection and viral rebound dynamics in pediatric populations may provide insights into the mechanisms of viral control with potential implications for vaccine design and the development of effective targeted therapeutics for infants and children. Mathematical models have been a crucial tool to elucidate the complex processes driving viral infections within the host. Traditionally, acute HIV infection has been modeled with a standard model of viral dynamics initially developed to explore viral decay during treatment, while viral rebound has necessitated extensions of that standard model to incorporate explicit immune responses. Previous efforts to fit these models to viral load data have underscored differences between the two infection stages, such as increased viral clearance rate and increased death rate of infected cells during rebound. However, these findings have been predicated on viral load measurements from disparate adult individuals. In this study, we aim to bridge this gap, in infants, by comparing the dynamics of acute infection and viral rebound within the same individuals by leveraging an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model. Ten infant Rhesus macaques (RMs) orally challenged with SHIV.C.CH505 375H dCT and given ART at 8 weeks post-infection. These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We use the HIV standard viral dynamics model fitted to viral load measurements in a nonlinear mixed effects framework. We find that the primary difference between acute infection and rebound is the increased death rate of infected cells during rebound. We use these findings to generate hypotheses on the effects of adaptive immune responses. We leverage these findings to formulate hypotheses to elucidate the observed results and provide arguments to support the notion that delayed viral rebound is characterized by a stronger CD8+ T cell response.
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Affiliation(s)
- Ellie Mainou
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Emilie A Uffman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Caroline T Phan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mithra R Kumar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily J Fray
- Department of Biochemistry and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | - Janice McCarthy
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Jessica M Conway
- Department of Mathematics, Pennsylvania State University, University Park, PA, USA
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Phan T, Conway JM, Pagane N, Kreig J, Sambaturu N, Iyaniwura S, Li JZ, Ribeiro RM, Ke R, Perelson AS. Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592318. [PMID: 38746144 PMCID: PMC11092759 DOI: 10.1101/2024.05.03.592318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Most people living with HIV-1 experience rapid viral rebound once antiretroviral therapy is interrupted; however, a small fraction remain in viral remission for an extended duration. Understanding the factors that determine whether viral rebound is likely after treatment interruption can enable the development of optimal treatment regimens and therapeutic interventions to potentially achieve a functional cure for HIV-1. We built upon the theoretical framework proposed by Conway and Perelson to construct dynamic models of virus-immune interactions to study factors that influence viral rebound dynamics. We evaluated these models using viral load data from 24 individuals following antiretroviral therapy interruption. The best-performing model accurately captures the heterogeneity of viral dynamics and highlights the importance of the effector cell expansion rate. Our results show that post-treatment controllers and non-controllers can be distinguished based on the effector cell expansion rate in our models. Furthermore, these results demonstrate the potential of using dynamic models incorporating an effector cell response to understand early viral rebound dynamics post-antiretroviral therapy interruption.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jessica M Conway
- Department of Mathematics, Pennsylvania State University, College Township, PA, USA
- Department of Biology, Pennsylvania State University, College Township, PA, USA
| | - Nicole Pagane
- Program in Computational and Systems Biology, Massachusetts Institute of Technology; Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - Jasmine Kreig
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Narmada Sambaturu
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Sarafa Iyaniwura
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jonathan Z Li
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- Santa Fe Institute, Santa Fe, NM, USA
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4
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Ciupe SM, Conway JM. Incorporating Intracellular Processes in Virus Dynamics Models. Microorganisms 2024; 12:900. [PMID: 38792730 PMCID: PMC11124127 DOI: 10.3390/microorganisms12050900] [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: 04/13/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
In-host models have been essential for understanding the dynamics of virus infection inside an infected individual. When used together with biological data, they provide insight into viral life cycle, intracellular and cellular virus-host interactions, and the role, efficacy, and mode of action of therapeutics. In this review, we present the standard model of virus dynamics and highlight situations where added model complexity accounting for intracellular processes is needed. We present several examples from acute and chronic viral infections where such inclusion in explicit and implicit manner has led to improvement in parameter estimates, unification of conclusions, guidance for targeted therapeutics, and crossover among model systems. We also discuss trade-offs between model realism and predictive power and highlight the need of increased data collection at finer scale of resolution to better validate complex models.
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Affiliation(s)
- Stanca M. Ciupe
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Penn State University, State College, PA 16802, USA
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Chung WJ, Connick E, Wodarz D. Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants. Virus Evol 2024; 10:vead084. [PMID: 38516655 PMCID: PMC10956502 DOI: 10.1093/ve/vead084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 12/05/2023] [Accepted: 01/08/2024] [Indexed: 03/23/2024] Open
Abstract
In secondary lymphoid tissues, human immunodeficiency virus (HIV) can replicate in both the follicular and extrafollicular compartments. Yet, virus is concentrated in the follicular compartment in the absence of antiretroviral therapy, in part due to the lack of cytotoxic T lymphocyte (CTL)-mediated activity there. CTLs home to the extrafollicular compartment, where they can suppress virus load to relatively low levels. We use mathematical models to show that this compartmentalization can explain seemingly counter-intuitive observations. First, it can explain the observed constancy of the viral decline slope during antiviral therapy in the peripheral blood, irrespective of the presence of CTL in Simian Immunodeficiency Virus (SIV)-infected macaques, under the assumption that CTL-mediated lysis significantly contributes to virus suppression. Second, it can account for the relatively long times it takes for CTL escape mutants to emerge during chronic infection even if CTL-mediated lysis is responsible for virus suppression. The reason is the heterogeneity in CTL activity and the consequent heterogeneity in selection pressure between the follicular and extrafollicular compartments. Hence, to understand HIV dynamics more thoroughly, this analysis highlights the importance of measuring virus populations separately in the extrafollicular and follicular compartments rather than using virus load in peripheral blood as an observable; this hides the heterogeneity between compartments that might be responsible for the particular patterns seen in the dynamics and evolution of the HIV in vivo.
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Affiliation(s)
- Wen-Jian Chung
- Department of Population Health and Disease Prevention, University of California, 856 Health Sciences Quad, Irvine, CA 92697, USA
| | - Elizabeth Connick
- Division of Infectious Diseases, Department of Medicine, University of Arizona, 1501 N. Campbell Ave, P.O. Box 245039, Tucson, AZ 85724, USA
| | - Dominik Wodarz
- Department of Ecology, Behavior, and Evolution, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Docken SS, McCormick K, Pampena MB, Samer S, Lindemuth E, Pinkevych M, Viox EG, Wu Y, Schlub TE, Cromer D, Keele BF, Paiardini M, Betts MR, Bar KJ, Davenport MP. Preferential selection of viral escape mutants by CD8+ T cell 'sieving' of SIV reactivation from latency. PLoS Pathog 2023; 19:e1011755. [PMID: 38032851 PMCID: PMC10688670 DOI: 10.1371/journal.ppat.1011755] [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: 06/30/2023] [Accepted: 10/15/2023] [Indexed: 12/02/2023] Open
Abstract
HIV rapidly rebounds after interruption of antiretroviral therapy (ART). HIV-specific CD8+ T cells may act to prevent early events in viral reactivation. However, the presence of viral immune escape mutations may limit the effect of CD8+ T cells on viral rebound. Here, we studied the impact of CD8 immune pressure on post-treatment rebound of barcoded SIVmac293M in 14 Mamu-A*01 positive rhesus macaques that initiated ART on day 14, and subsequently underwent two analytic treatment interruptions (ATIs). Rebound following the first ATI (seven months after ART initiation) was dominated by virus that retained the wild-type sequence at the Mamu-A*01 restricted Tat-SL8 epitope. By the end of the two-month treatment interruption, the replicating virus was predominantly escaped at the Tat-SL8 epitope. Animals reinitiated ART for 3 months prior to a second treatment interruption. Time-to-rebound and viral reactivation rate were significantly slower during the second treatment interruption compared to the first. Tat-SL8 escape mutants dominated early rebound during the second treatment interruption, despite the dominance of wild-type virus in the proviral reservoir. Furthermore, the escape mutations detected early in the second treatment interruption were well predicted by those replicating at the end of the first, indicating that escape mutant virus in the second interruption originated from the latent reservoir as opposed to evolving de novo post rebound. SL8-specific CD8+ T cell levels in blood prior to the second interruption were marginally, but significantly, higher (median 0.73% vs 0.60%, p = 0.016). CD8+ T cell depletion approximately 95 days after the second treatment interruption led to the reappearance of wild-type virus. This work suggests that CD8+ T cells can actively suppress the rebound of wild-type virus, leading to the dominance of escape mutant virus after treatment interruption.
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Affiliation(s)
- Steffen S. Docken
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Kevin McCormick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - M. Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sadia Samer
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Emily Lindemuth
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Elise G. Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Yuhuang Wu
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Timothy E. Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Deborah Cromer
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
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Policicchio BB, Cardozo-Ojeda EF, Xu C, Ma D, He T, Raehtz KD, Sivanandham R, Kleinman AJ, Perelson AS, Apetrei C, Pandrea I, Ribeiro RM. CD8 + T cells control SIV infection using both cytolytic effects and non-cytolytic suppression of virus production. Nat Commun 2023; 14:6657. [PMID: 37863982 PMCID: PMC10589330 DOI: 10.1038/s41467-023-42435-8] [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] [Received: 08/18/2022] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Whether CD8+ T lymphocytes control human immunodeficiency virus infection by cytopathic or non-cytopathic mechanisms is not fully understood. Multiple studies highlighted non-cytopathic effects, but one hypothesis is that cytopathic effects of CD8+ T cells occur before viral production. Here, to examine the role of CD8+ T cells prior to virus production, we treated SIVmac251-infected macaques with an integrase inhibitor combined with a CD8-depleting antibody, or with either reagent alone. We analyzed the ensuing viral dynamics using a mathematical model that included infected cells pre- and post- viral DNA integration to compare different immune effector mechanisms. Macaques receiving the integrase inhibitor alone experienced greater viral load decays, reaching lower nadirs on treatment, than those treated also with the CD8-depleting antibody. Models including CD8+ cell-mediated reduction of viral production (non-cytolytic) were found to best explain the viral profiles across all macaques, in addition an effect in killing infected cells pre-integration (cytolytic) was supported in some of the best models. Our results suggest that CD8+ T cells have both a cytolytic effect on infected cells before viral integration, and a direct, non-cytolytic effect by suppressing viral production.
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Affiliation(s)
- Benjamin B Policicchio
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | | | - Cuiling Xu
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Dongzhu Ma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Tianyu He
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kevin D Raehtz
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Ranjit Sivanandham
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Adam J Kleinman
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Cristian Apetrei
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Ivona Pandrea
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- Laboratório de Biomatemática, Faculdade de Medicina da Universidade de Lisboa (previous address), Lisboa, Portugal.
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Nakamura-Hoshi M, Nomura T, Nishizawa M, Hau TTT, Yamamoto H, Okazaki M, Ishii H, Yonemitsu K, Suzaki Y, Ami Y, Matano T. HTLV-1 Proliferation after CD8 + Cell Depletion by Monoclonal Anti-CD8 Antibody Administration in Latently HTLV-1-Infected Cynomolgus Macaques. Microbiol Spectr 2023; 11:e0151823. [PMID: 37367230 PMCID: PMC10434050 DOI: 10.1128/spectrum.01518-23] [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] [Received: 04/11/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) induces chronic asymptomatic latent infection with a substantial proviral load but without significant viral replication in vivo. Cumulative studies have indicated involvement of CD8-positive (CD8+) cells, including virus-specific CD8+ T cells in the control of HTLV-1 replication. However, whether HTLV-1 expression from latently infected cells in vivo occurs in the absence of CD8+ cells remains unclear. Here, we examined the impact of CD8+ cell depletion by monoclonal anti-CD8 antibody administration on proviral load in HTLV-1-infected cynomolgus macaques. Five cynomolgus macaques were infected with HTLV-1 by inoculation with HTLV-1-producing cells. Administration of monoclonal anti-CD8 antibody in the chronic phase resulted in complete depletion of peripheral CD8+ T cells for approximately 2 months. All five macaques showed an increase in proviral load following CD8+ cell depletion, which peaked just before the reappearance of peripheral CD8+ T cells. Tax-specific CD8+ T-cell responses were detected in these recovered CD8+ T cells. Importantly, anti-HTLV-1 antibodies also increased after CD8+ cell depletion, indicating HTLV-1 antigen expression. These results provide evidence indicating that HTLV-1 can proliferate from the latent phase in the absence of CD8+ cells and suggest that CD8+ cells are responsible for the control of HTLV-1 replication. IMPORTANCE HTLV-1 can cause serious diseases such as adult T-cell leukemia (ATL) in humans after chronic asymptomatic latent infection with substantial proviral load. Proviruses are detectable in peripheral lymphocytes in HTLV-1 carriers, and the association of a higher proviral load with a higher risk of disease progression has been observed. However, neither substantial viral structural protein expression nor viral replication was detectable in vivo. Cumulative studies have indicated involvement of CD8+ cells, including virus-specific CD8+ T cells in the control of HTLV-1 replication. In the present study, we showed that CD8+ cell depletion by monoclonal anti-CD8 antibody administration results in HTLV-1 expression and an increase in proviral load in HTLV-1-infected cynomolgus macaques. Our results indicate that HTLV-1 can proliferate in the absence of CD8+ cells, suggesting that CD8+ cells are responsible for the control of HTLV-1 replication. This study provides insights into the mechanism of virus-host immune interaction in latent HTLV-1 infection.
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Affiliation(s)
| | - Takushi Nomura
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Masako Nishizawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Trang Thi Thu Hau
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Yamamoto
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Midori Okazaki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Ishii
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenzo Yonemitsu
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuriko Suzaki
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasushi Ami
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
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9
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Li S, Zhang MY, Yuan J, Zhang YX. Nano-vaccines for gene delivery against HIV-1 infection. Expert Rev Vaccines 2023; 22:315-326. [PMID: 36945780 DOI: 10.1080/14760584.2023.2193266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Over the last four decades, human immunodeficiency virus type 1 (HIV-1) infection has been a major public health concern. It is acknowledged that an effective vaccine remains the best hope for eliminating the HIV-1 pandemic. The prophylaxis of HIV-1 infection remains a central theme because of the absence of an available HIV-1 vaccine. The incapability of conventional delivery strategies to induce potent immunity is a crucial task to overcome and ultimately lead to a major obstacle in HIV-1 vaccine research. AREAS COVERED The literature search was conducted in the following databases: PubMed, Web of Science, and Embase. Nano-platforms based vaccines have proven prophylaxis of various diseases for effectively activating the immune system. Nano-vaccines, including non-viral and viral vectored nano-vaccines, are in a position to improve the effectiveness of HIV-1 antigen delivery and enhance the innate and adaptive immune responses against HIV-1. Compared to traditional vaccination strategies, genetic immunization can elicit a long-term immune response to provide protective immunity for HIV-1 prevention. EXPERT OPINION The research progress on nano-vaccines for gene delivery against HIV-1 was discussed. The vaccine strategies based on nano-platforms that are being applied to stimulate effective HIV-1-specific cellular and humoral immune responses were particularly emphasized.
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Affiliation(s)
- Shuang Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jie Yuan
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
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10
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CD8 + T cell depletion does not induce an expansion of viral reservoir in HIV model. Nat Microbiol 2023; 8:191-192. [PMID: 36690862 DOI: 10.1038/s41564-023-01321-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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11
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Statzu M, Jin W, Fray EJ, Wong AKH, Kumar MR, Ferrer E, Docken SS, Pinkevych M, McBrien JB, Fennessey CM, Keele BF, Liang S, Harper JL, Mutascio S, Franchitti L, Wang H, Cicetti D, Bosinger SE, Carnathan DG, Vanderford TH, Margolis DM, Garcia-Martinez JV, Chahroudi A, Paiardini M, Siliciano J, Davenport MP, Kulpa DA, Siliciano RS, Silvestri G. CD8 + lymphocytes do not impact SIV reservoir establishment under ART. Nat Microbiol 2023; 8:299-308. [PMID: 36690860 PMCID: PMC9894752 DOI: 10.1038/s41564-022-01311-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/15/2022] [Indexed: 01/24/2023]
Abstract
Persistence of the human immunodeficiency virus type-1 (HIV-1) latent reservoir in infected individuals remains a problem despite fully suppressive antiretroviral therapy (ART). While reservoir formation begins during acute infection, the mechanisms responsible for its establishment remain unclear. CD8+ T cells are important during the initial control of viral replication. Here we examined the effect of CD8+ T cells on formation of the latent reservoir in simian immunodeficiency virus (SIV)-infected macaques by performing experimental CD8+ depletion either before infection or before early (that is, day 14 post-infection) ART initiation. We found that CD8+ depletion resulted in slower decline of viremia, indicating that CD8+ lymphocytes reduce the average lifespan of productively infected cells during acute infection and early ART, presumably through SIV-specific cytotoxic T lymphocyte (CTL) activity. However, CD8+ depletion did not change the frequency of infected CD4+ T cells in the blood or lymph node as measured by the total cell-associated viral DNA or intact provirus DNA assay. In addition, the size of the persistent reservoir remained the same when measuring the kinetics of virus rebound after ART interruption. These data indicate that during early SIV infection, the viral reservoir that persists under ART is established largely independent of CTL control.
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Grants
- P30 AI050409 NIAID NIH HHS
- 75N91019D00024 NCI NIH HHS
- P51 OD011132 NIH HHS
- R01 AI143414 NIAID NIH HHS
- UM1 AI164562 NIAID NIH HHS
- UM1 AI164567 NIAID NIH HHS
- R01 AI125064 NIAID NIH HHS
- CU | National Cancer Institute, Cairo University (NCI)
- National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024/HHSN261201500003I.
- This work was supported by UM1AI164562, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases (to G.S., D.A.K., M.P.1), and NIH NIAID R01-AI143414 (to G.S. and D.A.K), and R01-AI125064 (to G.S., A.C., D.A.K.).
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Affiliation(s)
- Maura Statzu
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Wang Jin
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Kam Ho Wong
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Ferrer
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steffen S Docken
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Mykola Pinkevych
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Julia B McBrien
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shan Liang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Justin L Harper
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Simona Mutascio
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Hong Wang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Davide Cicetti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Diane G Carnathan
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David M Margolis
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - J Victor Garcia-Martinez
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - Ann Chahroudi
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Janet Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Deanna A Kulpa
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Robert S Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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12
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Abstract
Posttreatment controllers (PTCs) are rare HIV-infected individuals who can limit viral rebound after antiretroviral therapy interruption (ATI), but the mechanisms of this remain unclear. To investigate these mechanisms, we quantified various HIV RNA transcripts (via reverse transcription droplet digital PCR [RT-ddPCR]) and cellular transcriptomes (via RNA-seq) in blood cells from PTCs and noncontrollers (NCs) before and two time points after ATI. HIV transcription initiation did not significantly increase after ATI in PTCs or in NCs, whereas completed HIV transcripts increased at early ATI in both groups and multiply-spliced HIV transcripts increased only in NCs. Compared to NCs, PTCs showed lower levels of HIV DNA, more cell-associated HIV transcripts per total RNA at all times, no increase in multiply-spliced HIV RNA at early or late ATI, and a reduction in the ratio of completed/elongated HIV RNA after early ATI. NCs expressed higher levels of the IL-7 pathway before ATI and expressed higher levels of multiple cytokine, inflammation, HIV transcription, and cell death pathways after ATI. Compared to the baseline, the NCs upregulated interferon and cytokine (especially TNF) pathways during early and late ATI, whereas PTCs upregulated interferon and p53 pathways only at early ATI and downregulated gene translation during early and late ATI. In NCs, viral rebound after ATI is associated with increases in HIV transcriptional completion and splicing, rather than initiation. Differences in HIV and cellular transcription may contribute to posttreatment control, including an early limitation of spliced HIV RNA, a delayed reduction in completed HIV transcripts, and the differential expression of the IL-7, p53, and TNF pathways. IMPORTANCE The findings presented here provide new insights into how HIV and cellular gene expression change after stopping ART in both noncontrollers and posttreatment controllers. Posttreatment control is associated with an early ability to limit increases in multiply-spliced HIV RNA, a delayed (and presumably immune-mediated) ability to reverse an initial rise in processive/completed HIV transcripts, and multiple differences in cellular gene expression pathways. These differences may represent correlates or mechanisms of posttreatment control and may provide insight into the development and/or monitoring of therapeutic strategies that are aimed at a functional HIV cure.
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13
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Multiple modes of antigen exposure induce clonotypically diverse epitope-specific CD8+ T cells across multiple tissues in nonhuman primates. PLoS Pathog 2022; 18:e1010611. [PMID: 35797339 PMCID: PMC9262242 DOI: 10.1371/journal.ppat.1010611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Antigen-specific CD8+ T cells play a key role in the host’s antiviral response. T cells recognize viral epitopes via the T cell receptor (TCR), which contains the complementarity-determining region-3 (CDR3), comprising the variable, diversity and joining regions of the TCRβ gene. During chronic simian immunodeficiency virus (SIV) infection of Asian macaque nonhuman primates, tissue-specific clonotypes are identifiable among SIV-specific CD8+ T cells. Here, we sought to determine level of antigen exposure responsible for the tissue-specific clonotypic structure. We examined whether the priming event and/or chronic antigen exposure is response for tissue-specific TCR repertoires. We evaluated the TCR repertoire of SIV-specific CD8+ T cells after acute antigen exposure following inoculation with a SIV DNA vaccine, longitudinally during the acute and chronic phases of SIV, and after administration of antiretrovirals (ARVs). Finally, we assessed the TCR repertoire of cytomegalovirus (CMV)-specific CD8+ T cells to establish if TCR tissue-specificity is shared among viruses that chronically replicate. TCR sequences unique to anatomical sites were identified after acute antigen exposure via vaccination and upon acute SIV infection. Tissue-specific clones also persisted into chronic infection and the clonotypic structure continued to evolve after ARV administration. Finally, tissue-specific clones were also observed in CMV-specific CD8+ T cells. Together, these data suggest that acute antigen priming is sufficient to induce tissue-specific clones and that this clonal hierarchy can persist when antigen loads are naturally or therapeutically reduced, providing mechanistic insight into tissue-residency. During viral infection, CD8+ T cells that bind a specific viral particle through their T cell receptor (TCR) can help control viral replication. Infection with simian immunodeficiency virus (SIV) in nonhuman primates is a commonly used animal model of HIV infection. Here we assess the TCR sequences of CD8+ T cells specific for the SIV gag gene during vaccination with an experimental SIV vaccine and throughout SIV infection, including during treatment with antiretroviral drugs. We identified unique TCR sequences in specific tissues, which were not identified in the blood or in other tissues, both in response to vaccination and throughout SIV infection with and without antiretroviral treatment. We also observed tissue-specific TCR sequences in CD8+ T cells specific for Cytomegalovius, another virus that causes a chronic infection in humans. Together, our findings identify the conditions required to form a tissue-specific TCR repertoire.
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14
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Kumar Singh A, Padwal V, Palav H, Velhal S, Nagar V, Patil P, Patel V. Highly dampened HIV-specific cytolytic effector T cell responses define viremic non-progression. Immunobiology 2022; 227:152234. [PMID: 35671626 DOI: 10.1016/j.imbio.2022.152234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/30/2022] [Indexed: 11/05/2022]
Abstract
This study reports on HIV-specific T cell responses in HIV-1 infected Viremic Non-Progressors (VNPs), a rare group of people living with HIV that exhibit asymptomatic infection over several years accompanied by stable CD4+ T cell counts in spite of ongoing viral replication. We attempted to identify key virus-specific functional attributes that could underlie the apparently paradoxical virus-host equilibrium observed in VNPs. Our results revealed modulation of HIV-specific CD4+ and CD8+ effector T cell responses in VNPs towards a dominant non-cytolytic profile with concomitantly diminished degranulation (CD107a+) ability. Further, the HIV specific CD8+ effector T cell response was primarily enriched for MIP-1β producing cells. As expected, concordant with better viral suppression, VCs exhibit a robust cytolytic T cell response. Interestingly, PuPs shared features common to both these responses but did not exhibit a CD4+ central memory IFN-γ producing Gag-specific response that was shared by both non-progressor (VC and VNP) groups, suggesting CD4 helper response is critical for non-progression. Our study also revealed that cytolytic response in VNPs is primarily limited to polyfunctional cells while both monofunctional and polyfunctional cells significantly contribute to cytolytic responses in VCs. To further understand mechanisms underlying the unique HIV-specific effector T cell response described here in VNPs we also evaluated and demonstrated a possible role for altered gut homing in these individuals. Our findings inform immunotherapeutic interventions to achieve functional cures in the context of ART resistance and serious non AIDS events.
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Affiliation(s)
- Amit Kumar Singh
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Varsha Padwal
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Harsha Palav
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Shilpa Velhal
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Vidya Nagar
- Department of Medicine, Grant Medical College & Sir J. J. Group of Hospitals, Mumbai, Maharashtra, India
| | - Priya Patil
- Department of Medicine, Grant Medical College & Sir J. J. Group of Hospitals, Mumbai, Maharashtra, India
| | - Vainav Patel
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India.
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15
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Barbian HJ, Seaton MS, Narasipura SD, Wallace J, Rajan R, Sha BE, Al-Harthi L. β-catenin regulates HIV latency and modulates HIV reactivation. PLoS Pathog 2022; 18:e1010354. [PMID: 35255110 PMCID: PMC8939789 DOI: 10.1371/journal.ppat.1010354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/22/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
Latency is the main obstacle towards an HIV cure, with cure strategies aiming to either elicit or prevent viral reactivation. While these strategies have shown promise, they have only succeeded in modulating latency in a fraction of the latent HIV reservoir, suggesting that the mechanisms controlling HIV latency are not completely understood, and that comprehensive latency modulation will require targeting of multiple latency maintenance pathways. We show here that the transcriptional co-activator and the central mediator of canonical Wnt signaling, β-catenin, inhibits HIV transcription in CD4+ T cells via TCF-4 LTR binding sites. Further, we show that inhibiting the β-catenin pathway reactivates HIV in a primary TCM cell model of HIV latency, primary cells from cART-controlled HIV donors, and in CD4+ latent cell lines. β-catenin inhibition or activation also enhanced or inhibited the activity of several classes of HIV latency reversing agents, respectively, in these models, with significant synergy of β-catenin and each LRA class tested. In sum, we identify β-catenin as a novel regulator of HIV latency in vitro and ex vivo, adding new therapeutic targets that may be combined for comprehensive HIV latency modulation in HIV cure efforts.
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Affiliation(s)
- Hannah J. Barbian
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Melanie S. Seaton
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Srinivas D. Narasipura
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Jennillee Wallace
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Reshma Rajan
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Beverly E. Sha
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinios United States of America
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, United States of America
- * E-mail:
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16
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White JA, Simonetti FR, Beg S, McMyn NF, Dai W, Bachmann N, Lai J, Ford WC, Bunch C, Jones JL, Ribeiro RM, Perelson AS, Siliciano JD, Siliciano RF. Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proc Natl Acad Sci U S A 2022; 119:e2120326119. [PMID: 35110411 PMCID: PMC8833145 DOI: 10.1073/pnas.2120326119] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4+ T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ∼3 mo, the decay slope changes, and CD4+ T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie F McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas Bachmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - William C Ford
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christina Bunch
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joyce L Jones
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ruy M Ribeiro
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- HHMI, Baltimore, MD 21205
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17
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Arya RK, Verros GD, Thapliyal D. Towards a Mathematical Model for the Viral Progression in the Pharynx. Healthcare (Basel) 2021; 9:healthcare9121766. [PMID: 34946492 PMCID: PMC8701019 DOI: 10.3390/healthcare9121766] [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: 11/23/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/03/2022] Open
Abstract
In this work, a comprehensive model for the viral progression in the pharynx has been developed. This one-dimension model considers both Fickian diffusion and convective flow coupled with chemical reactions, such as virus population growth, infected and uninfected cell accumulation as well as virus clearance. The effect of a sterilizing agent such as an alcoholic solution on the viral progression in the pharynx was taken into account and a parametric analysis for the effect of kinetic rate parameters on virus propagation was made. Moreover, different conditions caused by further medical treatment, such as a decrease in virus yield per infected cell, were examined. It is shown that the infection fails to establish by decreasing the virus yield per infected cell. It is believed that this work could be used to further investigate the medical treatment of viral progression in the pharynx.
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Affiliation(s)
- Raj Kumar Arya
- Department of Chemical Engineering, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar 144011, India;
- Correspondence: or
| | - George D. Verros
- Laboratory of Polymer and Colour Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki (AUTH), P.O. Box 454, Plagiari, Epanomi, 57500 Thessaloniki, Greece;
| | - Devyani Thapliyal
- Department of Chemical Engineering, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar 144011, India;
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18
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Sharan R, Ganatra SR, Bucsan AN, Cole J, Singh DK, Alvarez X, Gough M, Alvarez C, Blakley A, Ferdin J, Thippeshappa R, Singh B, Escobedo R, Shivanna V, Dick EJ, Hall-Ursone S, Khader SA, Mehra S, Rengarajan J, Kaushal D. Antiretroviral therapy timing impacts latent tuberculosis infection reactivation in a tuberculosis/simian immunodeficiency virus coinfection model. J Clin Invest 2021; 132:153090. [PMID: 34855621 PMCID: PMC8803324 DOI: 10.1172/jci153090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Studies using the nonhuman primate model of Mycobacteriumtuberculosis/simian immunodeficiency virus coinfection have revealed protective CD4+ T cell–independent immune responses that suppress latent tuberculosis infection (LTBI) reactivation. In particular, chronic immune activation rather than the mere depletion of CD4+ T cells correlates with reactivation due to SIV coinfection. Here, we administered combinatorial antiretroviral therapy (cART) 2 weeks after SIV coinfection to study whether restoration of CD4+ T cell immunity occurred more broadly, and whether this prevented reactivation of LTBI compared to cART initiated 4 weeks after SIV. Earlier initiation of cART enhanced survival, led to better control of viral replication, and reduced immune activation in the periphery and lung vasculature, thereby reducing the rate of SIV-induced reactivation. We observed robust CD8+ T effector memory responses and significantly reduced macrophage turnover in the lung tissue. However, skewed CD4+ T effector memory responses persisted and new TB lesions formed after SIV coinfection. Thus, reactivation of LTBI is governed by very early events of SIV infection. Timing of cART is critical in mitigating chronic immune activation. The potential novelty of these findings mainly relates to the development of a robust animal model of human M. tuberculosis/HIV coinfection that allows the testing of underlying mechanisms.
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Affiliation(s)
- Riti Sharan
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Shashank R Ganatra
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Allison N Bucsan
- Department of Molecular Microbiology, Washington University, St. Louis, St. Louis, United States of America
| | - Journey Cole
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Dhiraj K Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Xavier Alvarez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Maya Gough
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Cynthia Alvarez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Alyssa Blakley
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Justin Ferdin
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Rajesh Thippeshappa
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Bindu Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Ruby Escobedo
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Vinay Shivanna
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Edward J Dick
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Shannan Hall-Ursone
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University, St. Louis, St. Louis, United States of America
| | - Smriti Mehra
- Divisions of Bacteriology and Parasitology, Tulane National Primate Research Center, Covington, United States of America
| | - Jyothi Rengarajan
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, United States of America
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, United States of America
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19
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Bricker KM, Chahroudi A, Mavigner M. New Latency Reversing Agents for HIV-1 Cure: Insights from Nonhuman Primate Models. Viruses 2021; 13:1560. [PMID: 34452425 PMCID: PMC8402914 DOI: 10.3390/v13081560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 01/30/2023] Open
Abstract
Antiretroviral therapy (ART) controls human immunodeficiency virus 1 (HIV-1) replication and prevents disease progression but does not eradicate HIV-1. The persistence of a reservoir of latently infected cells represents the main barrier to a cure. "Shock and kill" is a promising strategy involving latency reversing agents (LRAs) to reactivate HIV-1 from latently infected cells, thus exposing the infected cells to killing by the immune system or clearance agents. Here, we review advances to the "shock and kill" strategy made through the nonhuman primate (NHP) model, highlighting recently identified latency reversing agents and approaches such as mimetics of the second mitochondrial activator of caspase (SMACm), experimental CD8+ T cell depletion, immune checkpoint blockade (ICI), and toll-like receptor (TLR) agonists. We also discuss the advantages and limits of the NHP model for HIV cure research and methods developed to evaluate the efficacy of in vivo treatment with LRAs in NHPs.
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Affiliation(s)
- Katherine M. Bricker
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Emory + Children’s Center for Childhood Infections and Vaccines, Atlanta, GA 30322, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
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20
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Rausch JW, Le Grice SFJ. Characterizing the Latent HIV-1 Reservoir in Patients with Viremia Suppressed on cART: Progress, Challenges, and Opportunities. Curr HIV Res 2021; 18:99-113. [PMID: 31889490 PMCID: PMC7475929 DOI: 10.2174/1570162x18666191231105438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Modern combination antiretroviral therapy (cART) can bring HIV-1 in blood plasma to level undetectable by standard tests, prevent the onset of acquired immune deficiency syndrome (AIDS), and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, cART is not curative, as within a few weeks of treatment cessation, HIV viremia in most patients rebounds to pre-cART levels. The primary source of this rebound, and the principal barrier to a cure, is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of resting memory CD4+ T cells. In this review, prevailing models for how the latent reservoir is established and maintained, residual viremia and viremic rebound upon withdrawal of cART, and the types and characteristics of cells harboring latent HIV-1 will be discussed. Selected technologies currently being used to advance our understanding of HIV latency will also be presented, as will a perspective on which areas of advancement are most essential for producing the next generation of HIV-1 therapeutics.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
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21
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Abstract
The CD8+ T cell noncytotoxic antiviral response (CNAR) was discovered during studies of asymptomatic HIV-infected subjects more than 30 years ago. In contrast to CD8+ T cell cytotoxic lymphocyte (CTL) activity, CNAR suppresses HIV replication without target cell killing. This activity has characteristics of innate immunity: it acts on all retroviruses and thus is neither epitope specific nor HLA restricted. The HIV-associated CNAR does not affect other virus families. It is mediated, at least in part, by a CD8+ T cell antiviral factor (CAF) that blocks HIV transcription. A variety of assays used to measure CNAR/CAF and the effects on other retrovirus infections are described. Notably, CD8+ T cell noncytotoxic antiviral responses have now been observed with other virus families but are mediated by different cytokines. Characterizing the protein structure of CAF has been challenging despite many biologic, immunologic, and molecular studies. It represents a low-abundance protein that may be identified by future next-generation sequencing approaches. Since CNAR/CAF is a natural noncytotoxic activity, it could provide promising strategies for HIV/AIDS therapy, cure, and prevention.
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Affiliation(s)
- Maelig G Morvan
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Fernando C Teque
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Jay A Levy
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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22
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Kula-Pacurar A, Rodari A, Darcis G, Van Lint C. Shocking HIV-1 with immunomodulatory latency reversing agents. Semin Immunol 2021; 51:101478. [PMID: 33972164 DOI: 10.1016/j.smim.2021.101478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
The "shock-and-kill" strategy is one of the most explored HIV-1 cure approaches to eliminate latent virus. This strategy is based on HIV-1 reactivation using latency reversing agents (LRAs) to reactivate latent proviruses (the "shock" phase) and to induce subsequent elimination of the reactivated cells by immune responses or virus-induced cytopathic effects (the "kill" phase). Studies using immunomodulatory LRAs such as blockers of immune checkpoint molecules, toll-like receptor agonists, cytokines and CD8+ T cell depleting antibodies showed promising potential as LRAs inducing directly or indirectly cellular pathways known to control HIV transcription. However, the precise molecular mechanisms by which these immunomodulatory LRAs reverse latency remain incompletely understood. Together with the heterogenous nature of HIV-1 latency, this lack of understanding complicates efforts to develop more efficient and safer cure strategies. Hence, deciphering those mechanisms is pivotal in designing approaches to eliminate latent HIV infection.
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Affiliation(s)
- Anna Kula-Pacurar
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Anthony Rodari
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, Liège, Belgium
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium.
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23
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Cardozo-Ojeda EF, Duke ER, Peterson CW, Reeves DB, Mayer BT, Kiem HP, Schiffer JT. Thresholds for post-rebound SHIV control after CCR5 gene-edited autologous hematopoietic cell transplantation. eLife 2021; 10:57646. [PMID: 33432929 PMCID: PMC7803377 DOI: 10.7554/elife.57646] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/27/2020] [Indexed: 01/10/2023] Open
Abstract
Autologous, CCR5 gene-edited hematopoietic stem and progenitor cell (HSPC) transplantation is a promising strategy for achieving HIV remission. However, only a fraction of HSPCs can be edited ex vivo to provide protection against infection. To project the thresholds of CCR5-edition necessary for HIV remission, we developed a mathematical model that recapitulates blood T cell reconstitution and plasma simian-HIV (SHIV) dynamics from SHIV-1157ipd3N4-infected pig-tailed macaques that underwent autologous transplantation with CCR5 gene editing. The model predicts that viral control can be obtained following analytical treatment interruption (ATI) when: (1) transplanted HSPCs are at least fivefold higher than residual endogenous HSPCs after total body irradiation and (2) the fraction of protected HSPCs in the transplant achieves a threshold (76–94%) sufficient to overcome transplantation-dependent loss of SHIV immunity. Under these conditions, if ATI is withheld until transplanted gene-modified cells engraft and reconstitute to a steady state, spontaneous viral control is projected to occur.
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Affiliation(s)
- E Fabian Cardozo-Ojeda
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
| | - Elizabeth R Duke
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States.,Department of Medicine, University of Washington, Seattle, United States
| | - Christopher W Peterson
- Department of Medicine, University of Washington, Seattle, United States.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Daniel B Reeves
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
| | - Bryan T Mayer
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
| | - Hans-Peter Kiem
- Department of Medicine, University of Washington, Seattle, United States.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Pathology, University of Washington, Seattle, United States
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States.,Department of Medicine, University of Washington, Seattle, United States.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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24
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Ganatra SR, Bucşan AN, Alvarez X, Kumar S, Chatterjee A, Quezada M, Fish A, Singh DK, Singh B, Sharan R, Lee TH, Shanmugasundaram U, Velu V, Khader SA, Mehra S, Rengarajan J, Kaushal D. Antiretroviral therapy does not reduce tuberculosis reactivation in a tuberculosis-HIV coinfection model. J Clin Invest 2020; 130:5171-5179. [PMID: 32544085 PMCID: PMC7524506 DOI: 10.1172/jci136502] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/04/2020] [Indexed: 12/12/2022] Open
Abstract
While the advent of combination antiretroviral therapy (ART) has significantly improved survival, tuberculosis (TB) remains the leading cause of death in the HIV-infected population. We used Mycobacterium tuberculosis/simian immunodeficiency virus-coinfected (M. tuberculosis/SIV-coinfected) macaques to model M. tuberculosis/HIV coinfection and study the impact of ART on TB reactivation due to HIV infection. Although ART significantly reduced viral loads and increased CD4+ T cell counts in blood and bronchoalveolar lavage (BAL) samples, it did not reduce the relative risk of SIV-induced TB reactivation in ART-treated macaques in the early phase of treatment. CD4+ T cells were poorly restored specifically in the lung interstitium, despite their significant restoration in the alveolar compartment of the lung as well as in the periphery. IDO1 induction in myeloid cells in the inducible bronchus-associated lymphoid tissue (iBALT) likely contributed to dysregulated T cell homing and impaired lung immunity. Thus, although ART was indispensable for controlling viral replication, restoring CD4+ T cells, and preventing opportunistic infection, it appeared inadequate in reversing the clinical signs of TB reactivation during the relatively short duration of ART administered in this study. This finding warrants the modeling of concurrent treatment of TB and HIV to potentially reduce the risk of reactivation of TB due to HIV to inform treatment strategies in patients with M. tuberculosis/HIV coinfection.
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Affiliation(s)
- Shashank R. Ganatra
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Allison N. Bucşan
- Tulane National Primate Research Center (TNPRC), Covington, Louisiana, USA
| | - Xavier Alvarez
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
- Tulane National Primate Research Center (TNPRC), Covington, Louisiana, USA
| | - Shyamesh Kumar
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ayan Chatterjee
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Melanie Quezada
- Emory Vaccine Center and
- Yerkes National Primate Research Center (YNPRC), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Abigail Fish
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Dhiraj K. Singh
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Bindu Singh
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Riti Sharan
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Tae-Hyung Lee
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Uma Shanmugasundaram
- Emory Vaccine Center and
- Yerkes National Primate Research Center (YNPRC), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Vijayakumar Velu
- Emory Vaccine Center and
- Yerkes National Primate Research Center (YNPRC), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shabaana A. Khader
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Smriti Mehra
- Tulane National Primate Research Center (TNPRC), Covington, Louisiana, USA
| | - Jyothi Rengarajan
- Emory Vaccine Center and
- Yerkes National Primate Research Center (YNPRC), Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center (SNPRC), Texas Biomedical Research Institute, San Antonio, Texas, USA
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25
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Zanoni M, Palesch D, Pinacchio C, Statzu M, Tharp GK, Paiardini M, Chahroudi A, Bosinger SE, Yoon J, Cox B, Silvestri G, Kulpa DA. Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription. PLoS Pathog 2020; 16:e1008821. [PMID: 32941545 PMCID: PMC7523993 DOI: 10.1371/journal.ppat.1008821] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 09/29/2020] [Accepted: 07/18/2020] [Indexed: 12/31/2022] Open
Abstract
MHC-I-restricted, virus-specific cytotoxic CD8+ T cells (CTLs) may control human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication via the recognition and killing of productively infected CD4+ T cells. Several studies in SIV-infected macaques suggest that CD8+ T cells may also decrease virus production by suppressing viral transcription. Here, we show that non-HIV-specific, TCR-activated non-cytolytic CD8+ T cells suppress HIV transcription via a virus- and MHC-independent immunoregulatory mechanism that modulates CD4+ T cell proliferation and activation. We also demonstrate that this CD8+ T cell-mediated effect promotes the survival of infected CD4+ T cells harboring integrated, inducible virus. Finally, we used RNA sequencing and secretome analyses to identify candidate cellular pathways that are involved in the virus-silencing mediated by these CD8+ T cells. This study characterizes a previously undescribed mechanism of immune-mediated HIV silencing that may be involved in the establishment and maintenance of the reservoir under antiretroviral therapy and therefore represent a major obstacle to HIV eradication.
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Affiliation(s)
- Michelle Zanoni
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - David Palesch
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Claudia Pinacchio
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Maura Statzu
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Gregory K. Tharp
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Jack Yoon
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Bryan Cox
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
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26
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Immune outcomes of Zika virus infection in nonhuman primates. Sci Rep 2020; 10:13069. [PMID: 32747639 PMCID: PMC7400481 DOI: 10.1038/s41598-020-69978-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/21/2020] [Indexed: 11/23/2022] Open
Abstract
Although the Zika virus (ZIKV) epidemic is subsiding, immune responses that are important for controlling acute infection have not been definitively characterized. Nonhuman primate (NHP) models were rapidly developed to understand the disease and to test vaccines, and these models have since provided an understanding of the immune responses that correlate with protection during natural infection and vaccination. Here, we infected a small group of male rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques with a minimally passaged Brazilian ZIKV isolate and used multicolor flow cytometry and transcriptional profiling to describe early immune patterns following infection. We found evidence of strong innate antiviral responses together with induction of neutralizing antibodies and T cell responses. We also assessed the relative importance of CD8 T cells in controlling infection by carrying out CD8 T cell depletion in an additional two animals of each species. CD8 depletion appeared to dysregulate early antiviral responses and possibly increase viral persistence, but the absence of CD8 T cells ultimately did not impair control of the virus. Together, these data describe immunological trends in two NHP species during acute ZIKV infection, providing an account of early responses that may be important in controlling infection.
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27
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Nguyen S, Sada-Japp A, Petrovas C, Betts MR. Jigsaw falling into place: A review and perspective of lymphoid tissue CD8+ T cells and control of HIV. Mol Immunol 2020; 124:42-50. [PMID: 32526556 PMCID: PMC7279761 DOI: 10.1016/j.molimm.2020.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/28/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
CD8+ T cells are crucial for immunity against viral infections, including HIV. Several characteristics of CD8+ T cells, such as polyfunctionality and cytotoxicity, have been correlated with effective control of HIV. However, most of these correlates have been established in the peripheral blood. Meanwhile, HIV primarily replicates in lymphoid tissues. Therefore, it is unclear which aspects of CD8+ T cell biology are shared and which are different between blood and lymphoid tissues in the context of HIV infection. In this review, we will recapitulate the latest advancements of our knowledge on lymphoid tissue CD8+ T cells during HIV infection and discuss the insights these advancements might provide for the development of a HIV cure.
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Affiliation(s)
- Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alberto Sada-Japp
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Constantinos Petrovas
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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28
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Pinzone MR, Bertuccio MP, VanBelzen DJ, Zurakowski R, O'Doherty U. Next-Generation Sequencing in a Direct Model of HIV Infection Reveals Important Parallels to and Differences from In Vivo Reservoir Dynamics. J Virol 2020; 94:e01900-19. [PMID: 32051279 PMCID: PMC7163122 DOI: 10.1128/jvi.01900-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) represents a powerful tool to unravel the genetic make-up of the HIV reservoir, but limited data exist on its use in vitro Moreover, most NGS studies do not separate integrated from unintegrated DNA, even though selection pressures on these two forms should be distinct. We reasoned we could use NGS to compare the infection of resting and activated CD4 T cells in vitro to address how the metabolic state affects reservoir formation and dynamics. To address these questions, we obtained HIV sequences 2, 4, and 8 days after NL4-3 infection of metabolically activated and quiescent CD4 T cells (cultured with 2 ng/ml interleukin-7). We compared the composition of integrated and total HIV DNA by isolating integrated HIV DNA using pulsed-field electrophoresis before performing sequencing. After a single-round infection, the majority of integrated HIV DNA was intact in both resting and activated T cells. The decay of integrated intact proviruses was rapid and similar in both quiescent and activated T cells. Defective forms accumulated relative to intact ones analogously to what is observed in vivo Massively deleted viral sequences formed more frequently in resting cells, likely due to lower deoxynucleoside triphosphate (dNTP) levels and the presence of multiple restriction factors. To our surprise, the majority of these deleted sequences did not integrate into the human genome. The use of NGS to study reservoir dynamics in vitro provides a model that recapitulates important aspects of reservoir dynamics. Moreover, separating integrated from unintegrated HIV DNA is important in some clinical settings to properly study selection pressures.IMPORTANCE The major implication of our work is that the decay of intact proviruses in vitro is extremely rapid, perhaps as a result of enhanced expression. Gaining a better understanding of why intact proviruses decay faster in vitro might help the field identify strategies to purge the reservoir in vivo When used wisely, in vitro models are a powerful tool to study the selective pressures shaping the viral landscape. Our finding that massively deleted sequences rarely succeed in integrating has several ramifications. It demonstrates that the total HIV DNA can differ substantially in character from the integrated HIV DNA under certain circumstances. The presence of unintegrated HIV DNA has the potential to obscure selection pressures and confound the interpretation of clinical studies, especially in the case of trials involving treatment interruptions.
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Affiliation(s)
- Marilia Rita Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Paola Bertuccio
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - D Jake VanBelzen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Ryan Zurakowski
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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29
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Nguyen S, Deleage C, Darko S, Ransier A, Truong DP, Agarwal D, Japp AS, Wu VH, Kuri-Cervantes L, Abdel-Mohsen M, Del Rio Estrada PM, Ablanedo-Terrazas Y, Gostick E, Hoxie JA, Zhang NR, Naji A, Reyes-Terán G, Estes JD, Price DA, Douek DC, Deeks SG, Buggert M, Betts MR. Elite control of HIV is associated with distinct functional and transcriptional signatures in lymphoid tissue CD8 + T cells. Sci Transl Med 2019; 11:eaax4077. [PMID: 31852798 PMCID: PMC7265335 DOI: 10.1126/scitranslmed.aax4077] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/03/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
Abstract
The functional properties of circulating CD8+ T cells have been associated with immune control of HIV. However, viral replication occurs predominantly in secondary lymphoid tissues, such as lymph nodes (LNs). We used an integrated single-cell approach to characterize effective HIV-specific CD8+ T cell responses in the LNs of elite controllers (ECs), defined as individuals who suppress viral replication in the absence of antiretroviral therapy (ART). Higher frequencies of total memory and follicle-homing HIV-specific CD8+ T cells were detected in the LNs of ECs compared with the LNs of chronic progressors (CPs) who were not receiving ART. Moreover, HIV-specific CD8+ T cells potently suppressed viral replication without demonstrable cytolytic activity in the LNs of ECs, which harbored substantially lower amounts of CD4+ T cell-associated HIV DNA and RNA compared with the LNs of CPs. Single-cell RNA sequencing analyses further revealed a distinct transcriptional signature among HIV-specific CD8+ T cells from the LNs of ECs, typified by the down-regulation of inhibitory receptors and cytolytic molecules and the up-regulation of multiple cytokines, predicted secreted factors, and components of the protein translation machinery. Collectively, these results provide a mechanistic framework to expedite the identification of novel antiviral factors, highlighting a potential role for the localized deployment of noncytolytic functions as a determinant of immune efficacy against HIV.
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Affiliation(s)
- Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Duc P Truong
- Department of Mathematics, Southern Methodist University, Dallas, TX 75205, USA
| | - Divyansh Agarwal
- Department of Statistics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alberto Sada Japp
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vincent H Wu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Perla M Del Rio Estrada
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico
| | - Yuria Ablanedo-Terrazas
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico
| | - Emma Gostick
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - James A Hoxie
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy R Zhang
- Department of Statistics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ali Naji
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gustavo Reyes-Terán
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, OR 97239, USA
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR 97239, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco General Hospital, San Francisco, CA 94110, USA
| | - Marcus Buggert
- Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, 14186 Stockholm, Sweden
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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30
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Fiege JK, Stone IA, Dumm RE, Waring BM, Fife BT, Agudo J, Brown BD, Heaton NS, Langlois RA. Long-term surviving influenza infected cells evade CD8+ T cell mediated clearance. PLoS Pathog 2019; 15:e1008077. [PMID: 31557273 PMCID: PMC6782110 DOI: 10.1371/journal.ppat.1008077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 10/08/2019] [Accepted: 09/11/2019] [Indexed: 01/02/2023] Open
Abstract
Influenza A virus (IAV) is a seasonal pathogen with the potential to cause devastating pandemics. IAV infects multiple epithelial cell subsets in the respiratory tract, eliciting damage to the lungs. Clearance of IAV is primarily dependent on CD8+ T cells, which must balance control of the infection with immunopathology. Using a virus expressing Cre recombinase to permanently label infected cells in a Cre-inducible reporter mouse, we previously discovered infected club cells that survive both lytic virus replication and CD8+ T cell-mediated clearance. In this study, we demonstrate that ciliated epithelial cells, type I and type II alveolar cells can also become survivor cells. Survivor cells are stable in the lung long-term and demonstrate enhanced proliferation compared to uninfected cells. When we investigated how survivor cells evade CD8+ T cell killing we observed that survivor cells upregulated the inhibitory ligand PD-L1, but survivor cells did not use PD-L1 to evade CD8+ T cell killing. Instead our data suggest that survivor cells are not inherently resistant to CD8+ T cell killing, but instead no longer present IAV antigen and cannot be detected by CD8+ T cells. Finally, we evaluate the failure of CD8+ T cells to kill these previously infected cells. This work demonstrates that additional cell types can survive IAV infection and that these cells robustly proliferate and are stable long term. By sparing previously infected cells, the adaptive immune system may be minimizing pathology associated with IAV infection.
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Affiliation(s)
- Jessica K. Fiege
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Ian A. Stone
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Rebekah E. Dumm
- Duke University School of Medicine, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Barbara M. Waring
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Brian T. Fife
- University of Minnesota, Department of Medicine and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Judith Agudo
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York City, New York, United States of America
| | - Brian D. Brown
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York City, New York, United States of America
| | - Nicholas S. Heaton
- Duke University School of Medicine, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Ryan A. Langlois
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
- * E-mail:
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Sutton MS, Ellis-Connell A, Balgeman AJ, Barry G, Weiler AM, Hetzel SJ, Zhou Y, Lau-Kilby AW, Mason RD, Biris KK, Mascola JR, Sullivan NJ, Roederer M, Friedrich TC, O'Connor SL. CD8β Depletion Does Not Prevent Control of Viral Replication or Protection from Challenge in Macaques Chronically Infected with a Live Attenuated Simian Immunodeficiency Virus. J Virol 2019; 93:e00537-19. [PMID: 31092584 PMCID: PMC6639280 DOI: 10.1128/jvi.00537-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/11/2019] [Indexed: 11/20/2022] Open
Abstract
We evaluated the contribution of CD8αβ+ T cells to control of live-attenuated simian immunodeficiency virus (LASIV) replication during chronic infection and subsequent protection from pathogenic SIV challenge. Unlike previous reports with a CD8α-specific depleting monoclonal antibody (mAb), the CD8β-specific mAb CD8β255R1 selectively depleted CD8αβ+ T cells without also depleting non-CD8+ T cell populations that express CD8α, such as natural killer (NK) cells and γδ T cells. Following infusion with CD8β255R1, plasma viremia transiently increased coincident with declining peripheral CD8αβ+ T cells. Interestingly, plasma viremia returned to predepletion levels even when peripheral CD8αβ+ T cells did not. Although depletion of CD8αβ+ T cells in the lymph node (LN) was incomplete, frequencies of these cells were 3-fold lower (P = 0.006) in animals that received CD8β255R1 than in those that received control IgG. It is possible that these residual SIV-specific CD8αβ+ T cells may have contributed to suppression of viremia during chronic infection. We also determined whether infusion of CD8β255R1 in the LASIV-vaccinated animals increased their susceptibility to infection following intravenous challenge with pathogenic SIVmac239. We found that 7/8 animals infused with CD8β255R1, and 3/4 animals infused with the control IgG, were resistant to SIVmac239 infection. These results suggest that infusion with CD8β255R1 did not eliminate the protection afforded to LASIV vaccination. This provides a comprehensive description of the impact of CD8β255R1 infusion on the immunological composition in cynomolgus macaques, compared to an isotype-matched control IgG, while showing that the control of LASIV viremia and protection from challenge can occur even after CD8β255R1 administration.IMPORTANCE Studies of SIV-infected macaques that deplete CD8+ T cells in vivo with monoclonal antibodies have provided compelling evidence for their direct antiviral role. These studies utilized CD8α-specific mAbs that target both the major (CD8αβ+) and minor (CD8αα+) populations of CD8+ T cells but additionally deplete non-CD8+ T cell populations that express CD8α, such as NK cells and γδ T cells. In the current study, we administered the CD8β-specific depleting mAb CD8β255R1 to cynomolgus macaques chronically infected with a LASIV to selectively deplete CD8αβ+ T cells without removing CD8αα+ lymphocytes. We evaluated the impact on control of virus replication and protection from pathogenic SIVmac239 challenge. These results underscore the utility of CD8β255R1 for studying the direct contribution of CD8αβ+ T cells in various disease states.
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Affiliation(s)
- Matthew S Sutton
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy Ellis-Connell
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexis J Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gabrielle Barry
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Scott J Hetzel
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yan Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Annie W Lau-Kilby
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristin K Biris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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32
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Cardozo EF, Apetrei C, Pandrea I, Ribeiro RM. The dynamics of simian immunodeficiency virus after depletion of CD8+ cells. Immunol Rev 2019; 285:26-37. [PMID: 30129200 DOI: 10.1111/imr.12691] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus infection is still one of the most important causes of morbidity and mortality in the world, with a disproportionate human and economic burden especially in poorer countries. Despite many years of intense research, an aspect that still is not well understood is what (immune) mechanisms control the viral load during the prolonged asymptomatic stage of infection. Because CD8+ T cells have been implicated in this control by multiple lines of evidence, there has been a focus on understanding the potential mechanisms of action of this immune effector population. One type of experiment used to this end has been depleting these cells with monoclonal antibodies in the simian immunodeficiency virus-macaque model and then studying the effect of that depletion on the viral dynamics. Here we review what these experiments have told us. We emphasize modeling studies to interpret the changes in viral load observed in these experiments, including discussion of alternative models, assumptions and interpretations, as well as potential future experiments.
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Affiliation(s)
- Erwing Fabian Cardozo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ivona Pandrea
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.,Laboratorio de Biomatematica, Faculdade de Medicina da Universidade de Lisboa, Portugal
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Defining Kinetic Properties of HIV-Specific CD8⁺ T-Cell Responses in Acute Infection. Microorganisms 2019; 7:microorganisms7030069. [PMID: 30836625 PMCID: PMC6462943 DOI: 10.3390/microorganisms7030069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/22/2019] [Accepted: 02/24/2019] [Indexed: 12/14/2022] Open
Abstract
Multiple lines of evidence indicate that CD8 + T cells are important in the control of HIV-1 (HIV) replication. However, CD8 + T cells induced by natural infection cannot eliminate the virus or reduce viral loads to acceptably low levels in most infected individuals. Understanding the basic quantitative features of CD8 + T-cell responses induced during HIV infection may therefore inform us about the limits that HIV vaccines, which aim to induce protective CD8 + T-cell responses, must exceed. Using previously published experimental data from a cohort of HIV-infected individuals with sampling times from acute to chronic infection we defined the quantitative properties of CD8 + T-cell responses to the whole HIV proteome. In contrast with a commonly held view, we found that the relative number of HIV-specific CD8 + T-cell responses (response breadth) changed little over the course of infection (first 400 days post-infection), with moderate but statistically significant changes occurring only during the first 35 symptomatic days. This challenges the idea that a change in the T-cell response breadth over time is responsible for the slow speed of viral escape from CD8 + T cells in the chronic infection. The breadth of HIV-specific CD8 + T-cell responses was not correlated with the average viral load for our small cohort of patients. Metrics of relative immunodominance of HIV-specific CD8 + T-cell responses such as Shannon entropy or the Evenness index were also not significantly correlated with the average viral load. Our mathematical-model-driven analysis suggested extremely slow expansion kinetics for the majority of HIV-specific CD8 + T-cell responses and the presence of intra- and interclonal competition between multiple CD8 + T-cell responses; such competition may limit the magnitude of CD8 + T-cell responses, specific to different epitopes, and the overall number of T-cell responses induced by vaccination. Further understanding of mechanisms underlying interactions between the virus and virus-specific CD8 + T-cell response will be instrumental in determining which T-cell-based vaccines will induce T-cell responses providing durable protection against HIV infection.
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34
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Baral S, Raja R, Sen P, Dixit NM. Towards multiscale modeling of the CD8 + T cell response to viral infections. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1446. [PMID: 30811096 PMCID: PMC6614031 DOI: 10.1002/wsbm.1446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/22/2022]
Abstract
The CD8+ T cell response is critical to the control of viral infections. Yet, defining the CD8+ T cell response to viral infections quantitatively has been a challenge. Following antigen recognition, which triggers an intracellular signaling cascade, CD8+ T cells can differentiate into effector cells, which proliferate rapidly and destroy infected cells. When the infection is cleared, they leave behind memory cells for quick recall following a second challenge. If the infection persists, the cells may become exhausted, retaining minimal control of the infection while preventing severe immunopathology. These activation, proliferation and differentiation processes as well as the mounting of the effector response are intrinsically multiscale and collective phenomena. Remarkable experimental advances in the recent years, especially at the single cell level, have enabled a quantitative characterization of several underlying processes. Simultaneously, sophisticated mathematical models have begun to be constructed that describe these multiscale phenomena, bringing us closer to a comprehensive description of the CD8+ T cell response to viral infections. Here, we review the advances made and summarize the challenges and opportunities ahead. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Cell Fates Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models.
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Affiliation(s)
- Subhasish Baral
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Pramita Sen
- 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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Abstract
The interplay between immune response and HIV is intensely studied via mathematical modeling, with significant insights but few direct answers. In this short review, we highlight advances and knowledge gaps across different aspects of immunity. In particular, we identify the innate immune response and its role in priming the adaptive response as ripe for modeling. The latter have been the focus of most modeling studies, but we also synthesize key outstanding questions regarding effector mechanisms of cellular immunity and development of broadly neutralizing antibodies. Thus far, most modeling studies aimed to infer general immune mechanisms; we foresee that significant progress will be made next by detailed quantitative fitting of models to data, and prediction of immune responses.
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Affiliation(s)
- Jessica M Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park PA 16802, USA
| | - Ruy M Ribeiro
- Laboratorio de Biomatematica, Faculdade de Medicina da Universidade de Lisboa, Portugal and Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Cao Y, Cartwright EK, Silvestri G, Perelson AS. CD8+ lymphocyte control of SIV infection during antiretroviral therapy. PLoS Pathog 2018; 14:e1007350. [PMID: 30308068 PMCID: PMC6199003 DOI: 10.1371/journal.ppat.1007350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/23/2018] [Accepted: 09/21/2018] [Indexed: 12/19/2022] Open
Abstract
CD8+ lymphocytes play an important role in suppressing in vivo viral replication in HIV infection. However, both the extent to which and the mechanisms by which CD8+ lymphocytes contribute to viral control are not completely understood. A recent experiment depleted CD8+ lymphocytes in simian immunodeficiency virus (SIV)-infected rhesus macaques (RMs) on antiretroviral treatment (ART) to study the role of CD8+ lymphocytes. CD8+ lymphocytes depletion resulted in temporary plasma viremia in all studied RMs. Viral control was restored when CD8+ lymphocytes repopulated. We developed a viral dynamic model to fit the viral load (VL) data from the CD8 depletion experiment. We explicitly modeled the dynamics of the latent reservoir and the SIV-specific effector cell population including their exhaustion and their potential cytolytic and noncytolytic functions. We found that the latent reservoir significantly contributes to the size of the peak VL after CD8 depletion, while drug efficacy plays a lesser role. Our model suggests that the overall CD8+ lymphocyte cytolytic killing rate is dynamically changing depending on the levels of antigen-induced effector cell activation and exhaustion. Based on estimated parameters, our model suggests that before ART or without ART the overall CD8 cytolytic killing rate is small due to exhaustion. However, after the start of ART, the overall CD8 cytolytic killing rate increases due to an expansion of SIV-specific CD8 effector cells. Further, we estimate that the cytolytic killing rate can be significantly larger than the cytopathic death rate in some animals during the second phase of ART-induced viral decay. Lastly, our model provides a new explanation for the puzzling findings by Klatt et al. and Wong et al. that CD8 depletion done immediately before ART has no noticeable effect on the first phase viral decay slope seen after ART initiation Overall, by incorporating effector cells and their exhaustion, our model can explain the effects of CD8 depletion on VL during ART, reveals a detailed dynamic role of CD8+ lymphocytes in controlling viral infection, and provides a unified explanation for CD8 depletion experimental data. CD8+ lymphocytes play an important role in suppressing in vivo viral replication in HIV infection. However, both the extent to which and the mechanisms by which CD8+ lymphocytes contribute to viral control are not completely understood. By mathematically modeling data from a recent CD8 depletion experiment done in antiretroviral (ART) treated animals, our results suggest that the overall CD8+ lymphocyte cytolytic killing rate is dynamically changing depending on the levels of antigen-induced effector cell activation and exhaustion, i.e. before ART or without ART the overall CD8 cytolytic killing rate is small due to exhaustion. However, after the start of ART, the overall CD8 cytolytic killing rate increases due to an expansion of SIV-specific CD8 effector cells. By incorporating effector cells and their exhaustion, our model explains the effects on viral load of CD8 depletion done before ART or during ART, reveals a detailed dynamic role of CD8+ lymphocytes in controlling viral infection, and provides a unified explanation for CD8 depletion experimental data.
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Affiliation(s)
- Youfang Cao
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, United States of America
- Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Emily K. Cartwright
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, United States of America
- * E-mail:
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37
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Bhattacharyya M, Whitney JB, Seaman M, Barouch DH, Penaloza-MacMaster P. T-cell subset differentiation and antibody responses following antiretroviral therapy during simian immunodeficiency virus infection. Immunology 2018; 155:458-466. [PMID: 30014618 DOI: 10.1111/imm.12985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/29/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022] Open
Abstract
Antiretroviral therapy (ART) for the treatment of human immunodeficiency virus (HIV) infection represents a major breakthrough in the treatment of HIV/acquired immune-deficiency syndrome. However, it remains unclear how ART influences virus-specific immune responses and understanding this is important for developing novel cure and eradication interventions for HIV-1. In the present study, we evaluate how ART impacts T-cell and antibody responses in simian immunodeficiency virus (SIV) -infected rhesus macaques. We evaluated CD4 and CD8 T-cell responses by multiparameter flow cytometry, viral loads by quantitative RT-PCR by a two-step process using SIV-specific primers and antibody neutralization function by luciferase-based TZM-bl assays. We demonstrate that macaques treated with ART exhibit phenotypic and qualitative effects on T-cell and antibody responses. Macaques on ART exhibited low numbers of virus-specific T-cell responses, and these responses appeared to be partially biased towards central memory subsets. More importantly, there were significantly reduced neutralizing antibody responses in macaques treated with ART. Collectively, these data improve the understanding of how virus-specific immune responses are generated during ART, and suggest the potential importance of therapeutic vaccines to maintain adaptive immunity during treated infection.
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Affiliation(s)
- Mitra Bhattacharyya
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - James B Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michael Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Pablo Penaloza-MacMaster
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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38
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Reuter MA, Del Rio Estrada PM, Buggert M, Petrovas C, Ferrando-Martinez S, Nguyen S, Sada Japp A, Ablanedo-Terrazas Y, Rivero-Arrieta A, Kuri-Cervantes L, Gunzelman HM, Gostick E, Price DA, Koup RA, Naji A, Canaday DH, Reyes-Terán G, Betts MR. HIV-Specific CD8 + T Cells Exhibit Reduced and Differentially Regulated Cytolytic Activity in Lymphoid Tissue. Cell Rep 2018; 21:3458-3470. [PMID: 29262326 PMCID: PMC5764192 DOI: 10.1016/j.celrep.2017.11.075] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/29/2017] [Accepted: 11/21/2017] [Indexed: 11/26/2022] Open
Abstract
Elimination of lymphoid tissue reservoirs is a key component of HIV eradication strategies. CD8+ T cells play a critical role in control of HIV, but their functional attributes in lymph nodes (LNs) remain unclear. Here, we show that memory, follicular CXCR5+, and HIV-specific CD8+ T cells from LNs do not manifest the properties of cytolytic CD8+ T cells. While the frequency of follicular CXCR5+ CD8+ T cells was strongly inversely associated with peripheral viremia, this association was not dependent on cytolytic CXCR5+ CD8+ T cells. Moreover, the poor cytolytic activity of LN CD8+ T cells was linked to a compartmentalized dissociation between effector programming and the transcription factor T-bet. In line with this, activation of LN CD8+ T cells only partially induced the acquisition of cytolytic functions relative to peripheral blood CD8+ T cells. These results suggest that a state of immune privilege against CD8+ T cell-mediated cytolysis exists in lymphoid tissue, potentially facilitating the persistence of HIV.
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Affiliation(s)
- Morgan A Reuter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Marcus Buggert
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | | | | | - Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alberto Sada Japp
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Heidi M Gunzelman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Ali Naji
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David H Canaday
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH, USA; Division of Geriatric Research, Louis Stokes VA Medical Center, Cleveland, OH, USA
| | - Gustavo Reyes-Terán
- Departamento de Investigación en Enfermedades Infecciosas, INER, Mexico City, Mexico
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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39
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Dynamics of Simian Immunodeficiency Virus Two-Long-Terminal-Repeat Circles in the Presence and Absence of CD8 + Cells. J Virol 2018; 92:JVI.02100-17. [PMID: 29643246 DOI: 10.1128/jvi.02100-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 04/08/2018] [Indexed: 12/28/2022] Open
Abstract
CD8+ cells play a key role in human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection, but their specific mechanism(s) of action in controlling the virus is unclear. Two-long-terminal-repeat (2-LTR) circles are extrachromosomal products generated upon failed integration of HIV/SIV. To understand the specific effects of CD8+ cells on infected cells, we analyzed the dynamics of 2-LTR circles in SIVmac251-infected rhesus macaques (RMs) treated with an integrase inhibitor (INT). Twenty RMs underwent CD8+ cell depletion and received raltegravir (RAL) monotherapy or a combination of both. Blood, lymph nodes (LNs), and gut biopsy specimens were routinely sampled. Plasma viral loads (pVLs) and 2-LTR circles from peripheral blood mononuclear cells (PBMCs) and LN lymphocytes were measured with quantitative reverse transcription-PCR (qRT-PCR). In the CD8 depletion group, an ∼1-log increase in pVLs and a slow increase in PBMC 2-LTRs occurred following depletion. In the INT group, a strong decline in pVLs upon treatment initiation and no change in 2-LTR levels were observed. In the INT and CD8+ cell depletion group, an increase in pVLs following CD8 depletion similar to that in the CD8 depletion group was observed, with a modest decline following INT initiation, and 2-LTR circles significantly increased in PBMCs and LNs. Analyzing the 2-LTR data across all treatment groups with a mathematical model indicates that the data best support an effect of CD8+ cells in killing cells prior to viral integration. Sensitivity analyses of these results confirm that effect but also allow for additional effects, which the data do not discriminate well. Overall, we show that INT does not significantly increase the levels of 2-LTR circles. However, CD8+ cell depletion increases the 2-LTR levels, which are enhanced in the presence of an INT.IMPORTANCE CD8+ T cells play an essential role in controlling HIV and SIV infection, but the specific mechanisms involved remain poorly understood. Due to failed viral infection, HIV and SIV can form 2-LTR extrachromosomal circles that can be quantified. We present novel data on the dynamics of these 2-LTR forms in a SIV-infected macaque model under three different treatment conditions: depletion of CD8+ cells, administration of the integrase inhibitor in a monotherapy, which favors the formation of 2-LTR circles, and a combination of the two treatments. We used a new mathematical model to help interpret the data, and the results suggest that CD8+ cells exert a killing effect on infected cells prior to virus integration. These results provide new insights into the mechanisms of action of CD8+ cells in SIV infection. Confirmation of our results would be an important step in understanding immune control of HIV.
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40
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Murray JM, Ribeiro RM. Special Issue "Mathematical Modeling of Viral Infections". Viruses 2018; 10:v10060303. [PMID: 29866993 PMCID: PMC6024780 DOI: 10.3390/v10060303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/23/2022] Open
Affiliation(s)
- John M Murray
- School of Mathematics and Statistics, UNSW Australia, Sydney 2052, Australia.
- Cancer Research Division, Cancer Council NSW, Woolloomooloo NSW 2011, Australia.
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Laboratorio de Biomatematica, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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41
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Buggert M, Nguyen S, McLane LM, Steblyanko M, Anikeeva N, Paquin-Proulx D, Del Rio Estrada PM, Ablanedo-Terrazas Y, Noyan K, Reuter MA, Demers K, Sandberg JK, Eller MA, Streeck H, Jansson M, Nowak P, Sönnerborg A, Canaday DH, Naji A, Wherry EJ, Robb ML, Deeks SG, Reyes-Teran G, Sykulev Y, Karlsson AC, Betts MR. Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease. PLoS Pathog 2018; 14:e1006973. [PMID: 29652923 PMCID: PMC5919077 DOI: 10.1371/journal.ppat.1006973] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/25/2018] [Accepted: 03/13/2018] [Indexed: 11/21/2022] Open
Abstract
CD4+ T cells subsets have a wide range of important helper and regulatory functions in the immune system. Several studies have specifically suggested that circulating effector CD4+ T cells may play a direct role in control of HIV replication through cytolytic activity or autocrine β-chemokine production. However, it remains unclear whether effector CD4+ T cells expressing cytolytic molecules and β-chemokines are present within lymph nodes (LNs), a major site of HIV replication. Here, we report that expression of β-chemokines and cytolytic molecules are enriched within a CD4+ T cell population with high levels of the T-box transcription factors T-bet and eomesodermin (Eomes). This effector population is predominately found in peripheral blood and is limited in LNs regardless of HIV infection or treatment status. As a result, CD4+ T cells generally lack effector functions in LNs, including cytolytic capacity and IFNγ and β-chemokine expression, even in HIV elite controllers and during acute/early HIV infection. While we do find the presence of degranulating CD4+ T cells in LNs, these cells do not bear functional or transcriptional effector T cell properties and are inherently poor to form stable immunological synapses compared to their peripheral blood counterparts. We demonstrate that CD4+ T cell cytolytic function, phenotype, and programming in the peripheral blood is dissociated from those characteristics found in lymphoid tissues. Together, these data challenge our current models based on blood and suggest spatially and temporally dissociated mechanisms of viral control in lymphoid tissues. CD4+ T cells have classically been divided into different subsets based on their different abilities to help and regulate specific parts of the immune system. Recent work in the HIV field has demonstrated that HIV-specific CD4+ T cells with unique effector functions, such as cytolytic activity and β-chemokine production, can play a direct role in control of HIV replication. However, HIV infection is generally considered to be a disease centered in lymphoid tissues, where unique CD4+ T helper cell subsets are present to orchestrate the maturation and priming of adaptive immunity. In this study, we identify that two specific transcription factors, T-bet and Eomes, mark cytolytic and β-chemokine producing CD4+ T cells. While this effector CD4+ T cell population is part of immunosurveillance mechanisms in blood, we find that lymph nodes largely lack this effector population–independent of HIV infection or disease progression status. These results indicate that current effector CD4+ T cell mediated correlates of HIV control are limited to blood and not representative of potential correlates of control in lymphoid tissues.
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Affiliation(s)
- Marcus Buggert
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Center for Infection Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- * E-mail: (MB); (MRB)
| | - Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Laura M. McLane
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Maria Steblyanko
- Microbiology and Immunology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Nadia Anikeeva
- Microbiology and Immunology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Dominic Paquin-Proulx
- Center for Infection Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Perla M. Del Rio Estrada
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yuria Ablanedo-Terrazas
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Kajsa Noyan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Morgan A. Reuter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Korey Demers
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Johan K. Sandberg
- Center for Infection Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Michael A. Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Hendrik Streeck
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
- Institute for HIV Research, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marianne Jansson
- Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Piotr Nowak
- Center for Infection Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Center for Infection Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David H. Canaday
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH, United States of America
- Geriatric Research, Education and Clinical Center, Louis Stokes VA Medical Center, Cleveland, OH, United States of America
| | - Ali Naji
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - E. John Wherry
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco General Hospital, San Francisco, CA, United States of America
| | - Gustavo Reyes-Teran
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yuri Sykulev
- Microbiology and Immunology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
- Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Annika C. Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- * E-mail: (MB); (MRB)
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42
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McBrien JB, Kumar NA, Silvestri G. Mechanisms of CD8 + T cell-mediated suppression of HIV/SIV replication. Eur J Immunol 2018; 48:898-914. [PMID: 29427516 DOI: 10.1002/eji.201747172] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/29/2018] [Accepted: 02/02/2018] [Indexed: 12/13/2022]
Abstract
In this article, we summarize the role of CD8+ T cells during natural and antiretroviral therapy (ART)-treated HIV and SIV infections, discuss the mechanisms responsible for their suppressive activity, and review the rationale for CD8+ T cell-based HIV cure strategies. Evidence suggests that CD8+ T cells are involved in the control of virus replication during HIV and SIV infections. During early HIV infection, the cytolytic activity of CD8+ T cells is responsible for control of viremia. However, it has been proposed that CD8+ T cells also use non-cytolytic mechanisms to control SIV infection. More recently, CD8+ T cells were shown to be required to fully suppress virus production in ART-treated SIV-infected macaques, suggesting that CD8+ T cells are involved in the control of virus transcription in latently infected cells that persist under ART. A better understanding of the complex antiviral activities of CD8+ T cells during HIV/SIV infection will pave the way for immune interventions aimed at harnessing these functions to target the HIV reservoir.
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Affiliation(s)
- Julia Bergild McBrien
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Nitasha A Kumar
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
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43
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Takata H, Buranapraditkun S, Kessing C, Fletcher JLK, Muir R, Tardif V, Cartwright P, Vandergeeten C, Bakeman W, Nichols CN, Pinyakorn S, Hansasuta P, Kroon E, Chalermchai T, O'Connell R, Kim J, Phanuphak N, Robb ML, Michael NL, Chomont N, Haddad EK, Ananworanich J, Trautmann L. Delayed differentiation of potent effector CD8 + T cells reducing viremia and reservoir seeding in acute HIV infection. Sci Transl Med 2017; 9:9/377/eaag1809. [PMID: 28202771 DOI: 10.1126/scitranslmed.aag1809] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/21/2016] [Accepted: 01/10/2017] [Indexed: 12/11/2022]
Abstract
CD8+ T cells play a critical role in controlling HIV viremia and could be important in reducing HIV-infected cells in approaches to eradicate HIV. The simian immunodeficiency virus model provided the proof of concept for a CD8+ T cell-mediated reservoir clearance but showed conflicting evidence on the role of these cells to eliminate HIV-infected cells. In humans, HIV-specific CD8+ T cell responses have not been associated with a reduction of the HIV-infected cell pool in vivo. We studied HIV-specific CD8+ T cells in the RV254 cohort of individuals initiating ART in the earliest stages of acute HIV infection (AHI). We showed that the HIV-specific CD8+ T cells generated as early as AHI stages 1 and 2 before peak viremia are delayed in expanding and acquiring effector functions but are endowed with higher memory potential. In contrast, the fully differentiated HIV-specific CD8+ T cells at peak viremia in AHI stage 3 were more prone to apoptosis but were associated with a steeper viral load decrease after ART initiation. Their capacity to persist in vivo after ART initiation correlated with a lower HIV DNA reservoir. These findings demonstrate that HIV-specific CD8+ T cell magnitude and differentiation are delayed in the earliest stages of infection. These results also demonstrate that potent HIV-specific CD8+ T cells contribute to the reduction of the pool of HIV-producing cells and the HIV reservoir seeding in vivo and provide the rationale to design interventions aiming at inducing these potent responses to cure HIV infection.
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Affiliation(s)
- Hiroshi Takata
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Supranee Buranapraditkun
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Cari Kessing
- The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Roshell Muir
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University, Philadelphia, PA 19102, USA
| | - Virginie Tardif
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University, Philadelphia, PA 19102, USA
| | - Pearline Cartwright
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Claire Vandergeeten
- Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, FL 34987, USA
| | - Wendy Bakeman
- Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, FL 34987, USA
| | - Carmen N Nichols
- Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, FL 34987, USA
| | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Pokrath Hansasuta
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Eugene Kroon
- SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Thep Chalermchai
- SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Robert O'Connell
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jerome Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | | | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Nicolas Chomont
- Department of Microbiology, Infectiology, and Immunology, Centre de Recherche Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, Quebec, Canada
| | - Elias K Haddad
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University, Philadelphia, PA 19102, USA
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Lydie Trautmann
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
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44
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Schwartz EJ, Vaidya NK, Dorman KS, Carpenter S, Mealey RH. Dynamics of lentiviral infection in vivo in the absence of adaptive immune responses. Virology 2017; 513:108-113. [PMID: 29055819 DOI: 10.1016/j.virol.2017.09.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022]
Abstract
Understanding the dynamics of acute viral infection is crucial for developing strategies to prevent and control infection. In this study, lentiviral dynamics in a host without adaptive immunity were examined in order to determine kinetic parameters of infection and quantify the effect of neutralizing antibodies in preventing infection, using mathematical modeling of data from equine infectious anemia virus (EIAV) infection of horses with severe combined immunodeficiency (SCID). Estimated parameters were used to calculate the basic reproductive number and virus doubling time and found that the rate that antibodies neutralized virus was ~18 times greater than the virus clearance rate. These results establish EIAV replication kinetics in SCID horses and the minimal efficacy of antibodies that blocked infection. Furthermore, they indicate that EIAV is at most mildly cytopathic. This study advances our understanding of EIAV infection and may have important implications for the control of other viral infections, including HIV.
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Affiliation(s)
- Elissa J Schwartz
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA; Department of Mathematics and Statistics, Washington State University, Pullman, WA 99164, USA.
| | - Naveen K Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
| | - Karin S Dorman
- Department of Statistics, Iowa State University, Ames, IA 50011, USA; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Susan Carpenter
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Robert H Mealey
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
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45
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Murray AJ, Kwon KJ, Farber DL, Siliciano RF. The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence. THE JOURNAL OF IMMUNOLOGY 2017; 197:407-17. [PMID: 27382129 DOI: 10.4049/jimmunol.1600343] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/12/2016] [Indexed: 12/15/2022]
Abstract
Combination antiretroviral therapy (ART) for HIV-1 infection reduces plasma virus levels to below the limit of detection of clinical assays. However, even with prolonged suppression of viral replication with ART, viremia rebounds rapidly after treatment interruption. Thus, ART is not curative. The principal barrier to cure is a remarkably stable reservoir of latent HIV-1 in resting memory CD4(+) T cells. In this review, we consider explanations for the remarkable stability of the latent reservoir. Stability does not appear to reflect replenishment from new infection events but rather normal physiologic processes that provide for immunologic memory. Of particular importance are proliferative processes that drive clonal expansion of infected cells. Recent evidence suggests that in some infected cells, proliferation is a consequence of proviral integration into host genes associated with cell growth. Efforts to cure HIV-1 infection by targeting the latent reservoir may need to consider the potential of latently infected cells to proliferate.
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Affiliation(s)
- Alexandra J Murray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032; Department of Surgery, Columbia University Medical Center, New York, NY 10032; and
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205; Howard Hughes Medical Institute, Baltimore MD 21250
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46
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Killian MS, Teque F, Sudhagoni R. Analysis of the CD8 + T cell anti-HIV activity in heterologous cell co-cultures reveals the benefit of multiple HLA class I matches. Immunogenetics 2017; 70:99-113. [PMID: 28735348 DOI: 10.1007/s00251-017-1021-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/17/2017] [Indexed: 01/15/2023]
Abstract
CD8+ T lymphocytes can reduce the production of human immunodeficiency virus 1 (HIV-1) by CD4+ T cells by cytotoxic and non-cytotoxic mechanisms. To investigate the involvement of human leukocyte antigen (HLA) class I compatibility in anti-HIV responses, we co-cultured primary CD8+ T cells, isolated from the peripheral blood of HIV-1-infected individuals, with panels of autologous and heterologous acutely HIV-1-infected primary CD4+ T cells. Altogether, CD8+ T cell anti-HIV activity was evaluated in more than 200 co-cultures. Marked heterogeneity in HIV-1 replication levels was observed among the co-cultures sharing a common CD8+ T cell source. The co-cultures that exhibited greater than 50% reduction in HIV production were found to have significantly increased numbers of matching HLA class I alleles (Yates chi-square = 54.21; p < 0.001). With CD8+ T cells from HIV controllers and asymptomatic viremic individuals, matching HLA-B and/or HLA-C alleles were more predictive of strong anti-HIV activity than matching HLA-A alleles. Overall, HLA class I genotype matches were more closely associated with CD8+ T cell anti-HIV activity than supertype pairings. Antibodies against HLA class I and CD3 reduced the CD8+ T cell anti-HIV activity. Stimulated CD8+ T cells exhibited increased anti-HIV activity and reduced dependency on HLA compatibility. These findings provide evidence that the maximal suppression of HIV replication by CD8+ T cells requires the recognition of multiple epitopes. These studies provide insight for HIV vaccine development, and the analytic approach can be useful for the functional characterization of HLA class I alleles and tentative HLA class I supertypes.
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Affiliation(s)
- M Scott Killian
- Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark St, Vermillion, SD, 57069, USA. .,Department of Public Health, School of Health Sciences, University of South Dakota, Vermillion, SD, 57069, USA.
| | - Fernando Teque
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ramu Sudhagoni
- Department of Public Health, School of Health Sciences, University of South Dakota, Vermillion, SD, 57069, USA
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47
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Beauchemin CAA, Miura T, Iwami S. Duration of SHIV production by infected cells is not exponentially distributed: Implications for estimates of infection parameters and antiviral efficacy. Sci Rep 2017; 7:42765. [PMID: 28202942 PMCID: PMC5311941 DOI: 10.1038/srep42765] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/12/2017] [Indexed: 01/21/2023] Open
Abstract
The duration of the eclipse phase, from cell infection to the production and release of the first virion progeny, immediately followed by the virus-production phase, from the first to the last virion progeny, are important steps in a viral infection, by setting the pace of infection progression and modulating the response to antiviral therapy. Using a mathematical model (MM) and data for the infection of HSC-F cells with SHIV in vitro, we reconfirm our earlier finding that the eclipse phase duration follows a fat-tailed distribution, lasting 19 h (18–20 h). Most importantly, for the first time, we show that the virus-producing phase duration, which lasts 11 h (9.8–12 h), follows a normal-like distribution, and not an exponential distribution as is typically assumed. We explore the significance of this finding and its impact on analysis of plasma viral load decays in HIV patients under antiviral therapy. We find that incorrect assumptions about the eclipse and virus-producing phase distributions can lead to an overestimation of antiviral efficacy. Additionally, our predictions for the rate of plasma HIV decay under integrase inhibitor therapy offer an opportunity to confirm whether HIV production duration in vivo also follows a normal distribution, as demonstrated here for SHIV infections in vitro.
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Affiliation(s)
- Catherine A A Beauchemin
- Department of Physics, Ryerson University, Toronto, M5B 2K3, Canada.,Interdisciplinary Theoretical Science (iTHES) Research Group, RIKEN, Wako, 351-0198, Japan
| | - Tomoyuki Miura
- Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Shingo Iwami
- Department of Biology, Kyushu University, Fukuoka, 819-0395, Japan.,CREST and PRESTO, Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
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48
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Verma M, Erwin S, Abedi V, Hontecillas R, Hoops S, Leber A, Bassaganya-Riera J, Ciupe SM. Modeling the Mechanisms by Which HIV-Associated Immunosuppression Influences HPV Persistence at the Oral Mucosa. PLoS One 2017; 12:e0168133. [PMID: 28060843 PMCID: PMC5218576 DOI: 10.1371/journal.pone.0168133] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 11/24/2016] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus (HIV)-infected patients are at an increased risk of co-infection with human papilloma virus (HPV), and subsequent malignancies such as oral cancer. To determine the role of HIV-associated immune suppression on HPV persistence and pathogenesis, and to investigate the mechanisms underlying the modulation of HPV infection and oral cancer by HIV, we developed a mathematical model of HIV/HPV co-infection. Our model captures known immunological and molecular features such as impaired HPV-specific effector T helper 1 (Th1) cell responses, and enhanced HPV infection due to HIV. We used the model to determine HPV prognosis in the presence of HIV infection, and identified conditions under which HIV infection alters HPV persistence in the oral mucosa system. The model predicts that conditions leading to HPV persistence during HIV/HPV co-infection are the permissive immune environment created by HIV and molecular interactions between the two viruses. The model also determines when HPV infection continues to persist in the short run in a co-infected patient undergoing antiretroviral therapy. Lastly, the model predicts that, under efficacious antiretroviral treatment, HPV infections will decrease in the long run due to the restoration of CD4+ T cell numbers and protective immune responses.
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Affiliation(s)
- Meghna Verma
- Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States of America
| | - Samantha Erwin
- Department of Mathematics, Virginia Tech, Blacksburg, VA, United States of America
| | - Vida Abedi
- Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States of America
| | - Raquel Hontecillas
- Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States of America
| | - Stefan Hoops
- Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States of America
| | - Andrew Leber
- Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States of America
| | - Josep Bassaganya-Riera
- Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States of America
| | - Stanca M Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA, United States of America
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49
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Roberts ER, Carnathan DG, Li H, Shaw GM, Silvestri G, Betts MR. Collapse of Cytolytic Potential in SIV-Specific CD8+ T Cells Following Acute SIV Infection in Rhesus Macaques. PLoS Pathog 2016; 12:e1006135. [PMID: 28036372 PMCID: PMC5231392 DOI: 10.1371/journal.ppat.1006135] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/12/2017] [Accepted: 12/16/2016] [Indexed: 12/23/2022] Open
Abstract
Poor maintenance of cytotoxic factor expression among HIV-specific CD8+ T cells, in part caused by dysregulated expression of the transcription factor T-bet, is associated with HIV disease progression. However, the precise evolution and context in which CD8+ T cell cytotoxic functions become dysregulated in HIV infection remain unclear. Using the rhesus macaque (RM) SIV infection model, we evaluated the kinetics of SIV-specific CD8+ T cell cytolytic factor expression in peripheral blood, lymph node, spleen, and gut mucosa from early acute infection through chronic infection. We identified rapid acquisition of perforin and granzyme B expression in SIV-specific CD8+ T cells in blood, secondary lymphoid tissues and gut mucosa that collapsed rapidly during the transition to chronic infection. The evolution of this expression profile was linked to low expression of T-bet and occurred independent of epitope specificity, viral escape patterns and tissue origin. Importantly, during acute infection SIV-specific CD8+ T cells that maintained T-bet expression retained the ability to express granzyme B after stimulation, but this relationship was lost in chronic infection. Together, these data demonstrate the loss of cytolytic machinery in SIV-specific CD8+ T cells in blood and at tissue sites of viral reservoir and active replication during the transition from acute to chronic infection. This phenomenon occurs despite persistent high levels of viremia suggesting that an inability to maintain properly regulated cytotoxic T cell responses in all tissue sites enables HIV/SIV to avoid immune clearance, establish persistent viral reservoirs in lymphoid tissues and gut mucosa, and lead ultimately to immunopathogenesis and death.
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Affiliation(s)
- Emily R. Roberts
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Biomedical Graduate Studies in Immunology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Diane G. Carnathan
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Hui Li
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Guido Silvestri
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Michael R. Betts
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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HIV Dynamics With Immune Responses: Perspectives From Mathematical Modeling. CURRENT CLINICAL MICROBIOLOGY REPORTS 2016. [DOI: 10.1007/s40588-016-0049-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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