1
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Pitchai FNN, Tanner EJ, Khetan N, Vasen G, Levrel C, Kumar AJ, Pandey S, Ordonez T, Barnette P, Spencer D, Jung SY, Glazier J, Thompson C, Harvey-Vera A, Son HI, Son HI, Strathdee SA, Holguin L, Urak R, Burnett J, Burgess W, Busman-Sahay K, Estes JD, Hessell A, Fennessey CM, Keele BF, Haigwood NL, Weinberger LS. Engineered deletions of HIV replicate conditionally to reduce disease in nonhuman primates. Science 2024; 385:eadn5866. [PMID: 39116226 DOI: 10.1126/science.adn5866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 06/06/2024] [Indexed: 08/10/2024]
Abstract
Antiviral therapies with reduced frequencies of administration and high barriers to resistance remain a major goal. For HIV, theories have proposed that viral-deletion variants, which conditionally replicate with a basic reproductive ratio [R0] > 1 (termed "therapeutic interfering particles" or "TIPs"), could parasitize wild-type virus to constitute single-administration, escape-resistant antiviral therapies. We report the engineering of a TIP that, in rhesus macaques, reduces viremia of a highly pathogenic model of HIV by >3log10 following a single intravenous injection. Animal lifespan was significantly extended, TIPs conditionally replicated and were continually detected for >6 months, and sequencing data showed no evidence of viral escape. A single TIP injection also suppressed virus replication in humanized mice and cells from persons living with HIV. These data provide proof of concept for a potential new class of single-administration antiviral therapies.
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Affiliation(s)
- Fathima N Nagoor Pitchai
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Elizabeth J Tanner
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Neha Khetan
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Gustavo Vasen
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Clara Levrel
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Arjun J Kumar
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Shilpi Pandey
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Tracy Ordonez
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Philip Barnette
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - David Spencer
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
- Absci Corporation, Vancouver, WA, USA
| | - Seung-Yong Jung
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Joshua Glazier
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Cassandra Thompson
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Hye-In Son
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- US-Mexico Border Health Commission, Tijuana, Mexico
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Hye-In Son
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Steffanie A Strathdee
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Leo Holguin
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ryan Urak
- Center for Gene Therapy, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - John Burnett
- Center for Gene Therapy, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William Burgess
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
- Faculty of Health, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- School of Health and Biomedical Sciences College of Science, Engineering and Health RMIT University, Melbourne, Australia
| | - Ann Hessell
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 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
| | - Nancy L Haigwood
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Leor S Weinberger
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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2
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Mainou E, Ribeiro RM, Conway JM. Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection. PLoS Comput Biol 2024; 20:e1012129. [PMID: 38848426 PMCID: PMC11189221 DOI: 10.1371/journal.pcbi.1012129] [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: 06/16/2023] [Revised: 06/20/2024] [Accepted: 05/02/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the dynamics of acute HIV infection can offer valuable insights into the early stages of viral behavior, potentially helping uncover various aspects of HIV pathogenesis. The standard viral dynamics model explains HIV viral dynamics during acute infection reasonably well. However, the model makes simplifying assumptions, neglecting some aspects of HIV infection. For instance, in the standard model, target cells are infected by a single HIV virion. Yet, cellular multiplicity of infection (MOI) may have considerable effects in pathogenesis and viral evolution. Further, when using the standard model, we take constant infected cell death rates, simplifying the dynamic immune responses. Here, we use four models-1) the standard viral dynamics model, 2) an alternate model incorporating cellular MOI, 3) a model assuming density-dependent death rate of infected cells and 4) a model combining (2) and (3)-to investigate acute infection dynamics in 43 people living with HIV very early after HIV exposure. We find that all models qualitatively describe the data, but none of the tested models is by itself the best to capture different kinds of heterogeneity. Instead, different models describe differing features of the dynamics more accurately. For example, while the standard viral dynamics model may be the most parsimonious across study participants by the corrected Akaike Information Criterion (AICc), we find that viral peaks are better explained by a model allowing for cellular MOI, using a linear regression analysis as analyzed by R2. These results suggest that heterogeneity in within-host viral dynamics cannot be captured by a single model. Depending on the specific aspect of interest, a corresponding model should be employed.
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Affiliation(s)
- Ellie Mainou
- Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jessica M. Conway
- Department of Mathematics, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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3
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Albanese M, Chen HR, Gapp M, Muenchhoff M, Yang HH, Peterhoff D, Hoffmann K, Xiao Q, Ruhle A, Ambiel I, Schneider S, Mejías-Pérez E, Stern M, Wratil PR, Hofmann K, Amann L, Jocham L, Fuchs T, Ulivi AF, Besson-Girard S, Weidlich S, Schneider J, Spinner CD, Sutter K, Dittmer U, Humpe A, Baumeister P, Wieser A, Rothenfusser S, Bogner J, Roider J, Knolle P, Hengel H, Wagner R, Laketa V, Fackler OT, Keppler OT. Receptor transfer between immune cells by autoantibody-enhanced, CD32-driven trogocytosis is hijacked by HIV-1 to infect resting CD4 T cells. Cell Rep Med 2024; 5:101483. [PMID: 38579727 PMCID: PMC11031382 DOI: 10.1016/j.xcrm.2024.101483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/23/2023] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Immune cell phenotyping frequently detects lineage-unrelated receptors. Here, we report that surface receptors can be transferred from primary macrophages to CD4 T cells and identify the Fcγ receptor CD32 as driver and cargo of this trogocytotic transfer. Filamentous CD32+ nanoprotrusions deposit distinct plasma membrane patches onto target T cells. Transferred receptors confer cell migration and adhesion properties, and macrophage-derived membrane patches render resting CD4 T cells susceptible to infection by serving as hotspots for HIV-1 binding. Antibodies that recognize T cell epitopes enhance CD32-mediated trogocytosis. Such autoreactive anti-HIV-1 envelope antibodies can be found in the blood of HIV-1 patients and, consistently, the percentage of CD32+ CD4 T cells is increased in their blood. This CD32-mediated, antigen-independent cell communication mode transiently expands the receptor repertoire and functionality of immune cells. HIV-1 hijacks this mechanism by triggering the generation of trogocytosis-promoting autoantibodies to gain access to immune cells critical to its persistence.
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Affiliation(s)
- Manuel Albanese
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany; Department for Clinical Sciences and Community Health (DISCCO), University of Milan, Milan, Italy
| | - Hong-Ru Chen
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.
| | - Madeleine Gapp
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Hsiu-Hui Yang
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Katja Hoffmann
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Qianhao Xiao
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Adrian Ruhle
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Ina Ambiel
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Stephanie Schneider
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Ernesto Mejías-Pérez
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Paul R Wratil
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Katharina Hofmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Laura Amann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Linda Jocham
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Thimo Fuchs
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | | | - Simon Besson-Girard
- Institute for Stroke and Dementia Research, University Hospital, LMU München, Munich, Germany
| | - Simon Weidlich
- Technical University of Munich, School of Medicine, University Hospital Rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Jochen Schneider
- Technical University of Munich, School of Medicine, University Hospital Rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Christoph D Spinner
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Technical University of Munich, School of Medicine, University Hospital Rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Kathrin Sutter
- University Hospital Essen, University Duisburg-Essen, Institute for Virology and Institute for Translational HIV Research, Essen, Germany
| | - Ulf Dittmer
- University Hospital Essen, University Duisburg-Essen, Institute for Virology and Institute for Translational HIV Research, Essen, Germany
| | - Andreas Humpe
- Department of Transfusion Medicine, Cell Therapeutics, and Hemostaseology, Department of Anesthesiology, University Hospital Munich, Munich, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, LMU München, Munich, Germany
| | - Andreas Wieser
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Max von Pettenkofer Institute, Medical Microbiology and Hospital Epidemiology, Faculty of Medicine, LMU München, Munich, Germany; Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU München, Munich, Germany
| | - Simon Rothenfusser
- Division of Clinical Pharmacology, University Hospital, LMU München and Unit Clinical Pharmacology (EKliP), Helmholtz Center for Environmental Health, Munich, Germany
| | - Johannes Bogner
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Division of Infectious Diseases, University Hospital, Medizinische Klinik und Poliklinik IV, LMU München, Munich, Germany
| | - Julia Roider
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Division of Infectious Diseases, University Hospital, Medizinische Klinik und Poliklinik IV, LMU München, Munich, Germany
| | - Percy Knolle
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany; Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Hartmut Hengel
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Vibor Laketa
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany; Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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4
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Wan Z, Zhang C. How to report and make sense of a new HIV-1 circulating recombinant form? Front Microbiol 2024; 15:1343143. [PMID: 38450164 PMCID: PMC10915052 DOI: 10.3389/fmicb.2024.1343143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024] Open
Abstract
Co-circulation of multiple HIV-1 subtypes in the same high-risk groups leads to the on-going generation of various inter-subtype recombinants, including unique (URFs) and circulating (CRFs) recombinant forms, which brings a new challenge for the prevention and eradication of HIV/AIDS. Identification and prompt reporting of new CRFs will provide not only new insights into the understanding of genetic diversity and evolution of HIV-1, but also an early warning of potential prevalence of these variants. Currently, 140 HIV-1 CRFs have been described; however, their prevalence and clinical importance are less concerned. Apart from the mosaic genomic maps, less other valuable information, including the clinical and demographic data, genomic sequence characteristics, origin and evolutionary dynamics, as well as representative genomic fragments for determining the variants, are available for most of these CRFs. Accompanied with the growing increase of HIV-1 full-length genomic sequences, more and more CRFs will be identified in the near future due to the high recombination potential of HIV-1. Here, we discuss the prevalence and clinical importance of various HIV-1 CRFs and propose how to report and make sense of a new HIV-1 CRF.
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Affiliation(s)
- Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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5
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Romero EV, Feder AF. Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo. Mol Biol Evol 2024; 41:msad260. [PMID: 38197289 PMCID: PMC10777272 DOI: 10.1093/molbev/msad260] [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: 05/26/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
HIV's exceptionally high recombination rate drives its intrahost diversification, enabling immune escape and multidrug resistance within people living with HIV. While we know that HIV's recombination rate varies by genomic position, we have little understanding of how recombination varies throughout infection or between individuals as a function of the rate of cellular coinfection. We hypothesize that denser intrahost populations may have higher rates of coinfection and therefore recombination. To test this hypothesis, we develop a new approach (recombination analysis via time series linkage decay or RATS-LD) to quantify recombination using autocorrelation of linkage between mutations across time points. We validate RATS-LD on simulated data under short read sequencing conditions and then apply it to longitudinal, high-throughput intrahost viral sequencing data, stratifying populations by viral load (a proxy for density). Among sampled viral populations with the lowest viral loads (<26,800 copies/mL), we estimate a recombination rate of 1.5×10-5 events/bp/generation (95% CI: 7×10-6 to 2.9×10-5), similar to existing estimates. However, among samples with the highest viral loads (>82,000 copies/mL), our median estimate is approximately 6 times higher. In addition to co-varying across individuals, we also find that recombination rate and viral load are associated within single individuals across different time points. Our findings suggest that rather than acting as a constant, uniform force, recombination can vary dynamically and drastically across intrahost viral populations and within them over time. More broadly, we hypothesize that this phenomenon may affect other facultatively asexual populations where spatial co-localization varies.
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Affiliation(s)
- Elena V Romero
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alison F Feder
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
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6
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Lécuyer D, Nardacci R, Tannous D, Gutierrez-Mateyron E, Deva Nathan A, Subra F, Di Primio C, Quaranta P, Petit V, Richetta C, Mostefa-Kara A, Del Nonno F, Falasca L, Marlin R, Maisonnasse P, Delahousse J, Pascaud J, Deprez E, Naigeon M, Chaput N, Paci A, Saada V, Ghez D, Mariette X, Costa M, Pistello M, Allouch A, Delelis O, Piacentini M, Le Grand R, Perfettini JL. The purinergic receptor P2X7 and the NLRP3 inflammasome are druggable host factors required for SARS-CoV-2 infection. Front Immunol 2023; 14:1270081. [PMID: 37920468 PMCID: PMC10619763 DOI: 10.3389/fimmu.2023.1270081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
Purinergic receptors and NOD-like receptor protein 3 (NLRP3) inflammasome regulate inflammation and viral infection, but their effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remain poorly understood. Here, we report that the purinergic receptor P2X7 and NLRP3 inflammasome are cellular host factors required for SARS-CoV-2 infection. Lung autopsies from patients with severe coronavirus disease 2019 (COVID-19) reveal that NLRP3 expression is increased in host cellular targets of SARS-CoV-2 including alveolar macrophages, type II pneumocytes and syncytia arising from the fusion of infected macrophages, thus suggesting a potential role of NLRP3 and associated signaling pathways to both inflammation and viral replication. In vitro studies demonstrate that NLRP3-dependent inflammasome activation is detected upon macrophage abortive infection. More importantly, a weak activation of NLRP3 inflammasome is also detected during the early steps of SARS-CoV-2 infection of epithelial cells and promotes the viral replication in these cells. Interestingly, the purinergic receptor P2X7, which is known to control NLRP3 inflammasome activation, also favors the replication of D614G and alpha SARS-CoV-2 variants. Altogether, our results reveal an unexpected relationship between the purinergic receptor P2X7, the NLRP3 inflammasome and the permissiveness to SARS-CoV-2 infection that offers novel opportunities for COVID-19 treatment.
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Affiliation(s)
- Déborah Lécuyer
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
| | - Roberta Nardacci
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
- UniCamillus - Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Désirée Tannous
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
- NH TherAguix SAS, Meylan, France
| | - Emie Gutierrez-Mateyron
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
| | - Aurélia Deva Nathan
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
| | - Frédéric Subra
- Université Paris-Saclay, ENS Paris-Saclay, CNRS UMR 8113, IDA FR3242, Laboratory of Biology and Applied Pharmacology (LBPA), Gif-sur-Yvette, France
| | - Cristina Di Primio
- Institute of Neuroscience, Italian National Research Council, Pisa, Italy
- Laboratory of Biology BIO@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Paola Quaranta
- Institute of Neuroscience, Italian National Research Council, Pisa, Italy
- Retrovirus Center, Department of Translational Research, Universita of Pisa, Pisa, Italy
| | - Vanessa Petit
- Université Paris-Saclay, Inserm U1274, CEA, Genetic Stability, Stem Cells and Radiation, Fontenay-aux-Roses, France
| | - Clémence Richetta
- Université Paris-Saclay, ENS Paris-Saclay, CNRS UMR 8113, IDA FR3242, Laboratory of Biology and Applied Pharmacology (LBPA), Gif-sur-Yvette, France
| | - Ali Mostefa-Kara
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
| | - Franca Del Nonno
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Laura Falasca
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Romain Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA- HB/IDMIT), Fontenay-aux-Roses, France
| | - Pauline Maisonnasse
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA- HB/IDMIT), Fontenay-aux-Roses, France
| | - Julia Delahousse
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
| | - Juliette Pascaud
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA- HB/IDMIT), Fontenay-aux-Roses, France
- Assistance Publique, Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Eric Deprez
- Université Paris-Saclay, ENS Paris-Saclay, CNRS UMR 8113, IDA FR3242, Laboratory of Biology and Applied Pharmacology (LBPA), Gif-sur-Yvette, France
| | - Marie Naigeon
- Gustave Roussy Cancer Center, Villejuif, France
- Université Paris-Saclay, Inserm, CNRS, Analyse Moléculaire, Modélisation et Imagerie de la Maladie Cancéreuse, Laboratoire d'Immunomonitoring en Oncologie, Villejuif, France
- Université Paris-Saclay, Faculté de Pharmacie, Chatenay-Malabry, France
| | - Nathalie Chaput
- Université Paris-Saclay, Inserm, CNRS, Analyse Moléculaire, Modélisation et Imagerie de la Maladie Cancéreuse, Laboratoire d'Immunomonitoring en Oncologie, Villejuif, France
- Université Paris-Saclay, Faculté de Pharmacie, Chatenay-Malabry, France
- Université Paris-Saclay, Gustave Roussy Cancer Center, CNRS, Stabilité Génétique et Oncogenèse, Villejuif, France
| | - Angelo Paci
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
- Université Paris-Saclay, Faculté de Pharmacie, Chatenay-Malabry, France
- Department of Biology and Pathology, Gustave Roussy Cancer Center, Villejuif, France
| | - Véronique Saada
- Department of Biology and Pathology, Gustave Roussy Cancer Center, Villejuif, France
| | - David Ghez
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Department of Hematology, Gustave Roussy Cancer Center, Villejuif, France
| | - Xavier Mariette
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA- HB/IDMIT), Fontenay-aux-Roses, France
- Assistance Publique, Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin Bicêtre, France
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France
| | - Mario Costa
- Institute of Neuroscience, Italian National Research Council, Pisa, Italy
- Laboratory of Biology BIO@SNS, Scuola Normale Superiore, Pisa, Italy
- Centro Pisano Ricerca e Implementazione Clinical Flash Radiotherapy "CPFR@CISUP", "S. Chiara" Hospital, Pisa, Italy
| | - Mauro Pistello
- Retrovirus Center, Department of Translational Research, Universita of Pisa, Pisa, Italy
- Virology Operative Unit, Pisa University Hospital, Pisa, Italy
| | - Awatef Allouch
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
- NH TherAguix SAS, Meylan, France
| | - Olivier Delelis
- Université Paris-Saclay, ENS Paris-Saclay, CNRS UMR 8113, IDA FR3242, Laboratory of Biology and Applied Pharmacology (LBPA), Gif-sur-Yvette, France
| | - Mauro Piacentini
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA- HB/IDMIT), Fontenay-aux-Roses, France
| | - Jean-Luc Perfettini
- Université Paris-Saclay, Inserm UMR1030, Laboratory of Molecular Radiotherapy and Therapeutic Innovation, Villejuif, France
- Gustave Roussy Cancer Center, Villejuif, France
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7
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Romero EV, Feder AF. Elevated HIV viral load is associated with higher recombination rate in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539643. [PMID: 37873119 PMCID: PMC10592651 DOI: 10.1101/2023.05.05.539643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
HIV's exceptionally high recombination rate drives its intra-host diversification, enabling immune escape and multi-drug resistance within people living with HIV. While we know that HIV's recombination rate varies by genomic position, we have little understanding of how recombination varies throughout infection or between individuals as a function of the rate of cellular coinfection. We hypothesize that denser intra-host populations may have higher rates of coinfection and therefore recombination. To test this hypothesis, we develop a new approach (Recombination Analysis via Time Series Linkage Decay, or RATS-LD) to quantify recombination using autocorrelation of linkage between mutations across time points. We validate RATS-LD on simulated data under short read sequencing conditions and then apply it to longitudinal, high-throughput intra-host viral sequencing data, stratifying populations by viral load (a proxy for density). Among sampled viral populations with the lowest viral loads (< 26,800 copies/mL), we estimate a recombination rate of 1.5 × 10-5 events/bp/generation (95% CI: 7 × 10-6 - 2.9 × 10-5), similar to existing estimates. However, among samples with the highest viral loads (> 82,000 copies/mL), our median estimate is approximately 6 times higher. In addition to co-varying across individuals, we also find that recombination rate and viral load are associated within single individuals across different time points. Our findings suggest that rather than acting as a constant, uniform force, recombination can vary dynamically and drastically across intra-host viral populations and within them over time. More broadly, we hypothesize that this phenomenon may affect other facultatively asexual populations where spatial co-localization varies.
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Affiliation(s)
- Elena V. Romero
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alison F. Feder
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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8
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Mulinge MM, Oluoch JO, Abisi HK, Otieno LE, Anzala O, Wamalwa DC, Nduati RW, Kimani J, Herbeck J, McKinnon L. Age and CD4+ T cell counts are inversely associated with HIV drug resistance mutations in treatment naive female sex workers. Medicine (Baltimore) 2023; 102:e34060. [PMID: 37327289 PMCID: PMC10270489 DOI: 10.1097/md.0000000000034060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023] Open
Abstract
The increasing prevalence of human immunodeficiency virus (HIV) drug resistance mutations (HIVDRM) in untreated seropositive persons has consequences for future treatment options. This is extremely important in key populations such as female sex workers (FSWs), where the prevalence of pretreatment drug resistance (PDR) and associated risk factors are unknown. In this study, we analyzed PDR and associated risk factors in recently diagnosed and treatment-naive FSWs in Nairobi, Kenya. In this cross-sectional study, we used 64 HIV-seropositive plasma samples collected from FSWs between November 2020 and April 2021. To identify HIVDRM, the pol gene was amplified and genotyped using sanger sequencing. The effects of age, tropism, CD4+ T cell count, subtype, and location on HIVDRM counts were examined using Poisson regression. Overall, the prevalence of PDR was 35.9% (95% CI: 24.3-48.9), which was strongly influenced by K103N and M184V mutations, which confer resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTI), respectively. Subtype A1 was predominant followed by subtype D with a notable increase in inter-subtype recombinants. We found statistically significant evidence that age was inversely related to HIVDRM. A FSW who is 1 year older had 12% less HIVDRM (incidence rate ratios [IRR]: 0.88; 95% CI: 0.82-0.95; P < .001), after adjusting for CD4+ T cell count, subtype, location, and tropism. Similarly, an increase in CD4+ T cell count by 1 unit, was associated with 0.4% fewer HIVDRM (IRR: 0.996; 95% CI: 0.994-0.998; P = .001), while controlling for the other variables. HIV-1 tropism was not associated with HIVDRM counts. In conclusion, our findings show a high prevalence of NNRTIs. Lower CD4+ T cell counts and younger age were significant risk factors that influenced HIVDRM loads. This finding underscores the relevance of targeted interventions and the importance of continuing to focus on FSWs as a way of addressing the HIV epidemic.
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Affiliation(s)
- Martin M. Mulinge
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research (KAVI-ICR), University of Nairobi, Nairobi, Kenya
| | - Jeff O. Oluoch
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Hellen K. Abisi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Leon E. Otieno
- Molecular Medicine and Infectious Diseases Laboratory, University of Nairobi, Kenya
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research (KAVI-ICR), University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Dalton C. Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Ruth W. Nduati
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Joshua Kimani
- Partners for Health and Development in Africa (PHDA), Nairobi, Kenya
| | - Joshua Herbeck
- Department of Global Health, University of Washington, Seattle, WA
| | - Lyle McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
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9
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Rong SY, Guo T, Smith JT, Wang X. The role of cell-to-cell transmission in HIV infection: insights from a mathematical modeling approach. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:12093-12117. [PMID: 37501434 DOI: 10.3934/mbe.2023538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
HIV infection remains a serious global public health problem. Although current drug treatment is effective and can reduce plasma viral loads below the level of detection, it cannot eradicate the virus. The reasons for the low virus persistence despite long-term therapy have not been fully elucidated. In addition, multiple HIV infection, i.e., infection of a cell by multiple viruses, is common and can facilitate viral recombination and mutations, evading the immune system and conferring resistance to drug treatment. The mechanisms for multiple HIV infection formation and their respective contributions remain unclear. To answer these questions, we developed a mathematical modeling framework that encompasses cell-free viral infection and cell-to-cell spread. We fit sub-models that only have one transmission route and the full model containing both to the multi-infection data from HIV-infected patients, and show that the multi-infection data can only be reproduced if these two transmission routes are both considered. Computer simulations with the best-fitting parameter values indicate that cell-to-cell spread leads to the majority of multiple infection and also accounts for the majority of overall infection. Sensitivity analysis shows that cell-to-cell spread has reduced susceptibility to treatment and may explain low HIV persistence. Taken together, this work indicates that cell-to-cell spread plays a crucial role in the development of HIV multi-infection and low HIV persistence despite long-term therapy, and therefore has important implications for understanding HIV pathogenesis and developing more effective treatment strategies to control or even eliminate the disease.
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Affiliation(s)
| | - Ting Guo
- Aliyun School of Big Data, Changzhou University, Changzhou 213164, China
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
| | - J Tyler Smith
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
| | - Xia Wang
- School of Mathematics and Statistics, Xinyang Normal University, Xinyang 464000, China
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
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10
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Mahalingam SS, Jayaraman S, Bhaskaran N, Schneider E, Faddoul F, Paes da Silva A, Lederman MM, Asaad R, Adkins-Travis K, Shriver LP, Pandiyan P. Polyamine metabolism impacts T cell dysfunction in the oral mucosa of people living with HIV. Nat Commun 2023; 14:399. [PMID: 36693889 PMCID: PMC9873639 DOI: 10.1038/s41467-023-36163-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Metabolic changes in immune cells contribute to both physiological and pathophysiological outcomes of immune reactions. Here, by comparing protein expression, transcriptome, and salivary metabolome profiles of uninfected and HIV+ individuals, we found perturbations of polyamine metabolism in the oral mucosa of HIV+ patients. Mechanistic studies using an in vitro human tonsil organoid infection model revealed that HIV infection of T cells also resulted in increased polyamine synthesis, which was dependent on the activities of caspase-1, IL-1β, and ornithine decarboxylase-1. HIV-1 also led to a heightened expression of polyamine synthesis intermediates including ornithine decarboxylase-1 as well as an elevated dysfunctional regulatory T cell (TregDys)/T helper 17 (Th17) cell ratios. Blockade of caspase-1 and polyamine synthesis intermediates reversed the TregDys phenotype showing the direct role of polyamine pathway in altering T cell functions during HIV-1 infection. Lastly, oral mucosal TregDys/Th17 ratios and CD4 hyperactivation positively correlated with salivary putrescine levels, which were found to be elevated in the saliva of HIV+ patients. Thus, by revealing the role of aberrantly increased polyamine synthesis during HIV infection, our study unveils a mechanism by which chronic viral infections could drive distinct T cell effector programs and Treg dysfunction.
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Affiliation(s)
- S S Mahalingam
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - S Jayaraman
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - N Bhaskaran
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Faculty of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - E Schneider
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - F Faddoul
- Advanced Education in General Dentistry, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - A Paes da Silva
- Department of Periodontics, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - M M Lederman
- Department of Medicine, Division of Infectious Diseases & HIV Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,University Hospitals Cleveland Medical Center AIDS Clinical Trials Unit, Cleveland, OH, 44106, USA
| | - R Asaad
- University Hospitals Cleveland Medical Center AIDS Clinical Trials Unit, Cleveland, OH, 44106, USA
| | - K Adkins-Travis
- Department of Chemistry, Center for Metabolomics and Isotope Tracing, Washington University, Saint Louis, MO, 63110, USA
| | - L P Shriver
- Department of Chemistry, Center for Metabolomics and Isotope Tracing, Washington University, Saint Louis, MO, 63110, USA
| | - P Pandiyan
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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11
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HIV and Drug-Resistant Subtypes. Microorganisms 2023; 11:microorganisms11010221. [PMID: 36677513 PMCID: PMC9861097 DOI: 10.3390/microorganisms11010221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a human viral infectious disease caused by the positive-sense single-stranded (ss) RNA Human Immunodeficiency Virus (HIV) (Retroviridae family, Ortervirales order). HIV-1 can be distinguished into various worldwide spread groups and subtypes. HIV-2 also causes human immunodeficiency, which develops slowly and tends to be less aggressive. HIV-2 only partially homologates to HIV-1 despite the similar derivation. Antiretroviral therapy (ART) is the treatment approved to control HIV infection, based on multiple antiretroviral drugs that belong to different classes: (i) NNRTIs, (ii) NRTIs, (iii) PIs, (iv) INSTIs, and (v) entry inhibitors. These drugs, acting on different stages of the HIV life cycle, decrease the patient's total burden of HIV, maintain the function of the immune system, and prevent opportunistic infections. The appearance of several strains resistant to these drugs, however, represents a problem today that needs to be addressed as best as we can. New outbreaks of strains show a widespread geographic distribution and a highly variable mortality rate, even affecting treated patients significantly. Therefore, novel treatment approaches should be explored. The present review discusses updated information on HIV-1- and HIV-2-resistant strains, including details on different mutations responsible for drug resistance.
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12
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Mukhatayeva A, Mustafa A, Dzissyuk N, Issanov A, Mukhatayev Z, Bayserkin B, Vermund SH, Ali S. Antiretroviral therapy resistance mutations among HIV infected people in Kazakhstan. Sci Rep 2022; 12:17195. [PMID: 36229577 PMCID: PMC9562405 DOI: 10.1038/s41598-022-22163-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/10/2022] [Indexed: 01/05/2023] Open
Abstract
In Kazakhstan, the number of people living with HIV (PLHIV) has increased steadily by 39% since 2010. Development of antiretroviral therapy (ART) resistance mutations (ARTRM) is a major hurdle in achieving effective treatment and prevention against HIV. Using HIV pol sequences from 602 PLHIV from Kazakhstan, we analyzed ARTRMs for their association with factors that may promote development of ARTRMs. 56% PLHIV were infected with HIV subtype A6 and 42% with CRF02_AG. The ARTRM Q174K was associated with increased viral load and decreased CD4+ cell count, while infection with CRF02_AG was associated with a lower likelihood of Q174K. Interestingly, CRF02_AG was positively associated with the ARTRM L10V that, in turn, was observed frequently with darunavir administration. Infection with CRF02_AG was positively associated with the ARTRM S162A that, in turn, was frequently observed with the administration of nevirapine, also associated with lower CD4 counts. Zidovudine or Nevirapine receipt was associated with the development of the ARTRM E138A, that, in turn, was associated with lower CD4 counts. Determination of a patient's HIV variant can help guide ART choice in Kazakhstan. For example, PLHIV infected with CRF02_AG will benefit less from darunavir and nevirapine, and emtricitabine should replace zidovudine.
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Affiliation(s)
- Ainur Mukhatayeva
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Aidana Mustafa
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Natalya Dzissyuk
- Kazakh Scientific Center of Dermatology and Infectious Diseases, Almaty, Kazakhstan
| | - Alpamys Issanov
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Zhussipbek Mukhatayev
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Bauyrzhan Bayserkin
- Kazakh Scientific Center of Dermatology and Infectious Diseases, Almaty, Kazakhstan
| | | | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan.
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13
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Sivay MV, Maksimenko LV, Osipova IP, Nefedova AA, Gashnikova MP, Zyryanova DP, Ekushov VE, Totmenin AV, Nalimova TM, Ivlev VV, Kapustin DV, Pozdnyakova LL, Skudarnov SE, Ostapova TS, Yaschenko SV, Nazarova OI, Chernov AS, Ismailova TN, Maksutov RA, Gashnikova NM. Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic. Front Microbiol 2022; 13:946787. [PMID: 36118194 PMCID: PMC9470837 DOI: 10.3389/fmicb.2022.946787] [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: 05/18/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
HIV-1 epidemic in Russia is one of the fastest growing in the world reaching 1.14 million people living with HIV-1 (PLWH) in 2021. Since mid-1990s, the HIV-1 epidemic in Russia has started to grow substantially due to the multiple HIV-1 outbreaks among persons who inject drugs (PWID) leading to expansion of the HIV-1 sub-subtype A6 (former Soviet Union (FSU) subtype A). In 2006, a local HIV-1 sub-epidemic caused by the distribution of novel genetic lineage CRF63_02A6 was identified in Siberia. In this study, we used a comprehensive dataset of CRF63_02A6 pol gene sequences to investigate the spatiotemporal dynamic of the HIV-1 CRF63_02A6 sub-epidemic. This study includes all the available CRF63_02A6 HIV-1 pol gene sequences from Los Alamos National Laboratory (LANL) HIV Sequence Database. The HIV-1 subtypes of those sequences were conferred using phylogenetic analysis, and two automated HIV-1 subtyping tools Stanford HIVdb Program and COMET. Ancestral state reconstruction and origin date were estimated using Nextstrain. Evolutionary rate and phylodynamic analysis were estimated using BEAST v 1.10.4. CRF63_02A6 was assigned for 872 pol gene sequences using phylogenetic analysis approach. Predominant number (n = 832; 95.4%) of those sequences were from Russia; the remaining 40 (4.6%) sequences were from countries of Central Asia. Out of 872 CRF63_02A6 sequences, the corresponding genetic variant was assigned for 75.7 and 79.8% of sequences by Stanford and COMET subtyping tools, respectively. Dated phylogenetic analysis of the CRF63_02A6 sequences showed that the virus most likely originated in Novosibirsk, Russia, in 2005. Over the last two decades CRF63_02A6 has been widely distributed across Russia and has been sporadically detected in countries of Central Asia. Introduction of new genetic variant into mature sub-subtype A6 and CRF02_AGFSU epidemics could promote the increase of viral genetic diversity and emergence of new recombinant forms. Further HIV-1 studies are needed due to a continuing rapid virus distribution. Also, the implementation of HIV-1 prevention programs is required to reduce HIV-1 transmission. This study also highlights the discrepancies in HIV-1 subtyping approaches. The reference lists of HIV-1 sequences implemented in widely used HIV-1 automated subtyping tools need to be updated to provide reliable results.
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Affiliation(s)
- Mariya V. Sivay
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
- *Correspondence: Mariya V. Sivay, ;
| | - Lada V. Maksimenko
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Irina P. Osipova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Anastasiya A. Nefedova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Mariya P. Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Dariya P. Zyryanova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Vasiliy E. Ekushov
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Alexei V. Totmenin
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Tatyana M. Nalimova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Vladimir V. Ivlev
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | | | | | - Sergey E. Skudarnov
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk, Russia
| | - Tatyana S. Ostapova
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk, Russia
| | | | - Olga I. Nazarova
- Omsk City Center of Prevention and Control of AIDS and Other Infectious Diseases, Omsk, Russia
| | - Aleksander S. Chernov
- Tomsk Regional Center for Prevention and Control of AIDS and Other Infectious Diseases, Tomsk, Russia
| | - Tatyana N. Ismailova
- Tomsk Regional Center for Prevention and Control of AIDS and Other Infectious Diseases, Tomsk, Russia
| | - Rinat A. Maksutov
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Natalya M. Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
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14
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McTernan PM, Siggins RW, Catinis A, Amedee AM, Simon L, Molina PE. Chronic Binge Alcohol and Ovarian Hormone Loss Dysregulate Circulating Immune Cell SIV Co-Receptor Expression and Mitochondrial Homeostasis in SIV-Infected Rhesus Macaques. Biomolecules 2022; 12:946. [PMID: 35883501 PMCID: PMC9313096 DOI: 10.3390/biom12070946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 12/01/2022] Open
Abstract
Effective antiretroviral therapy (ART) has transitioned HIV to a chronic disease, with more than 50% of people living with HIV (PLWH) being over the age of 50. HIV targets activated CD4+ T cells expressing HIV-specific co-receptors (CCR5 and CXCR4). Previously, we reported that chronic binge alcohol (CBA)-administered male rhesus macaques had a higher percentage of gut CD4+ T cells expressing simian immunodeficiency virus (SIV) co-receptor CXCR4. Evidence also suggests that gonadal hormone loss increased activated peripheral T cells. Further, mitochondrial function is critical for HIV replication and alcohol dysregulates mitochondrial homeostasis. Hence, we tested the hypothesis that CBA and ovariectomy (OVX) increase circulating activated CD4+ T cells expressing SIV co-receptors and dysregulate mitochondrial homeostasis in SIV-infected female rhesus macaques. Results showed that at the study end-point, CBA/SHAM animals had increased peripheral CD4+ T cell SIV co-receptor expression, and a lower CD4+ T cell count compared to CBA/OVX animals. CBA and OVX animals had altered peripheral immune cell gene expression important for maintaining mitochondrial homeostasis. These results provide insights into how at-risk alcohol use could potentially impact viral expression in cellular reservoirs, particularly in SIV-infected ovariectomized rhesus macaques.
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Affiliation(s)
- Patrick M. McTernan
- Comprehensive Alcohol Research Center, New Orleans, LA 70112, USA; (P.M.M.); (R.W.S.); (A.M.A.); (L.S.)
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Robert W. Siggins
- Comprehensive Alcohol Research Center, New Orleans, LA 70112, USA; (P.M.M.); (R.W.S.); (A.M.A.); (L.S.)
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Anna Catinis
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Angela M. Amedee
- Comprehensive Alcohol Research Center, New Orleans, LA 70112, USA; (P.M.M.); (R.W.S.); (A.M.A.); (L.S.)
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Liz Simon
- Comprehensive Alcohol Research Center, New Orleans, LA 70112, USA; (P.M.M.); (R.W.S.); (A.M.A.); (L.S.)
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Patricia E. Molina
- Comprehensive Alcohol Research Center, New Orleans, LA 70112, USA; (P.M.M.); (R.W.S.); (A.M.A.); (L.S.)
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
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15
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Rheinemann L, Downhour DM, Davenport KA, McKeown AN, Sundquist WI, Elde NC. Recurrent evolution of an inhibitor of ESCRT-dependent virus budding and LINE-1 retrotransposition in primates. Curr Biol 2022; 32:1511-1522.e6. [PMID: 35245459 PMCID: PMC9007875 DOI: 10.1016/j.cub.2022.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022]
Abstract
Most antiviral proteins recognize specific features of viruses. In contrast, the recently described antiviral factor retroCHMP3 interferes with the "host endosomal complexes required for transport" (ESCRT) pathway to inhibit the budding of enveloped viruses. RetroCHMP3 arose independently on multiple occasions via duplication and truncation of the gene encoding the ESCRT-III factor CHMP3. However, since the ESCRT pathway is essential for cellular membrane fission reactions, ESCRT inhibition is potentially cytotoxic. This raises fundamental questions about how hosts can repurpose core cellular functions into antiviral functions without incurring a fitness cost due to excess cellular toxicity. We reveal the evolutionary process of detoxification for retroCHMP3 in New World monkeys using a combination of ancestral reconstructions, cytotoxicity, and virus release assays. A duplicated, full-length copy of retroCHMP3 in the ancestors of New World monkeys provides modest inhibition of virus budding while exhibiting subtle cytotoxicity. Ancient retroCHMP3 then accumulated mutations that reduced cytotoxicity but preserved virus inhibition before a truncating stop codon arose in the more recent ancestors of squirrel monkeys, resulting in potent inhibition. In species where full-length copies of retroCHMP3 still exist, their artificial truncation generated potent virus-budding inhibitors with little cytotoxicity, revealing the potential for future antiviral defenses in modern species. In addition, we discovered that retroCHMP3 restricts LINE-1 retrotransposition, revealing how different challenges to genome integrity might explain multiple independent origins of retroCHMP3 in different species to converge on new immune functions.
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Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Diane Miller Downhour
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Kristen A Davenport
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Alesia N McKeown
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA.
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16
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Lentiviral Nef Proteins Differentially Govern the Establishment of Viral Latency. J Virol 2022; 96:e0220621. [PMID: 35266804 DOI: 10.1128/jvi.02206-21] [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: 11/20/2022] Open
Abstract
Despite the clinical importance of latent human immunodeficiency virus type 1 (HIV-1) infection, our understanding of the biomolecular processes involved in HIV-1 latency control is still limited. This study was designed to address whether interactions between viral proteins, specifically HIV Nef, and the host cell could affect latency establishment. The study was driven by three reported observations. First, early reports suggested that human immunodeficiency virus type 2 (HIV-2) infection in patients produces a lower viral RNA/DNA ratio than HIV-1 infection, potentially indicating an increased propensity of HIV-2 to produce latent infection. Second, Nef, an early viral gene product, has been shown to alter the activation state of infected cells in a lentiviral lineage-dependent manner. Third, it has been demonstrated that the ability of HIV-1 to establish latent infection is a function of the activation state of the host cell at the time of infection. Based on these observations, we reasoned that HIV-2 Nef may have the ability to promote latency establishment. We demonstrate that HIV-1 latency establishment in T cell lines and primary T cells is indeed differentially modulated by Nef proteins. In the context of an HIV-1 backbone, HIV-1 Nef promoted active HIV-1 infection, while HIV-2 Nef strongly promoted latency establishment. Given that Nef represents the only difference in these HIV-1 vectors and is known to interact with numerous cellular factors, these data add support to the idea that latency establishment is a host cell-virus interaction phenomenon, but they also suggest that the HIV-1 lineage may have evolved mechanisms to counteract host cell suppression. IMPORTANCE Therapeutic attempts to eliminate the latent HIV-1 reservoir have failed, at least in part due to our incomplete biomolecular understanding of how latent HIV-1 infection is established and maintained. We here address the fundamental question of whether all lentiviruses actually possess a similar capacity to establish latent infections or whether there are differences between the lentiviral lineages driving differential latency establishment that could be exploited to develop improved latency reversal agents. Research investigating the viral RNA/DNA ratio in HIV-1 and HIV-2 patients could suggest that HIV-2 indeed has a much higher propensity to establish latent infections, a trait that we found, at least in part, to be attributable to the HIV-2 Nef protein. Reported Nef-mediated effects on host cell activation thus also affect latency establishment, and HIV-1 vectors that carry different lentiviral nef genes should become key tools to develop a better understanding of the biomolecular basis of HIV-1 latency establishment.
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17
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Zhang H, Cao S, Gao Y, Sun X, Jiang F, Zhao B, Ding H, Dong T, Han X, Shang H. HIV-1-Specific Immunodominant T-Cell Responses Drive the Dynamics of HIV-1 Recombination Following Superinfection. Front Immunol 2022; 12:820628. [PMID: 35095925 PMCID: PMC8794799 DOI: 10.3389/fimmu.2021.820628] [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] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
A series of HIV-1 CRF01_AE/CRF07_BC recombinants were previously found to have emerged gradually in a superinfected patient (patient LNA819). However, the extent to which T-cell responses influenced the development of these recombinants after superinfection is unclear. In this study, we undertook a recombination structure analysis of the gag, pol, and nef genes from longitudinal samples of patient LNA819. A total of 9 pol and 5 nef CRF01_AE/CRF07_BC recombinants were detected. The quasispecies makeup and the composition of the pol and nef gene recombinants changed continuously, suggestive of continuous evolution in vivo. T-cell responses targeting peptides of the primary strain and the recombination regions were screened. The results showed that Pol-LY10, Pol-RY9, and Nef-GL9 were the immunodominant epitopes. Pol-LY10 overlapped with the recombination breakpoints in multiple recombinants. For the LY10 epitope, escape from T-cell responses was mediated by both recombination with a CRF07_BC insertion carrying the T467E/T472V variants and T467N/T472V mutations originating in the CRF01_AE strain. In pol recombinants R8 and R9, the recombination breakpoints were located ~23 amino acids upstream of the RY9 epitope. The appearance of new recombination breakpoints harboring a CRF07_BC insertion carrying a R984K variant was associated with escape from RY9-specific T-cell responses. Although the Nef-GL9 epitope was located either within or 10~11 amino acids downstream of the recombination breakpoints, no variant of this epitope was observed in the nef recombinants. Instead, a F85V mutation originating in the CRF01_AE strain was the main immune escape mechanism. Understanding the cellular immune pressure on recombination is critical for monitoring the new circulating recombinant forms of HIV and designing epitope-based vaccines. Vaccines targeting antigens that are less likely to escape immune pressure by recombination and/or mutation are likely to be of benefit to patients with HIV-1.
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Affiliation(s)
- Hui Zhang
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Shuang Cao
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Clinical Laboratory, China Medical University Shengjing Hospital Nanhu Branch, Shenyang, China
| | - Yang Gao
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Xiao Sun
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Fanming Jiang
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Bin Zhao
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Haibo Ding
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Xiaoxu Han
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Hong Shang
- National Health Commission (NHC) Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
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18
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The Hippo signaling component LATS2 enhances innate immunity to inhibit HIV-1 infection through PQBP1-cGAS pathway. Cell Death Differ 2022; 29:192-205. [PMID: 34385679 PMCID: PMC8738759 DOI: 10.1038/s41418-021-00849-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023] Open
Abstract
As the most primordial signaling pathway in animal physiology, the Hippo pathway and innate immunity play crucial roles not only in sensing cellular conditions or infections, but also in various metabolite homeostasis and tumorigenesis. However, the correlation between cellular homeostasis and antiviral defense is not well understood. The core kinase LATS1/2, could either enhance or inhibit the anti-tumor immunity in different cellular contexts. In this study, we found that LATS2 can interact with PQBP1, the co-factor of cGAS, thus enhanced the cGAS-STING mediated innate immune response to HIV-1 challenge. LATS2 was observed to upregulate type-I interferon (IFN-I) and cytokines in response to HIV-1 reverse-transcribed DNA and inhibited HIV-1 infection. Due to the involvement of PQBP1, the function of LATS2 in regulating cGAS activity is not relying on the downstream YAP/TAZ as that in the canonical Hippo pathway. The related kinase activity of LATS2 was verified, and the potential phosphorylation site of PQBP1 was identified. Our study established a novel connection between Hippo signaling and innate immunity, thus may provide new potential intervention target on antiviral therapeutics.
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19
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Albanese M, Ruhle A, Mittermaier J, Mejías-Pérez E, Gapp M, Linder A, Schmacke NA, Hofmann K, Hennrich AA, Levy DN, Humpe A, Conzelmann KK, Hornung V, Fackler OT, Keppler OT. Rapid, efficient and activation-neutral gene editing of polyclonal primary human resting CD4 + T cells allows complex functional analyses. Nat Methods 2022; 19:81-89. [PMID: 34949807 PMCID: PMC8748193 DOI: 10.1038/s41592-021-01328-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
CD4+ T cells are central mediators of adaptive and innate immune responses and constitute a major reservoir for human immunodeficiency virus (HIV) in vivo. Detailed investigations of resting human CD4+ T cells have been precluded by the absence of efficient approaches for genetic manipulation limiting our understanding of HIV replication and restricting efforts to find a cure. Here we report a method for rapid, efficient, activation-neutral gene editing of resting, polyclonal human CD4+ T cells using optimized cell cultivation and nucleofection conditions of Cas9-guide RNA ribonucleoprotein complexes. Up to six genes, including HIV dependency and restriction factors, were knocked out individually or simultaneously and functionally characterized. Moreover, we demonstrate the knock in of double-stranded DNA donor templates into different endogenous loci, enabling the study of the physiological interplay of cellular and viral components at single-cell resolution. Together, this technique allows improved molecular and functional characterizations of HIV biology and general immune functions in resting CD4+ T cells.
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Affiliation(s)
- Manuel Albanese
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany.
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy.
| | - Adrian Ruhle
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Jennifer Mittermaier
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Ernesto Mejías-Pérez
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Madeleine Gapp
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Andreas Linder
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
- Department of Medicine II, University Hospital, LMU München, Munich, Germany
| | - Niklas A Schmacke
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Katharina Hofmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Alexandru A Hennrich
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - David N Levy
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
| | - Andreas Humpe
- Department of Transfusion Medicine, Cell Therapeutics, and Hemostaseology, Department of Anesthesiology, University Hospital Munich, Munich, Germany
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany.
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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20
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Wang L, Sandmeyer A, Hübner W, Li H, Huser T, Chen BK. A Replication-Competent HIV Clone Carrying GFP-Env Reveals Rapid Env Recycling at the HIV-1 T Cell Virological Synapse. Viruses 2021; 14:v14010038. [PMID: 35062242 PMCID: PMC8781834 DOI: 10.3390/v14010038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/08/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 infection is enhanced by cell-cell adhesions between infected and uninfected T cells called virological synapses (VS). VS are initiated by the interactions of cell-surface HIV-1 envelope glycoprotein (Env) and CD4 on target cells and act as sites of viral assembly and viral transfer between cells. To study the process that recruits and retains HIV-1 Env at the VS, a replication-competent HIV-1 clone carrying an Env-sfGFP fusion protein was designed to enable live tracking of Env within infected cells. Combined use of surface pulse-labeling of Env and fluorescence recovery after photobleaching (FRAP) studies, enabled the visualization of the targeted accumulation and sustained recycling of Env between endocytic compartments (EC) and the VS. We observed dynamic exchange of Env at the VS, while the viral structural protein, Gag, was largely immobile at the VS. The disparate exchange rates of Gag and Env at the synapse support that the trafficking and/or retention of a majority of Env towards the VS is not maintained by entrapment by a Gag lattice or immobilization by binding to CD4 on the target cell. A FRAP study of an Env endocytosis mutant showed that recycling is not required for accumulation at the VS, but is required for the rapid exchange of Env at the VS. We conclude that the mechanism of Env accumulation at the VS and incorporation into nascent particles involves continuous internalization and targeted secretion rather than irreversible interactions with the budding virus, but that this recycling is largely dispensable for VS formation and viral transfer across the VS.
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Affiliation(s)
- Lili Wang
- Department of Medicine, Division of Infectious Disease, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (L.W.); (H.L.)
| | - Alice Sandmeyer
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany; (A.S.); (W.H.); (T.H.)
| | - Wolfgang Hübner
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany; (A.S.); (W.H.); (T.H.)
| | - Hongru Li
- Department of Medicine, Division of Infectious Disease, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (L.W.); (H.L.)
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany; (A.S.); (W.H.); (T.H.)
| | - Benjamin K. Chen
- Department of Medicine, Division of Infectious Disease, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (L.W.); (H.L.)
- Correspondence:
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21
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Kreger J, Komarova NL, Wodarz D. A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV. PLoS Comput Biol 2021; 17:e1009713. [PMID: 34936647 PMCID: PMC8730440 DOI: 10.1371/journal.pcbi.1009713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 01/05/2022] [Accepted: 12/02/2021] [Indexed: 11/30/2022] Open
Abstract
To study viral evolutionary processes within patients, mathematical models have been instrumental. Yet, the need for stochastic simulations of minority mutant dynamics can pose computational challenges, especially in heterogeneous systems where very large and very small sub-populations coexist. Here, we describe a hybrid stochastic-deterministic algorithm to simulate mutant evolution in large viral populations, such as acute HIV-1 infection, and further include the multiple infection of cells. We demonstrate that the hybrid method can approximate the fully stochastic dynamics with sufficient accuracy at a fraction of the computational time, and quantify evolutionary end points that cannot be expressed by deterministic models, such as the mutant distribution or the probability of mutant existence at a given infected cell population size. We apply this method to study the role of multiple infection and intracellular interactions among different virus strains (such as complementation and interference) for mutant evolution. Multiple infection is predicted to increase the number of mutants at a given infected cell population size, due to a larger number of infection events. We further find that viral complementation can significantly enhance the spread of disadvantageous mutants, but only in select circumstances: it requires the occurrence of direct cell-to-cell transmission through virological synapses, as well as a substantial fitness disadvantage of the mutant, most likely corresponding to defective virus particles. This, however, likely has strong biological consequences because defective viruses can carry genetic diversity that can be incorporated into functional virus genomes via recombination. Through this mechanism, synaptic transmission in HIV might promote virus evolvability. The evolution of human immunodeficiency virus within patients is an important part of the disease process. In particular, the presence of mutants that are resistant against anti-viral drugs can result in challenges to the long-term control of the infection. To study disease progression, computer simulations have been useful. However, in some cases these simulations can be difficult because of the complexity of the model. Here, we use a computational complexity reducing algorithm to simulate mutant dynamics in large populations, which can approximate the full model at a fraction of the time. The use of this algorithm allows us to study different transmission methods, viral processes that occur between virus strains within individual cells, and important quantities such as the mutant distribution or the probability of mutant existence at a given infected cell population size. We find that the direct synaptic cell-to-cell transmission of the virus through virological synapses can have strong biological consequences because it can promote potentially defective viruses that carry genetic diversity which can be incorporated into functional virus genomes during infection. Through this process, synaptic transmission in human immunodeficiency virus might promote virus evolvability.
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Affiliation(s)
- Jesse Kreger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
- * E-mail:
| | - Natalia L. Komarova
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
| | - Dominik Wodarz
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
- Department of Population Health and Disease Prevention Program in Public Health Susan and Henry Samueli College of Health Sciences, University of California, Irvine, California, United States of America
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22
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Koma T, Doi N, Takemoto M, Watanabe K, Yamamoto H, Nakashima S, Adachi A, Nomaguchi M. The Expression Level of HIV-1 Vif Is Optimized by Nucleotide Changes in the Genomic SA1D2prox Region during the Viral Adaptation Process. Viruses 2021; 13:2079. [PMID: 34696508 PMCID: PMC8537775 DOI: 10.3390/v13102079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
HIV-1 Vif plays an essential role in viral replication by antagonizing anti-viral cellular restriction factors, a family of APOBEC3 proteins. We have previously shown that naturally-occurring single-nucleotide mutations in the SA1D2prox region, which surrounds the splicing acceptor 1 and splicing donor 2 sites of the HIV-1 genome, dramatically alter the Vif expression level, resulting in variants with low or excessive Vif expression. In this study, we investigated how these HIV-1 variants with poor replication ability adapt and evolve under the pressure of APOBEC3 proteins. Adapted clones obtained through adaptation experiments exhibited an altered replication ability and Vif expression level compared to each parental clone. While various mutations were present throughout the viral genome, all replication-competent adapted clones with altered Vif expression levels were found to bear them within SA1D2prox, without exception. Indeed, the mutations identified within SA1D2prox were responsible for changes in the Vif expression levels and altered the splicing pattern. Moreover, for samples collected from HIV-1-infected patients, we showed that the nucleotide sequences of SA1D2prox can be chronologically changed and concomitantly affect the Vif expression levels. Taken together, these results demonstrated the importance of the SA1D2prox nucleotide sequence for modulating the Vif expression level during HIV-1 replication and adaptation.
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Affiliation(s)
- Takaaki Koma
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
| | - Naoya Doi
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
| | - Mai Takemoto
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Kyosuke Watanabe
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Hideki Yamamoto
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Satoshi Nakashima
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Akio Adachi
- Department of Microbiology, Kansai Medical University, Osaka 573-1010, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
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23
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Rheinemann L, Downhour DM, Bredbenner K, Mercenne G, Davenport KA, Schmitt PT, Necessary CR, McCullough J, Schmitt AP, Simon SM, Sundquist WI, Elde NC. RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis. Cell 2021; 184:5419-5431.e16. [PMID: 34597582 PMCID: PMC8929533 DOI: 10.1016/j.cell.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/03/2021] [Accepted: 09/03/2021] [Indexed: 11/26/2022]
Abstract
Many enveloped viruses require the endosomal sorting complexes required for transport (ESCRT) pathway to exit infected cells. This highly conserved pathway mediates essential cellular membrane fission events, which restricts the acquisition of adaptive mutations to counteract viral co-option. Here, we describe duplicated and truncated copies of the ESCRT-III factor CHMP3 that block ESCRT-dependent virus budding and arose independently in New World monkeys and mice. When expressed in human cells, these retroCHMP3 proteins potently inhibit release of retroviruses, paramyxoviruses, and filoviruses. Remarkably, retroCHMP3 proteins have evolved to reduce interactions with other ESCRT-III factors and have little effect on cellular ESCRT processes, revealing routes for decoupling cellular ESCRT functions from viral exploitation. The repurposing of duplicated ESCRT-III proteins thus provides a mechanism to generate broad-spectrum viral budding inhibitors without blocking highly conserved essential cellular ESCRT functions.
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Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Diane Miller Downhour
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kate Bredbenner
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY 10065, USA
| | - Gaelle Mercenne
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kristen A Davenport
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Phuong Tieu Schmitt
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christina R Necessary
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - John McCullough
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Anthony P Schmitt
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY 10065, USA.
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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24
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RNA Structures and Their Role in Selective Genome Packaging. Viruses 2021; 13:v13091788. [PMID: 34578369 PMCID: PMC8472981 DOI: 10.3390/v13091788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
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25
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Bhaskaran N, Schneider E, Faddoul F, Paes da Silva A, Asaad R, Talla A, Greenspan N, Levine AD, McDonald D, Karn J, Lederman MM, Pandiyan P. Oral immune dysfunction is associated with the expansion of FOXP3 +PD-1 +Amphiregulin + T cells during HIV infection. Nat Commun 2021; 12:5143. [PMID: 34446704 PMCID: PMC8390677 DOI: 10.1038/s41467-021-25340-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
Residual systemic inflammation and mucosal immune dysfunction persist in people living with HIV, despite treatment with combined anti-retroviral therapy, but the underlying immune mechanisms are poorly understood. Here we report that the altered immune landscape of the oral mucosa of HIV-positive patients on therapy involves increased TLR and inflammasome signaling, localized CD4+ T cell hyperactivation, and, counterintuitively, enrichment of FOXP3+ T cells. HIV infection of oral tonsil cultures in vitro causes an increase in FOXP3+ T cells expressing PD-1, IFN-γ, Amphiregulin and IL-10. These cells persist even in the presence of anti-retroviral drugs, and further expand when stimulated by TLR2 ligands and IL-1β. Mechanistically, IL-1β upregulates PD-1 expression via AKT signaling, and PD-1 stabilizes FOXP3 and Amphiregulin through a mechanism involving asparaginyl endopeptidase, resulting in FOXP3+ cells that are incapable of suppressing CD4+ T cells in vitro. The FOXP3+ T cells that are abundant in HIV-positive patients are phenotypically similar to the in vitro cultured, HIV-responsive FOXP3+ T cells, and their presence strongly correlates with CD4+ T cell hyper-activation. This suggests that FOXP3+ T cell dysregulation might play a role in the mucosal immune dysfunction of HIV patients on therapy.
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Affiliation(s)
- N Bhaskaran
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - E Schneider
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - F Faddoul
- Advanced Education in General Dentistry, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - A Paes da Silva
- Department of Periodontics, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - R Asaad
- University Hospitals Cleveland Medical Center AIDS Clinical Trials Unit, Division of Infectious Diseases & HIV Medicine, Cleveland, OH, USA
| | - A Talla
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - N Greenspan
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - A D Levine
- Department of Microbiology and Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - D McDonald
- Division of AIDS, NIAID, NIH, Bethesda, MD, USA
| | - J Karn
- Department of Microbiology and Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - M M Lederman
- University Hospitals Cleveland Medical Center AIDS Clinical Trials Unit, Division of Infectious Diseases & HIV Medicine, Cleveland, OH, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - P Pandiyan
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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26
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Bedwell GJ, Jang S, Li W, Singh PK, Engelman AN. rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo. Nucleic Acids Res 2021; 49:7330-7346. [PMID: 34165568 PMCID: PMC8287940 DOI: 10.1093/nar/gkab514] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/31/2021] [Accepted: 06/22/2021] [Indexed: 12/19/2022] Open
Abstract
HIV-1 integration favors recurrent integration gene (RIG) targets and genic proviruses can confer cell survival in vivo. However, the relationship between initial RIG integrants and how these evolve in patients over time are unknown. To address these shortcomings, we built phenomenological models of random integration in silico, which were used to identify 3718 RIGs as well as 2150 recurrent avoided genes from 1.7 million integration sites across 10 in vitro datasets. Despite RIGs comprising only 13% of human genes, they harbored 70% of genic HIV-1 integrations across in vitro and patient-derived datasets. Although previously reported to associate with super-enhancers, RIGs tracked more strongly with speckle-associated domains. While depletion of the integrase cofactor LEDGF/p75 significantly reduced recurrent HIV-1 integration in vitro, LEDGF/p75 primarily occupied non-speckle-associated regions of chromatin, suggesting a previously unappreciated dynamic aspect of LEDGF/p75 functionality in HIV-1 integration targeting. Finally, we identified only six genes from patient samples-BACH2, STAT5B, MKL1, MKL2, IL2RB and MDC1-that displayed enriched integration targeting frequencies and harbored proviruses that likely contributed to cell survival. Thus, despite the known preference of HIV-1 to target cancer-related genes for integration, we conclude that genic proviruses play a limited role to directly affect cell proliferation in vivo.
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Affiliation(s)
- Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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27
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Meng FZ, Liu JB, Wang X, Wang P, Hu WH, Hou W, Ho WZ. TLR7 Activation of Macrophages by Imiquimod Inhibits HIV Infection through Modulation of Viral Entry Cellular Factors. BIOLOGY 2021; 10:661. [PMID: 34356516 PMCID: PMC8301371 DOI: 10.3390/biology10070661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/15/2023]
Abstract
The Toll-like receptor (TLR) 7 is a viral sensor for detecting single-stranded ribonucleic acid (ssRNA), the activation of which can induce intracellular innate immunity against viral infections. Imiquimod, a synthetic ligand for TLR7, has been successfully used for the topical treatment of genital/perianal warts in immunocompetent individuals. We studied the effect of imiquimod on the human immunodeficiency virus (HIV) infection of primary human macrophages and demonstrated that the treatment of cells with imiquimod effectively inhibited infection with multiple strains (Bal, YU2, and Jago) of HIV. This anti-HIV activity of imiquimod was the most potent when macrophages were treated prior to infection. Infection of macrophages with pseudotyped HIV NL4-3-ΔEnv-eGFP-Bal showed that imiquimod could block the viral entry. Further mechanistic studies revealed that while imiquimod had little effect on the interferons (IFNs) expression, its treatment of macrophages resulted in the increased production of the CC chemokines (human macrophage inflammatory protein-1 alpha (MIP-1α), MIP-1β, and upon activation regulated normal T cells expressed and secreted (RANTES)), the natural ligands of HIV entry co-receptor CCR5, and decreased the expression of CD4 and CCR5. The addition of the antibodies against the CC chemokines to macrophage cultures could block imiquimod-mediated HIV inhibition. These findings provide experimental evidence to support the notion that TLR7 participates in the intracellular immunity against HIV in macrophages, suggesting the further clinical evaluation of imiquimod for its additional benefit of treating genital/perianal warts in people infected with HIV.
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Affiliation(s)
- Feng-Zhen Meng
- School of Basic Medical Sciences, Wuhan University, Wuhan 430000, China;
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA; (J.-B.L.); (X.W.); (P.W.); (W.-H.H.)
| | - Jin-Biao Liu
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA; (J.-B.L.); (X.W.); (P.W.); (W.-H.H.)
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA; (J.-B.L.); (X.W.); (P.W.); (W.-H.H.)
| | - Peng Wang
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA; (J.-B.L.); (X.W.); (P.W.); (W.-H.H.)
| | - Wen-Hui Hu
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA; (J.-B.L.); (X.W.); (P.W.); (W.-H.H.)
| | - Wei Hou
- School of Basic Medical Sciences, Wuhan University, Wuhan 430000, China;
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA; (J.-B.L.); (X.W.); (P.W.); (W.-H.H.)
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28
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Bauby H, Ward CC, Hugh-White R, Swanson CM, Schulz R, Goujon C, Malim MH. HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 + T Cells Early Postinfection. mBio 2021; 12:e0136921. [PMID: 34154423 PMCID: PMC8263007 DOI: 10.1128/mbio.01369-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
The interactions between a virus and its host are complex but can be broadly categorized as either viral manipulation of cellular functions or cellular responses to infection. These processes begin at the earliest point of contact between virus and cell and frequently result in changes to cellular gene expression, making genome-wide transcriptomics a useful tool to study them. Several previous studies have used transcriptomics to evaluate the cellular responses to human immunodeficiency virus type 1 (HIV-1) infection; however, none have examined events in primary CD4+ T cells during the first 24 h of infection. Here, we analyzed CD4+ T cells at 4.5, 8, 12, 24, and 48 h following infection. We describe global changes to host gene expression commencing at 4.5 h postinfection and evolving over the ensuing time points. We identify upregulation of genes related to innate immunity, cytokine production, and apoptosis and downregulation of those involved in transcription and translation. We further demonstrate that the viral accessory protein Vpr is necessary for almost all gene expression changes seen at 12 h postinfection and the majority of those seen at 48 h. Identifying this new role for Vpr not only provides fresh perspective on its possible function but also adds further insight into the interplay between HIV-1 and its host at the cellular level. IMPORTANCE HIV-1, while now treatable, remains an important human pathogen causing significant morbidity and mortality globally. The virus predominantly infects CD4+ T cells and, if not treated with medication, ultimately causes their depletion, resulting in AIDS and death. Further refining our understanding of the interaction between HIV-1 and these cells has the potential to inform further therapeutic development. Previous studies have used transcriptomics to assess gene expression changes in CD4+ T cells following HIV-1 infection; here, we provide a detailed examination of changes occurring in the first 24 h of infection. Importantly, we define the viral protein Vpr as essential for the changes observed at this early stage. This finding has significance for understanding the role of Vpr in infection and pathogenesis and also for interpreting previous transcriptomic analyses of HIV-1 infection.
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Affiliation(s)
- Hélène Bauby
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Christopher C. Ward
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rupert Hugh-White
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Reiner Schulz
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Caroline Goujon
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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29
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Kockler ZW, Gordenin DA. From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution. Cells 2021; 10:1557. [PMID: 34202997 PMCID: PMC8234929 DOI: 10.3390/cells10061557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
The current SARS-CoV-2 pandemic underscores the importance of understanding the evolution of RNA genomes. While RNA is subject to the formation of similar lesions as DNA, the evolutionary and physiological impacts RNA lesions have on viral genomes are yet to be characterized. Lesions that may drive the evolution of RNA genomes can induce breaks that are repaired by recombination or can cause base substitution mutagenesis, also known as base editing. Over the past decade or so, base editing mutagenesis of DNA genomes has been subject to many studies, revealing that exposure of ssDNA is subject to hypermutation that is involved in the etiology of cancer. However, base editing of RNA genomes has not been studied to the same extent. Recently hypermutation of single-stranded RNA viral genomes have also been documented though its role in evolution and population dynamics. Here, we will summarize the current knowledge of key mechanisms and causes of RNA genome instability covering areas from the RNA world theory to the SARS-CoV-2 pandemic of today. We will also highlight the key questions that remain as it pertains to RNA genome instability, mutations accumulation, and experimental strategies for addressing these questions.
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Affiliation(s)
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA;
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30
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Sevillano N, Green EM, Votteler J, Kim DY, Ren X, Yang B, Liu X, Lourenço AL, Hurley JH, Farr-Jones S, Gross JD, Cheng Y, Craik CS. Identification of recombinant Fabs for structural and functional characterization of HIV-host factor complexes. PLoS One 2021; 16:e0250318. [PMID: 33983947 PMCID: PMC8118348 DOI: 10.1371/journal.pone.0250318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/05/2021] [Indexed: 12/03/2022] Open
Abstract
Viral infection and pathogenesis is mediated by host protein—viral protein complexes that are important targets for therapeutic intervention as they are potentially less prone to development of drug resistance. We have identified human, recombinant antibodies (Fabs) from a phage display library that bind to three HIV-host complexes. We used these Fabs to 1) stabilize the complexes for structural studies; and 2) facilitate characterization of the function of these complexes. Specifically, we generated recombinant Fabs to Vif-CBF-β-ELOB-ELOC (VCBC); ESCRT-I complex and AP2-complex. For each complex we measured binding affinities with KD values of Fabs ranging from 12–419 nM and performed negative stain electron microscopy (nsEM) to obtain low-resolution structures of the HIV-Fab complexes. Select Fabs were converted to scFvs to allow them to fold intracellularly and perturb HIV-host protein complex assembly without affecting other pathways. To identify these recombinant Fabs, we developed a rapid screening pipeline that uses quantitative ELISAs and nsEM to establish whether the Fabs have overlapping or independent epitopes. This pipeline approach is generally applicable to other particularly challenging antigens that are refractory to immunization strategies for antibody generation including multi-protein complexes providing specific, reproducible, and renewable antibody reagents for research and clinical applications. The curated antibodies described here are available to the scientific community for further structural and functional studies on these critical HIV host-factor proteins.
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Affiliation(s)
- Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Evan M. Green
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Jörg Votteler
- Department of Biochemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Dong Young Kim
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Xuefeng Ren
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
| | - Bei Yang
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
| | - Xi Liu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - André Luiz Lourenço
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - James H. Hurley
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
| | - Shauna Farr-Jones
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, California, United States of America
| | - John D. Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California, San Francisco, California, United States of America
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
- * E-mail:
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31
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Kreger J, Garcia J, Zhang H, Komarova NL, Wodarz D, Levy DN. Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection. Virus Evol 2021; 7:veab026. [PMID: 34012557 PMCID: PMC8117450 DOI: 10.1093/ve/veab026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recombination has been shown to contribute to human immunodeficiency virus-1 (HIV-1) evolution in vivo, but the underlying dynamics are extremely complex, depending on the nature of the fitness landscapes and of epistatic interactions. A less well-studied determinant of recombinant evolution is the mode of virus transmission in the cell population. HIV-1 can spread by free virus transmission, resulting largely in singly infected cells, and also by direct cell-to-cell transmission, resulting in the simultaneous infection of cells with multiple viruses. We investigate the contribution of these two transmission pathways to recombinant evolution, by applying mathematical models to in vitro experimental data on the growth of fluorescent reporter viruses under static conditions (where both transmission pathways operate), and under gentle shaking conditions, where cell-to-cell transmission is largely inhibited. The parameterized mathematical models are then used to extrapolate the viral evolutionary dynamics beyond the experimental settings. Assuming a fixed basic reproductive ratio of the virus (independent of transmission pathway), we find that recombinant evolution is fastest if virus spread is driven only by cell-to-cell transmission and slows down if both transmission pathways operate. Recombinant evolution is slowest if all virus spread occurs through free virus transmission. This is due to cell-to-cell transmission 1, increasing infection multiplicity; 2, promoting the co-transmission of different virus strains from cell to cell; and 3, increasing the rate at which point mutations are generated as a result of more reverse transcription events. This study further resulted in the estimation of various parameters that characterize these evolutionary processes. For example, we estimate that during cell-to-cell transmission, an average of three viruses successfully integrated into the target cell, which can significantly raise the infection multiplicity compared to free virus transmission. In general, our study points towards the importance of infection multiplicity and cell-to-cell transmission for HIV evolution.
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Affiliation(s)
- Jesse Kreger
- Department of Mathematics, Rowland Hall, University of California, Irvine, CA 92697, USA
| | - Josephine Garcia
- Department of Basic Science, New York University College of Dentistry, 921 Schwartz Building, 345 East 24th Street, New York, NY 10010-9403, USA
| | - Hongtao Zhang
- Department of Basic Science, New York University College of Dentistry, 921 Schwartz Building, 345 East 24th Street, New York, NY 10010-9403, USA
| | - Natalia L Komarova
- Department of Mathematics, Rowland Hall, University of California, Irvine, CA 92697, USA
| | - Dominik Wodarz
- Department of Mathematics, Rowland Hall, University of California, Irvine, CA 92697, USA.,Department of Population Health and Disease Prevention, Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA
| | - David N Levy
- Department of Basic Science, New York University College of Dentistry, 921 Schwartz Building, 345 East 24th Street, New York, NY 10010-9403, USA
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32
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Cilento ME, Kirby KA, Sarafianos SG. Avoiding Drug Resistance in HIV Reverse Transcriptase. Chem Rev 2021; 121:3271-3296. [PMID: 33507067 DOI: 10.1021/acs.chemrev.0c00967] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV reverse transcriptase (RT) is an enzyme that plays a major role in the replication cycle of HIV and has been a key target of anti-HIV drug development efforts. Because of the high genetic diversity of the virus, mutations in RT can impart resistance to various RT inhibitors. As the prevalence of drug resistance mutations is on the rise, it is necessary to design strategies that will lead to drugs less susceptible to resistance. Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance. We also present novel strategies that can be useful to overcome RT's ability to escape therapies through drug resistance. While resistance may not be completely avoidable, designing drugs based on the strategies and principles discussed in this review could decrease the prevalence of drug resistance.
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Affiliation(s)
- Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
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33
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Abstract
Recent studies have renewed interest in developing novel antiviral therapeutics and vaccines based on defective interfering particles (DIPs)—a subset of viral deletion mutants that conditionally replicate. Identifying and engineering DIPs require that viral cis- and trans-acting elements be accurately mapped. It has long been known that noncoding genomic regions can be obligate cis elements acted upon in trans by gene products. In viruses, cis elements regulate gene expression, encapsidation, and other maturation processes, but mapping these elements relies on targeted iterative deletion or laborious prospecting for rare spontaneously occurring mutants. Here, we introduce a method to comprehensively map viral cis and trans elements at single-nucleotide resolution by high-throughput random deletion. Variable-size deletions are randomly generated by transposon integration, excision, and exonuclease chewback and then barcoded for tracking via sequencing (i.e., random deletion library sequencing [RanDeL-seq]). Using RanDeL-seq, we generated and screened >23,000 HIV-1 variants to generate a single-base resolution map of HIV-1’s cis and trans elements. The resulting landscape recapitulated HIV-1’s known cis-acting elements (i.e., long terminal repeat [LTR], Ψ, and Rev response element [RRE]) and, surprisingly, indicated that HIV-1’s central DNA flap (i.e., central polypurine tract [cPPT] to central termination sequence [CTS]) is as critical as the LTR, Ψ, and RRE for long-term passage. Strikingly, RanDeL-seq identified a previously unreported ∼300-bp region downstream of RRE extending to splice acceptor 7 that is equally critical for sustained viral passage. RanDeL-seq was also used to construct and screen a library of >90,000 variants of Zika virus (ZIKV). Unexpectedly, RanDeL-seq indicated that ZIKV’s cis-acting regions are larger than the untranscribed (UTR) termini, encompassing a large fraction of the nonstructural genes. Collectively, RanDeL-seq provides a versatile framework for generating viral deletion mutants, enabling discovery of replication mechanisms and development of novel antiviral therapeutics, particularly for emerging viral infections.
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34
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Li W, Singh PK, Sowd GA, Bedwell GJ, Jang S, Achuthan V, Oleru AV, Wong D, Fadel HJ, Lee K, KewalRamani VN, Poeschla EM, Herschhorn A, Engelman AN. CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration. mBio 2020; 11:e02254-20. [PMID: 32994325 PMCID: PMC7527728 DOI: 10.1128/mbio.02254-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Lentiviral DNA integration favors transcriptionally active chromatin. We previously showed that the interaction of human immunodeficiency virus type 1 (HIV-1) capsid with cleavage and polyadenylation specificity factor 6 (CPSF6) localizes viral preintegration complexes (PICs) to nuclear speckles for integration into transcriptionally active speckle-associated domains (SPADs). In the absence of the capsid-CPSF6 interaction, PICs uncharacteristically accumulate at the nuclear periphery and target heterochromatic lamina-associated domains (LADs) for integration. The integrase-binding protein lens epithelium-derived growth factor (LEDGF)/p75 in contrast to CPSF6 predominantly functions to direct HIV-1 integration to interior regions of transcription units. Though CPSF6 and LEDGF/p75 can reportedly interact with the capsid and integrase proteins of both primate and nonprimate lentiviruses, the extents to which these different viruses target SPADs versus LADs, as well as their dependencies on CPSF6 and LEDGF/p75 for integration targeting, are largely unknown. Here, we mapped 5,489,157 primate and nonprimate lentiviral integration sites in HEK293T and Jurkat T cells as well as derivative cells that were knocked out or knocked down for host factor expression. Despite marked preferences of all lentiviruses to target genes for integration, nonprimate lentiviruses only marginally favored SPADs, with corresponding upticks in LAD-proximal integration. While LEDGF/p75 knockout disrupted the intragenic integration profiles of all lentiviruses similarly, CPSF6 depletion specifically counteracted SPAD integration targeting by primate lentiviruses. CPSF6 correspondingly failed to appreciably interact with nonprimate lentiviral capsids. We conclude that primate lentiviral capsid proteins evolved to interact with CPSF6 to optimize PIC localization for integration into transcriptionally active SPADs.IMPORTANCE Integration is the defining step of the retroviral life cycle and underlies the inability to cure HIV/AIDS through the use of intensified antiviral therapy. The reservoir of latent, replication-competent proviruses that forms early during HIV infection reseeds viremia when patients discontinue medication. HIV cure research is accordingly focused on the factors that guide provirus formation and associated chromatin environments that regulate transcriptional reactivation, and studies of orthologous infectious agents such as nonprimate lentiviruses can inform basic principles of HIV biology. HIV-1 utilizes the integrase-binding protein LEDGF/p75 and the capsid interactor CPSF6 to target speckle-associated domains (SPADs) for integration. However, the extent to which these two host proteins regulate integration of other lentiviruses is largely unknown. Here, we mapped millions of retroviral integration sites in cell lines that were depleted for LEDGF/p75 and/or CPSF6. Our results reveal that primate lentiviruses uniquely target SPADs for integration in a CPSF6-dependent manner.
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Affiliation(s)
- Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory A Sowd
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Amarachi V Oleru
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Doris Wong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hind J Fadel
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - KyeongEun Lee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Alon Herschhorn
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Guo T, Qiu Z, Kitagawa K, Iwami S, Rong L. Modeling HIV multiple infection. J Theor Biol 2020; 509:110502. [PMID: 32998053 DOI: 10.1016/j.jtbi.2020.110502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/09/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
Multiple infection of target cells by human immunodeficiency virus (HIV) may lead to viral escape from host immune responses and drug resistance to antiretroviral therapy, bringing more challenges to the control of infection. The mechanisms underlying HIV multiple infection and their relative contributions are not fully understood. In this paper, we develop and analyze a mathematical model that includes sequential cell-free virus infection (i.e.one virus is transmitted each time in a sequential infection of target cells by virus) and cell-to-cell transmission (i.e.multiple viral genomes are transmitted simultaneously from infected to uninfected cells). By comparing model prediction with the distribution data of proviral genomes in HIV-infected spleen cells, we find that multiple infection can be well explained when the two modes of viral transmission are both included. Numerical simulation using the parameter estimates from data fitting shows that the majority of T cell infections are attributed to cell-to-cell transmission and this transmission mode also accounts for more than half of cell's multiple infections. These results suggest that cell-to-cell transmission plays a critical role in forming HIV multiple infection and thus has important implications for HIV evolution and pathogenesis.
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Affiliation(s)
- Ting Guo
- School of Science, Nanjing University of Science and Technology, Nanjing 210094, China; Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
| | - Zhipeng Qiu
- School of Science, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Kosaku Kitagawa
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8190395, Japan
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8190395, Japan
| | - Libin Rong
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA.
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36
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Udeze AO, Olaleye DO, Odaibo GN. Phylogeny of partial gag, pol and env genes show predominance of HIV-1G and CRF02_AG with emerging recombinants in south-eastern Nigeria. Heliyon 2020; 6:e04310. [PMID: 32775738 PMCID: PMC7403892 DOI: 10.1016/j.heliyon.2020.e04310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/06/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022] Open
Abstract
Human Immunodeficiency Virus is characterized by high degree of genetic diversity with marked differences in its geographic distribution even within a country. This study was designed to identify the strains of HIV-1 circulating among infected individuals in southeastern parts of Nigeria. Genomic DNA was extracted from blood samples of 30 HIV-1 infected individuals from Anambra, Delta and Imo states of southeastern Nigeria. Portions of the genome corresponding to entire p24 gag, entire protease and C2-V3 env genes were amplified by nested PCR, sequenced using Sanger's method and phylogenetically analysed. Out of the 30 samples sequenced, 17, 28 and 14 readable sequences were obtained for gag, pol and env regions respectively. The most prevalent subtypes were CRF02_AG (41.2% in gag, 57.1% in pol protease and 50.0% in env) and G (29.4% in gag, 35.7% in pol protease and 35.7% in env). Other subtypes identified include A (17.7% in gag, 7.1% in env) and J (7.1% in env). Also 2 sequences each in gag (11.8%) and pol protease (7.1%) regions were unclassified but preliminary analysis showed they are recombinants. Furthermore, 71.4% of the isolates with sequences in the 3 regions and 26.7% of those with sequences in 2 genomic regions were recombinant forms. CRF02_AG and subtype G are the predominant HIV-1 strains circulating among infected individuals in southeastern Nigeria. Preliminary analysis results of unclassified sequences suggest that they are new recombinants.
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Affiliation(s)
- Augustine O Udeze
- Department of Virology, College of Medicine, University College Hospital, Ibadan, Nigeria.,Virology Unit, Department of Microbiology, University of Ilorin, P.M.B 1515, Ilorin, Nigeria
| | - David O Olaleye
- Department of Virology, College of Medicine, University College Hospital, Ibadan, Nigeria
| | - Georgina N Odaibo
- Department of Virology, College of Medicine, University College Hospital, Ibadan, Nigeria
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37
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Li GH, Maric D, Major EO, Nath A. Productive HIV infection in astrocytes can be established via a nonclassical mechanism. AIDS 2020; 34:963-978. [PMID: 32379159 PMCID: PMC7429268 DOI: 10.1097/qad.0000000000002512] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Astrocytes are proposed to be a critical reservoir of HIV in the brain. However, HIV infection of astrocytes is inefficient in vitro except for cell-to-cell transmission from HIV-infected cells. Here, we explore mechanisms by which cell-free HIV bypasses entry and postentry barriers leading to a productive infection. METHODS HIV infection of astrocytes was investigated by a variety of techniques including transfection of CD4-expressing plasmid, treatment with lysosomotropic agents or using a transwell culture system loaded with HIV-infected lymphocytes. Infection was monitored by HIV-1 p24 in culture supernatants and integrated proviral DNA was quantified by Alu-PCR. RESULTS Persistent HIV infection could be established in astrocytes by transfection of proviral DNA, transduction with VSV-G-pseudotyped viruses, transient expression of CD4 followed by HIV infection, or simultaneous treatment with lysosomotropic chloroquine or Tat-HA2 peptide with HIV infection. In absence of these treatments, HIV entered via endocytosis as seen by electronmicroscopy and underwent lysosomal degradation without proviral integration, indicating endocytosis is a dead end for HIV in astrocytes. Nevertheless, productive infection was observed when astrocytes were in close proximity but physically separated from HIV-infected lymphocytes in the transwell cultures. This occurred with X4 or dual tropic R5X4 viruses and was blocked by an antibody or antagonist to CXCR4. CONCLUSION A CD4-independent, CXCR4-dependent mechanism of viral entry is proposed, by which immature HIV particles from infected lymphocytes might directly bind to CXCR4 on astrocytes and trigger virus--cell fusion during or after the process of viral maturation. This mechanism may contribute to the formation of brain HIV reservoirs.
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Affiliation(s)
- Guan-Han Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Eugene O. Major
- Laboratory of Molecular Medicine and Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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38
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Yin L, Zhao F, Sun H, Wang Z, Huang Y, Zhu W, Xu F, Mei S, Liu X, Zhang D, Wei L, Cen S, Hu S, Liang C, Guo F. CRISPR-Cas13a Inhibits HIV-1 Infection. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:147-155. [PMID: 32585623 PMCID: PMC7321785 DOI: 10.1016/j.omtn.2020.05.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/15/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas provides bacteria and archaea with immunity against invading phages and foreign plasmid DNA and has been successfully adapted for gene editing in a variety of species. The class 2 type VI CRISPR-Cas effector Cas13a targets and cleaves RNA, providing protection against RNA phages. Here we report the repurposing of CRISPR-Cas13a to inhibit human immunodeficiency virus type 1 (HIV-1) infection through targeting HIV-1 RNA and diminishing viral gene expression. We observed strong inhibition of HIV-1 infection by CRISPR-Cas13a in human cells. We showed that CRISPR-Cas13a not only diminishes the level of newly synthesized viral RNA, either from the transfected plasmid DNA or from the viral DNA, which is integrated into cellular DNA, but it also targets and destroys the viral RNA that enters cells within viral capsid, leading to strong inhibition of HIV-1 infection. Together, our results suggest that CRISPR-Cas13a provides a potential novel tool to treat viral diseases in humans.
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Affiliation(s)
- Lijuan Yin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Hong Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Zhen Wang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Weijun Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Di Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Siqi Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China.
| | - Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China.
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Kreger J, Komarova NL, Wodarz D. Effect of synaptic cell-to-cell transmission and recombination on the evolution of double mutants in HIV. J R Soc Interface 2020; 17:20190832. [PMID: 32208824 DOI: 10.1098/rsif.2019.0832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recombination in HIV infection can impact virus evolution in vivo in complex ways, as has been shown both experimentally and mathematically. The effect of free virus versus synaptic, cell-to-cell transmission on the evolution of double mutants, however, has not been investigated. Here, we do so by using a stochastic agent-based model. Consistent with data, we assume spatial constraints for synaptic but not for free-virus transmission. Two important effects of the viral spread mode are observed: (i) for disadvantageous mutants, synaptic transmission protects against detrimental effects of recombination on double mutant persistence. Under free virus transmission, recombination increases double mutant levels for negative epistasis, but reduces them for positive epistasis. This reduction for positive epistasis is much diminished under predominantly synaptic transmission, and recombination can, in fact, lead to increased mutant levels. (ii) The mode of virus spread also directly influences the evolutionary fate of double mutants. For disadvantageous mutants, double mutant production is the predominant driving force, and hence synaptic transmission leads to highest double mutant levels due to increased transmission efficiency. For advantageous mutants, double mutant spread is the most important force, and hence free virus transmission leads to fastest invasion due to better mixing. For neutral mutants, both production and spread of double mutants are important, and hence an optimal mixture of free virus and synaptic transmission maximizes double mutant fractions. Therefore, both free virus and synaptic transmission can enhance or delay double mutant evolution. Implications for drug resistance in HIV are discussed.
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Affiliation(s)
- Jesse Kreger
- Department of Mathematics, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA
| | - Natalia L Komarova
- Department of Mathematics, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA
| | - Dominik Wodarz
- Department of Mathematics, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA.,Department of Population Health and Disease Prevention Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA
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40
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Abstract
Genetic variation is a necessity of all biological systems. Viruses use all known mechanisms of variation; mutation, several forms of recombination, and segment reassortment in the case of viruses with a segmented genome. These processes are intimately connected with the replicative machineries of viruses, as well as with fundamental physical-chemical properties of nucleotides when acting as template or substrate residues. Recombination has been viewed as a means to rescue viable genomes from unfit parents or to produce large modifications for the exploration of phenotypic novelty. All types of genetic variation can act conjointly as blind processes to provide the raw materials for adaptation to the changing environments in which viruses must replicate. A distinction is made between mechanistically unavoidable and evolutionarily relevant mutation and recombination.
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41
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Crisci E, Svanberg C, Ellegård R, Khalid M, Hellblom J, Okuyama K, Bhattacharya P, Nyström S, Shankar EM, Eriksson K, Larsson M. HSV-2 Cellular Programming Enables Productive HIV Infection in Dendritic Cells. Front Immunol 2019; 10:2889. [PMID: 31867020 PMCID: PMC6909011 DOI: 10.3389/fimmu.2019.02889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Genital herpes is a common sexually transmitted infection caused by herpes simplex virus type 2 (HSV-2). Genital herpes significantly enhances the acquisition and transmission of HIV-1 by creating a microenvironment that supports HIV infection in the host. Dendritic cells (DCs) represent one of the first innate cell types that encounter HIV-1 and HSV-2 in the genital mucosa. HSV-2 infection has been shown to modulate DCs, rendering them more receptive to HIV infection. Here, we investigated the potential mechanisms underlying HSV-2-mediated augmentation of HIV-1 infection. We demonstrated that the presence of HSV-2 enhanced productive HIV-1 infection of DCs and boosted inflammatory and antiviral responses. The HSV-2 augmented HIV-1 infection required intact HSV-2 DNA, but not active HSV-2 DNA replication. Furthermore, the augmented HIV infection of DCs involved the cGAS-STING pathway. Interestingly, we could not see any involvement of TLR2 or TLR3 nor suppression of infection by IFN-β production. The conditioning by HSV-2 in dual exposed DCs decreased protein expression of IFI16, cGAS, STING, and TBK1, which is associated with signaling through the STING pathway. Dual exposure to HSV-2 and HIV-1 gave decreased levels of several HIV-1 restriction factors, especially SAMHD1, TREX1, and APOBEC3G. Activation of the STING pathway in DCs by exposure to both HSV-2 and HIV-1 most likely led to the proteolytic degradation of the HIV-1 restriction factors SAMHD1, TREX1, and APOBEC3G, which should release their normal restriction of HIV infection in DCs. This released their normal restriction of HIV infection in DCs. We showed that HSV-2 reprogramming of cellular signaling pathways and protein expression levels in the DCs provided a setting where HIV-1 can establish a higher productive infection in the DCs. In conclusion, HSV-2 reprogramming opens up DCs for HIV-1 infection and creates a microenvironment favoring HIV-1 transmission.
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Affiliation(s)
- Elisa Crisci
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Cecilia Svanberg
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Rada Ellegård
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Mohammad Khalid
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Julia Hellblom
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Kazuki Okuyama
- Division of Experimental Haematology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Pradyot Bhattacharya
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Sofia Nyström
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Esaki M. Shankar
- Division of Infection Biology and Medical Microbiology, Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, India
| | - Kristina Eriksson
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Marie Larsson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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Herzig E, Kim KC, Packard TA, Vardi N, Schwarzer R, Gramatica A, Deeks SG, Williams SR, Landgraf K, Killeen N, Martin DW, Weinberger LS, Greene WC. Attacking Latent HIV with convertibleCAR-T Cells, a Highly Adaptable Killing Platform. Cell 2019; 179:880-894.e10. [PMID: 31668804 DOI: 10.1016/j.cell.2019.10.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/19/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
Current approaches to reducing the latent HIV reservoir entail first reactivating virus-containing cells to become visible to the immune system. A critical second step is killing these cells to reduce reservoir size. Endogenous cytotoxic T-lymphocytes (CTLs) may not be adequate because of cellular exhaustion and the evolution of CTL-resistant viruses. We have designed a universal CAR-T cell platform based on CTLs engineered to bind a variety of broadly neutralizing anti-HIV antibodies. We show that this platform, convertibleCAR-T cells, effectively kills HIV-infected, but not uninfected, CD4 T cells from blood, tonsil, or spleen and only when armed with anti-HIV antibodies. convertibleCAR-T cells also kill within 48 h more than half of the inducible reservoir found in blood of HIV-infected individuals on antiretroviral therapy. The modularity of convertibleCAR-T cell system, which allows multiplexing with several anti-HIV antibodies yielding greater breadth and control, makes it a promising tool for attacking the latent HIV reservoir.
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Affiliation(s)
- Eytan Herzig
- Gladstone Center for HIV Cure Research, Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA; Departments of Medicine and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kaman Chan Kim
- Xyphos Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Thomas A Packard
- Gladstone Center for HIV Cure Research, Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA; Departments of Medicine and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Noam Vardi
- Gladstone Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Departments of Biochemistry and Biophysics and Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Roland Schwarzer
- Gladstone Center for HIV Cure Research, Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA; Departments of Medicine and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrea Gramatica
- Gladstone Center for HIV Cure Research, Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA; Departments of Medicine and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | | | - Kyle Landgraf
- Xyphos Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Nigel Killeen
- Xyphos Biosciences, Inc., South San Francisco, CA 94080, USA
| | - David W Martin
- Xyphos Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Leor S Weinberger
- Gladstone Center for HIV Cure Research, Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA; Gladstone Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Departments of Biochemistry and Biophysics and Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Warner C Greene
- Gladstone Center for HIV Cure Research, Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA; Departments of Medicine and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
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Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G. An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb. Nucleic Acids Res 2019; 47:1523-1531. [PMID: 30481318 PMCID: PMC6379670 DOI: 10.1093/nar/gky1197] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022] Open
Abstract
The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat–TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181–TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Paul T Wille
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Alisha N Jones
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Amy Davidson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Jasmina Bogdanovic
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Eric Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
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44
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Huang SH, McCann CD, Mota TM, Wang C, Lipkin SM, Jones RB. Have Cells Harboring the HIV Reservoir Been Immunoedited? Front Immunol 2019; 10:1842. [PMID: 31447850 PMCID: PMC6691121 DOI: 10.3389/fimmu.2019.01842] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/22/2019] [Indexed: 01/05/2023] Open
Abstract
Immunoediting is an important concept in oncology, delineating the mechanisms through which tumors are selected for resistance to immune-mediated elimination. The recent emergence of immunotherapies, such as checkpoint inhibitors, as pillars of cancer therapy has intensified interest in immunoediting as a constraint limiting the efficacy of these approaches. Immunoediting manifests at a number of levels for different cancers, for example through the establishment of immunosuppressive microenvironments within solid tumors. Of particular interest to the current review, selection also occurs at the cellular level; and recent studies have revealed novel mechanisms by which tumor cells acquire intrinsic resistance to immune recognition and elimination. While the selection of escape mutations in viral epitopes by HIV-specific T cells, which is a hallmark of chronic HIV infection, can be considered a form of immunoediting, few studies have considered the possibility that HIV-infected cells themselves may parallel tumors in having differential intrinsic susceptibilities to immune-mediated elimination. Such selection, on the level of an infected cell, may not play a significant role in untreated HIV, where infection is propagated by high levels of cell-free virus produced by cells that quickly succumb to viral cytopathicity. However, it may play an unappreciated role in individuals treated with effective antiretroviral therapy where viral replication is abrogated. In this context, an "HIV reservoir" persists, comprising long-lived infected cells which undergo extensive and dynamic clonal expansion. The ability of these cells to persist in infected individuals has generally been attributed to viral latency, thought to render them invisible to immune recognition, and/or to their compartmentalization in anatomical sites that are poorly accessible to immune effectors. Recent data from ex vivo studies have led us to propose that reservoir-harboring cells may additionally have been selected for intrinsic resistance to CD8+ T cells, limiting their elimination even in the context of antigen expression. Here, we draw on knowledge from tumor immunoediting to discuss potential mechanisms by which clones of HIV reservoir-harboring cells may resist elimination by CD8+ T cells. The establishment of such parallels may provide a premise for testing therapeutics designed to sensitize tumor cells to immune-mediated elimination as novel approaches aimed at curing HIV infection.
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Affiliation(s)
- Szu-Han Huang
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Chase D. McCann
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
- Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States
| | - Talia M. Mota
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Chao Wang
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Steven M. Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - R. Brad Jones
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
- Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States
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45
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Trinité B, Zhang H, Levy DN. NNRTI-induced HIV-1 protease-mediated cytotoxicity induces rapid death of CD4 T cells during productive infection and latency reversal. Retrovirology 2019; 16:17. [PMID: 31242909 PMCID: PMC6595680 DOI: 10.1186/s12977-019-0479-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/14/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Current efforts towards HIV-1 eradication focus on the reactivation and elimination of the latent viral reservoir, so-called shock and kill therapy. However, work from several groups indicates that infected cell death following virus reactivation is not guaranteed. Thus, it is imperative to develop strategies to foster specific elimination of cells carrying integrated proviruses. It has been shown that some non-nucleoside reverse transcriptase inhibitors (NNRTIs) including efavirenz can induce premature HIV-1 GagPol dimerization in productively infected cells, resulting in intracellular HIV-1 Protease (PR) activation and a reduction in HIV-1 expressing cells. RESULTS Here, we document that NNRTI-induced PR activation triggers apoptotic death of productively infected resting or activated T cells in as little as 2 h via caspase-dependent and independent pathways. Rilpivirine, efavirenz and etravirine were the most potent NNRTIs, whereas nevirapine had almost no effect. NNRTI-induced cell killing was prevented by inhibitors of HIV-1 Protease (PR) activity including indinavir and nelfinavir. HIV-1 transmitter founder viruses induced cell killing similarly to lab-adapted HIV-1 except when NNRTI resistance conferring mutations were present in reverse transcriptase. Mutations in PR that confer PR inhibitor (PI) resistance restore NNRTI-induced killing in the presence of PI. Finally, we show that NNRTIs can rapidly eliminate cells in which latent viruses are stimulated to active expression. CONCLUSIONS This work supports the notion that select NNRTIs might help promote the elimination of HIV-1 producing cells as an adjuvant during shock and kill therapy.
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Affiliation(s)
- Benjamin Trinité
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA. .,IrsiCaixa AIDS Research Institute, Badalona, Spain.
| | - Hongtao Zhang
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - David N Levy
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA.
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46
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Díaz-Muñoz SL. Uncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput Tools. mSystems 2019; 4:e00121-19. [PMID: 31164405 PMCID: PMC6584877 DOI: 10.1128/msystems.00121-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 01/05/2023] Open
Abstract
Virus-host interactions have received much attention in virology. Virus-virus interactions can occur when >1 virus infects a host and can be deemed social when one virus affects the fitness of another virus, as in the well-known case of superinfection exclusion. Coinfection and subsequent social interactions can change viral pathogenicity, host range, and genetic composition, with implications for human health and viral evolution. I propose that this field can be advanced by bringing new perspectives into virology (e.g., social evolution theory) and uniting disciplinary divides within virology (classical, host-focused, and ecoevolutionary). The development of novel high-throughput tools that meld molecular and evolutionary approaches can harness viral diversity as an experimental asset to understand complex viral social interactions. A greater knowledge of virus-virus interactions will lead to the reformulation of basic concepts of virology and advances in applied virology, with new treatments that harness interactions between viruses to fight viral and bacterial infections.
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Affiliation(s)
- Samuel L Díaz-Muñoz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
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47
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Majer C, Schüssler JM, König R. Intertwined: SAMHD1 cellular functions, restriction, and viral evasion strategies. Med Microbiol Immunol 2019; 208:513-529. [PMID: 30879196 DOI: 10.1007/s00430-019-00593-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/08/2019] [Indexed: 01/01/2023]
Abstract
SAMHD1 was initially described for its ability to efficiently restrict HIV-1 replication in myeloid cells and resting CD4+ T cells. However, a growing body of evidence suggests that SAMHD1-mediated restriction is by far not limited to lentiviruses, but seems to be a general concept that applies to most retroviruses and at least a number of DNA viruses. SAMHD1 anti-viral activity was long believed to be solely due to its ability to deplete cellular dNTPs by enzymatic degradation. However, since its discovery, several new functions have been attributed to SAMHD1. It has been demonstrated to bind nucleic acids, to modulate innate immunity, as well as to participate in the DNA damage response and resolution of stalled replication forks. Consequently, it is likely that SAMHD1-mediated anti-viral activity is not or not exclusively mediated through its dNTPase activity. Therefore, in this review, we summarize current knowledge on SAMHD1 cellular functions and systematically discuss how these functions could contribute to the restriction of a broad range of viruses besides retroviruses: herpesviruses, poxviruses and hepatitis B virus. Furthermore, we aim to highlight different ways how viruses counteract SAMHD1-mediated restriction to bypass the SAMHD1-mediated block to viral infection.
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Affiliation(s)
- Catharina Majer
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | | | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany. .,Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA. .,German Center for Infection Research (DZIF), 63225, Langen, Germany. .,Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany.
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48
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Capetti A, Rizzardini G. Choosing appropriate pharmacotherapy for drug-resistant HIV. Expert Opin Pharmacother 2019; 20:667-678. [DOI: 10.1080/14656566.2019.1570131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Amedeo Capetti
- Divisione Malattie Infettive, Aziende Socio Sanitarie Territoriale Fatebenefratelli Sacco, Milano, Italy
| | - Giuliano Rizzardini
- Divisione Malattie Infettive, Aziende Socio Sanitarie Territoriale Fatebenefratelli Sacco, Milano, Italy
- Faculty of Health Sciences, School of Clinical Medicine, Whitwaterstrand University, Johannesburg, South Africa
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49
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Nurtay A, Hennessy MG, Sardanyés J, Alsedà L, Elena SF. Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181179. [PMID: 30800366 PMCID: PMC6366233 DOI: 10.1098/rsos.181179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. The coexistence conditions are formulated in terms of the basic reproductive numbers of the strains, a maximum value of the mutation rate and the virulence of the pathogens. The analysis reveals that parameter space can be divided into five regions, each with distinct dynamics, that are organized around degenerate Bogdanov-Takens and zero-Hopf bifurcations, the latter of which gives rise to a curve of transcritical bifurcations of periodic orbits. These results provide new insights into the conditions by which viral populations may contain multiple coexisting strains in a stable manner.
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Affiliation(s)
- Anel Nurtay
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Parc Científic UV, Paterna, València 46980, Spain
| | - Matthew G. Hennessy
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Lluís Alsedà
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Parc Científic UV, Paterna, València 46980, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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50
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Wodarz D, Levy DN, Komarova NL. Multiple infection of cells changes the dynamics of basic viral evolutionary processes. Evol Lett 2018; 3:104-115. [PMID: 30788146 PMCID: PMC6369963 DOI: 10.1002/evl3.95] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/02/2018] [Indexed: 12/27/2022] Open
Abstract
The infection of cells by multiple copies of a given virus can impact viral evolution in a variety of ways, yet some of the most basic evolutionary dynamics remain underexplored. Using computational models, we investigate how infection multiplicity affects the fixation probability of mutants, the rate of mutant generation, and the timing of mutant invasion. An important insight from these models is that for neutral and disadvantageous phenotypes, rare mutants initially enjoy a fitness advantage in the presence of multiple infection of cells. This arises because multiple infection allows the rare mutant to enter more target cells and to spread faster, while it does not accelerate the spread of the resident wild-type virus. The rare mutant population can increase by entry into both uninfected and wild-type-infected cells, while the established wild-type population can initially only grow through entry into uninfected cells. Following this initial advantageous phase, the dynamics are governed by drift or negative selection, respectively, and a higher multiplicity reduces the chances that mutants fix in the population. Hence, while increased infection multiplicity promotes the presence of neutral and disadvantageous mutants in the short-term, it makes it less likely in the longer term. We show how these theoretical insights can be useful for the interpretation of experimental data on virus evolution at low and high multiplicities. The dynamics explored here provide a basis for the investigation of more complex viral evolutionary processes, including recombination, reassortment, as well as complementary/inhibitory interactions.
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Affiliation(s)
- Dominik Wodarz
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall University of California Irvine CA 92697.,Department of Mathematics, Rowland Hall University of California Irvine CA 92697
| | - David N Levy
- Department of Basic Science, 921 Schwartz Building New York University College of Dentistry New York NY 10010
| | - Natalia L Komarova
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall University of California Irvine CA 92697.,Department of Mathematics, Rowland Hall University of California Irvine CA 92697
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