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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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2
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Mthembu M, Claassen H, Khuzwayo S, Voillet V, Naidoo A, Nyamande K, Khan DF, Maharaj P, Mitha M, Mhlane Z, Karim F, Andersen-Nissen E, Ndung'u T, Pollara G, Wong EB. Dysfunctional effector memory CD8 T cells in the bronchoalveolar compartment of people living with HIV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539571. [PMID: 37205594 PMCID: PMC10187318 DOI: 10.1101/2023.05.05.539571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mechanisms by which HIV causes susceptibility to respiratory pathogens remain incompletely understood. We obtained whole blood and bronchoalveolar lavage (BAL) from people with latent TB infection in the presence or absence of antiretroviral-naïve HIV co-infection. Transcriptomic and flow cytometric analyses demonstrated HIV-associated cell proliferation plus type I interferon activity in blood and effector memory CD8 T-cells in BAL. Both compartments displayed reduced induction of CD8 T-cell-derived IL-17A in people with HIV, associated with elevated T-cell regulatory molecule expression. The data suggest that dysfunctional CD8 T-cell responses in uncontrolled HIV contribute to susceptibility to secondary bacterial infections, including tuberculosis.
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3
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de Gea-Grela A, Moreno S. Controversies in the Design of Strategies for the Cure of HIV Infection. Pathogens 2023; 12:322. [PMID: 36839593 PMCID: PMC9961067 DOI: 10.3390/pathogens12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
The cure for chronic human immunodeficiency virus (HIV) infections has been a goal pursued since the antiretroviral therapy that improved the clinical conditions of patients became available. However, the exclusive use of these drugs is not enough to achieve a cure, since the viral load rebounds when the treatment is discontinued, leading to disease progression. There are several theories and hypotheses about the biological foundations that prevent a cure. The main obstacle appears to be the existence of a latent viral reservoir that cannot be eliminated pharmacologically. This concept is the basis of the new strategies that seek a cure, known as kick and kill. However, there are other lines of study that recognize mechanisms of persistent viral replication in patients under effective treatment, and that would modify the current lines of research on the cure of HIV. Given the importance of these concepts, in this work, we propose to review the most recent evidence on these hypotheses, covering both the evidence that is positioned in favor and against, trying to expose what are some of the challenges that remain to be resolved in this field of research.
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Affiliation(s)
| | - Santiago Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Alcalá University, 28034 Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28034 Madrid, Spain
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4
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Campbell GR, Spector SA. Current strategies to induce selective killing of HIV-1-infected cells. J Leukoc Biol 2022; 112:1273-1284. [PMID: 35707952 PMCID: PMC9613504 DOI: 10.1002/jlb.4mr0422-636r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/24/2022] [Indexed: 01/02/2023] Open
Abstract
Although combination antiretroviral therapy (ART) has led to significant HIV-1 suppression and improvement in immune function, persistent viral reservoirs remain that are refractory to intensified ART. ART poses many challenges such as adherence to drug regimens, the emergence of resistant virus, and cumulative toxicity resulting from long-term therapy. Moreover, latent HIV-1 reservoir cells can be stochastically activated to produce viral particles despite effective ART and contribute to the rapid viral rebound that typically occurs within 2 weeks of ART interruption; thus, lifelong ART is required for continued viral suppression. Several strategies have been proposed to address the HIV-1 reservoir such as reactivation of HIV-1 transcription using latency reactivating agents with a combination of ART, host immune clearance and HIV-1-cytotoxicity to purge the infected cells-a "shock and kill" strategy. However, these approaches do not take into account the multiple transcriptional and translational blocks that contribute to HIV-1 latency or the complex heterogeneity of the HIV-1 reservoir, and clinical trials have thus far failed to produce the desired results. Here, we describe alternative strategies being pursued that are designed to kill selectively HIV-1-infected cells while sparing uninfected cells in the absence of enhanced humoral or adaptive immune responses.
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Affiliation(s)
- Grant R. Campbell
- Department of PediatricsDivision of Infectious DiseasesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Stephen A. Spector
- Department of PediatricsDivision of Infectious DiseasesUniversity of California San DiegoLa JollaCaliforniaUSA,Division of Infectious DiseasesRady Children's HospitalSan DiegoCaliforniaUSA
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5
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Genotypic and Phenotypic Diversity of the Replication-Competent HIV Reservoir in Treated Patients. Microbiol Spectr 2022; 10:e0078422. [PMID: 35770985 PMCID: PMC9431663 DOI: 10.1128/spectrum.00784-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In HIV infection, viral rebound after treatment discontinuation is considered to originate predominantly from viral genomes integrated in resting CD4+ T lymphocytes. Replication-competent proviral genomes represent a minority of the total HIV DNA. While the quantification of the HIV reservoir has been extensively studied, the diversity of genomes that compose the reservoir was less explored. Here, we measured the genotypic and phenotypic diversity in eight patients with different treatment histories. Between 4 and 14 (mean, 8) individual viral isolates per patient were obtained using a virus outgrowth assay, and their near-full-length genomes were sequenced. The mean pairwise distance (MPD) observed in different patients correlated with the time before undetectable viremia was achieved (r = 0.864, P = 0.0194), suggesting that the complexity of the replication-competent reservoir mirrors that present at treatment initiation. No correlation was instead observed between MPD and the duration of successful treatment (mean, 8 years; range, 2 to 21 years). For 5 of the 8 patients, genotypically identical viral isolates were observed in independent wells, suggesting clonal expansion of infected cells. Identical viruses represented between 25 and 60% of the isolates (mean, 48%). The proportion of identical viral isolates correlated with the duration of treatment (r = 0.822, P = 0.0190), suggesting progressive clonal expansion of infected cells during ART. A broader range of infectivity was also observed among isolates from patients with delayed viremia control (r = 0.79, P = 0.025). This work unveiled differences in the genotypic and phenotypic features of the replication-competent reservoir from treated patients and suggests that delaying treatment results in increased diversity of the reservoir. IMPORTANCE In HIV-infected and effectively treated individuals, integrated proviral genomes may persist for decades. The vast majority of the genomes, however, are defective, and only the replication-competent fraction represents a threat of viral reemergence. The quantification of the reservoir has been thoroughly explored, while the diversity of the genomes has been insufficiently studied. Its characterization, however, is relevant for the design of strategies aiming the reduction of the reservoir. Here, we explored the replication-competent near-full-length HIV genomes of eight patients who experienced differences in the delay before viremia control and in treatment duration. We found that delayed effective treatment was associated with increased genetic diversity of the reservoir. The duration of treatment did not impact the diversity but was associated with higher frequency of clonally expanded sequences. Thus, early treatment initiation has the double advantage of reducing both the size and the diversity of the reservoir.
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Insights into the HIV-1 Latent Reservoir and Strategies to Cure HIV-1 Infection. DISEASE MARKERS 2022; 2022:6952286. [PMID: 35664434 PMCID: PMC9157282 DOI: 10.1155/2022/6952286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/07/2022] [Accepted: 05/09/2022] [Indexed: 11/23/2022]
Abstract
Since the first discovery of human immunodeficiency virus 1 (HIV-1) in 1983, the targeted treatment, antiretroviral therapy (ART), has effectively limited the detected plasma viremia below a very low level and the technique has been improved rapidly. However, due to the persistence of the latent reservoir of replication-competent HIV-1 in patients treated with ART, a sudden withdrawal of the drug inevitably results in HIV viral rebound and HIV progression. Therefore, more understanding of the HIV-1 latent reservoir (LR) is the priority before developing a cure that thoroughly eliminates the reservoir. HIV-1 spreads through both the release of cell-free particles and by cell-to-cell transmission. Mounting evidence indicates that cell-to-cell transmission is more efficient than cell-free transmission of particles and likely influences the pathogenesis of HIV-1 infection. This mode of viral transmission also influences the generation and maintenance of the latent reservoir, which represents the main obstacle for curing the infection. In this review, the definition, establishment, and maintenance of the HIV-1 LR, along with the state-of-the-art quantitative approaches that directly quantify HIV-1 intact proviruses, are elucidated. Strategies to cure HIV infection are highlighted. This review will renew hope for a better and more thorough cure of HIV infection for mankind and encourage more clinical trials to achieve ART-free HIV remission.
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Mori L, Valente ST. Cure and Long-Term Remission Strategies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2407:391-428. [PMID: 34985678 DOI: 10.1007/978-1-0716-1871-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.
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Affiliation(s)
- Luisa Mori
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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8
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Ratti V, Nanda S, Eszterhas SK, Howell AL, Wallace DI. A mathematical model of HIV dynamics treated with a population of gene-edited haematopoietic progenitor cells exhibiting threshold phenomenon. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2021; 37:212-242. [PMID: 31265056 DOI: 10.1093/imammb/dqz011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/03/2019] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
Abstract
The use of gene-editing technology has the potential to excise the CCR5 gene from haematopoietic progenitor cells, rendering their differentiated CD4-positive (CD4+) T cell descendants HIV resistant. In this manuscript, we describe the development of a mathematical model to mimic the therapeutic potential of gene editing of haematopoietic progenitor cells to produce a class of HIV-resistant CD4+ T cells. We define the requirements for the permanent suppression of viral infection using gene editing as a novel therapeutic approach. We develop non-linear ordinary differential equation models to replicate HIV production in an infected host, incorporating the most appropriate aspects found in the many existing clinical models of HIV infection, and extend this model to include compartments representing HIV-resistant immune cells. Through an analysis of model equilibria and stability and computation of $R_0$ for both treated and untreated infections, we show that the proposed therapy has the potential to suppress HIV infection indefinitely and return CD4+ T cell counts to normal levels. A computational study for this treatment shows the potential for a successful 'functional cure' of HIV. A sensitivity analysis illustrates the consistency of numerical results with theoretical results and highlights the parameters requiring better biological justification. Simulations of varying level production of HIV-resistant CD4+ T cells and varying immune enhancements as the result of these indicate a clear threshold response of the model and a range of treatment parameters resulting in a return to normal CD4+ T cell counts.
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Affiliation(s)
| | - Seema Nanda
- Department of Mathematics, Dartmouth College, Hanover, USA
| | - Susan K Eszterhas
- Veterans Affairs Medical Center, White River Junction, USA.,Departments of Microbiology and Immunology, and Medicine, Geisel School of Medicine at Dartmouth, Lebanon, USA
| | - Alexandra L Howell
- Veterans Affairs Medical Center, White River Junction, USA.,Departments of Microbiology and Immunology, and Medicine, Geisel School of Medicine at Dartmouth, Lebanon, USA
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9
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Katusiime MG, Van Zyl GU, Cotton MF, Kearney MF. HIV-1 Persistence in Children during Suppressive ART. Viruses 2021; 13:v13061134. [PMID: 34204740 PMCID: PMC8231535 DOI: 10.3390/v13061134] [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: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
There is a growing number of perinatally HIV-1-infected children worldwide who must maintain life-long ART. In early life, HIV-1 infection is established in an immunologically inexperienced environment in which maternal ART and immune dynamics during pregnancy play a role in reservoir establishment. Children that initiated early antiretroviral therapy (ART) and maintained long-term suppression of viremia have smaller and less diverse HIV reservoirs than adults, although their proviral landscape during ART is reported to be similar to that of adults. The ability of these early infected cells to persist long-term through clonal expansion poses a major barrier to finding a cure. Furthermore, the effects of life-long HIV persistence and ART are yet to be understood, but growing evidence suggests that these individuals are at an increased risk for developing non-AIDS-related comorbidities, which underscores the need for an HIV cure.
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Affiliation(s)
- Mary Grace Katusiime
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD 21702, USA;
- Correspondence:
| | - Gert U. Van Zyl
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service Tygerberg, Cape Town 8000, South Africa;
| | - Mark F. Cotton
- Department of Pediatrics and Child Health, Tygerberg Children’s Hospital and Family Center for Research with Ubuntu, Stellenbosch University, Cape Town 7505, South Africa;
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD 21702, USA;
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10
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Gantner P, Pagliuzza A, Pardons M, Ramgopal M, Routy JP, Fromentin R, Chomont N. Single-cell TCR sequencing reveals phenotypically diverse clonally expanded cells harboring inducible HIV proviruses during ART. Nat Commun 2020; 11:4089. [PMID: 32796830 PMCID: PMC7427996 DOI: 10.1038/s41467-020-17898-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
Clonal expansions occur in the persistent HIV reservoir as shown by the duplication of proviral integration sites. However, the source of the proliferation of HIV-infected cells remains unclear. Here, we analyze the TCR repertoire of single HIV-infected cells harboring translation-competent proviruses in longitudinal samples from eight individuals on antiretroviral therapy (ART). When compared to uninfected cells, the TCR repertoire of reservoir cells is heavily biased: expanded clonotypes are present in all individuals, account for the majority of reservoir cells and are often maintained over time on ART. Infected T cell clones are detected at low frequencies in the long-lived central memory compartment and overrepresented in the most differentiated memory subsets. Our results indicate that clonal expansions highly contribute to the persistence of the HIV reservoir and suggest that reservoir cells displaying a differentiated phenotype are the progeny of infected central memory cells undergoing antigen-driven clonal expansion during ART. The cause of clonal expansions in the HIV reservoir remains unclear. Here, Gantner et al. perform single-cell TCR sequencing on longitudinal samples from eight individuals on antiretroviral therapy and find that antigens inducing clonal expansions of memory cells are major contributors to the HIV reservoir.
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Affiliation(s)
- Pierre Gantner
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Marion Pardons
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Moti Ramgopal
- Midway Immunology & Research Center, Fort Pierce, FL, USA
| | - Jean-Pierre Routy
- Division of Hematology & Chronic Viral Illness Service, McGill University Heath Centre, Montreal, QC, Canada
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada. .,Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada.
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11
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Abstract
Although antiretroviral therapies (ARTs) potently inhibit HIV replication, they do not eradicate the virus. HIV persists in cellular and anatomical reservoirs that show minimal decay during ART. A large number of studies conducted during the past 20 years have shown that HIV persists in a small pool of cells harboring integrated and replication-competent viral genomes. The majority of these cells do not produce viral particles and constitute what is referred to as the latent reservoir of HIV infection. Therefore, although HIV is not considered as a typical latent virus, it can establish a state of nonproductive infection under rare circumstances, particularly in memory CD4+ T cells, which represent the main barrier to HIV eradication. While it was originally thought that the pool of latently infected cells was largely composed of cells harboring transcriptionally silent genomes, recent evidence indicates that several blocks contribute to the nonproductive state of these cells. Here, we describe the virological and immunological factors that play a role in the establishment and persistence of the pool of latently infected cells and review the current approaches aimed at eliminating the latent HIV reservoir.
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Affiliation(s)
| | - Pierre Gantner
- Department of Microbiology, Infectiology and Immunology and
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier, Université de Montréal, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology and
- Centre de Recherche du Centre Hospitalier, Université de Montréal, Montreal, Quebec, Canada
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12
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Huang XS, Luo RH, Hu XL, Chen H, Xiang SY, Tang CR, Zhang CT, Shen XN, Zheng YT. The New NNRTI ACC007 Combined with Lamivudine and Tenofovir Disoproxil Fumarate Show Synergy Anti-HIV Activity In Vitro. Curr HIV Res 2020; 18:332-341. [PMID: 32562524 DOI: 10.2174/1570162x18666200620211922] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/11/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Acquired immunodeficiency syndrome can hardly be cured currently and people with human immunodeficiency virus (HIV) need lifelong treatment that may result in the emergence of drug resistance which leads to failed treatment. Thus, the development of new anti- HIV drugs and new treatment regimens are necessary. OBJECTIVE The aim of this study is to analyze the combined anti-HIV activity of tenofovir disoproxil fumarate, lamivudine and ACC007, a new non-nucleoside reverse transcriptase inhibitor. METHODS The antiviral activity of tenofovir disoproxil fumarate, lamivudine and ACC007 alone or in combination against different HIV-1 strains was determined by the detection of HIV-1 p24 level through enzyme-linked immunosorbent assay. RESULT ACC007 showed EC50 of nanomolar range (from 3.03 nM to 252.59 nM) against all HIV-1 strains used in this study except the HIV-1A17, with EC50 of 1.57 μM. The combined antiviral activity of ACC007, lamivudine and tenofovir disoproxil fumarate showed synergy antiviral activity against all HIV-1 strains used in this study. The three-drug combination showed moderate synergism against HIV-1A17, HIV-14755-5, HIV-1K103N and HIV-1V106M, with a combination index value ranging from 0.71 to 0.87, and showed synergism against the other HIV-1 strains with combination index value from 0.35 to 0.67. The combination with ACC007 significantly increases the dose reduction index value of lamivudine and tenofovir disoproxil fumarate, compared with two-drug combination. CONCLUSION ACC007 exhibits potent antiviral activity alone or with 3TC and TDF, and exerts synergistic effect against all HIV strains used in our investigation in vitro.
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Affiliation(s)
- Xu-Sheng Huang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Rong-Hua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Xiong-Lin Hu
- Nanjing Accelas Pharmaceutical Co. Ltd. Nanjing 210046, Jiangsu, China
| | - Huan Chen
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Si-Ying Xiang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Cheng-Run Tang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Chun-Tao Zhang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
| | - Xiao-Ning Shen
- Jiangsu Aidea Pharmaceutical Co. Ltd. Nanjing 210046, Jiangsu, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease
Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research
in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of
Sciences, Kunming 650223, Yunnan, China
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13
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Virnik K, Rosati M, Medvedev A, Scanlan A, Walsh G, Dayton F, Broderick KE, Lewis M, Bryson Y, Lifson JD, Ruprecht RM, Felber BK, Berkower I. Immunotherapy with DNA vaccine and live attenuated rubella/SIV gag vectors plus early ART can prevent SIVmac251 viral rebound in acutely infected rhesus macaques. PLoS One 2020; 15:e0228163. [PMID: 32130229 PMCID: PMC7055890 DOI: 10.1371/journal.pone.0228163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 01/29/2023] Open
Abstract
Anti-retroviral therapy (ART) has been highly successful in controlling HIV replication, reducing viral burden, and preventing both progression to AIDS and viral transmission. Yet, ART alone cannot cure the infection. Even after years of successful therapy, ART withdrawal leads inevitably to viral rebound within a few weeks or months. Our hypothesis: effective therapy must control both the replicating virus pool and the reactivatable latent viral reservoir. To do this, we have combined ART and immunotherapy to attack both viral pools simultaneously. The vaccine regimen consisted of DNA vaccine expressing SIV Gag, followed by a boost with live attenuated rubella/gag vectors. The vectors grow well in rhesus macaques, and they are potent immunogens when used in a prime and boost strategy. We infected rhesus macaques by high dose mucosal challenge with virulent SIVmac251 and waited three days to allow viral dissemination and establishment of a reactivatable viral reservoir before starting ART. While on ART, the control group received control DNA and empty rubella vaccine, while the immunotherapy group received DNA/gag prime, followed by boosts with rubella vectors expressing SIV gag over 27 weeks. Both groups had a vaccine "take" to rubella, and the vaccine group developed antibodies and T cells specific for Gag. Five weeks after the last immunization, we stopped ART and monitored virus rebound. All four control animals eventually had a viral rebound, and two were euthanized for AIDS. One control macaque did not rebound until 2 years after ART release. In contrast, there was only one viral rebound in the vaccine group. Three out of four vaccinees had no viral rebound, even after CD8 depletion, and they remain in drug-free viral remission more than 2.5 years later. The strategy of early ART combined with immunotherapy can produce a sustained SIV remission in macaques and may be relevant for immunotherapy of HIV in humans.
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Affiliation(s)
- Konstantin Virnik
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Margherita Rosati
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Alexei Medvedev
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Aaron Scanlan
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Gabrielle Walsh
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Frances Dayton
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Kate E. Broderick
- Inovio Pharmaceuticals, Inc., Plymouth Meeting, Pennsylvania, United States of America
| | - Mark Lewis
- BioQual, Inc., Rockville, Maryland, United States of America
| | - Yvonne Bryson
- Department of Pediatrics, Division of Infectious Disease, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ruth M. Ruprecht
- University of Louisiana at Lafayette, New Iberia Research Center, New Iberia, Louisiana, United States of America
| | - Barbara K. Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Ira Berkower
- Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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14
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Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion. Nat Commun 2019; 10:728. [PMID: 30760706 PMCID: PMC6374386 DOI: 10.1038/s41467-019-08431-7] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 12/31/2018] [Indexed: 01/17/2023] Open
Abstract
After initiating antiretroviral therapy (ART), a rapid decline in HIV viral load is followed by a long period of undetectable viremia. Viral outgrowth assay suggests the reservoir continues to decline slowly. Here, we use full-length sequencing to longitudinally study the proviral landscape of four subjects on ART to investigate the selective pressures influencing the dynamics of the treatment-resistant HIV reservoir. We find intact and defective proviruses that contain genetic elements favoring efficient protein expression decrease over time. Moreover, proviruses that lack these genetic elements, yet contain strong donor splice sequences, increase relatively to other defective proviruses, especially among clones. Our work suggests that HIV expression occurs to a significant extent during ART and results in HIV clearance, but this is obscured by the expansion of proviral clones. Paradoxically, clonal expansion may also be enhanced by HIV expression that leads to splicing between HIV donor splice sites and downstream human exons. How HIV reservoirs are shaped over time on antiviral therapy is poorly understood. Here, the authors analyze the dynamics of the HIV reservoir by longitudinal proviral sequencing revealing that HIV reservoir expression can contribute to its clearance and paradoxically even to its persistence.
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15
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A child with perinatal HIV infection and long-term sustained virological control following antiretroviral treatment cessation. Nat Commun 2019; 10:412. [PMID: 30679439 PMCID: PMC6345921 DOI: 10.1038/s41467-019-08311-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/03/2019] [Indexed: 11/27/2022] Open
Abstract
Understanding HIV remission in rare individuals who initiated antiretroviral therapy (ART) soon after infection and then discontinued, may inform HIV cure interventions. Here we describe features of virus and host of a perinatally HIV-1 infected child with long-term sustained virological control. The child received early limited ART in the Children with HIV Early antiRetroviral therapy (CHER) trial. At age 9.5 years, diagnostic tests for HIV are negative and the child has characteristics similar to uninfected children that include a high CD4:CD8 ratio, low T cell activation and low CCR5 expression. Virus persistence (HIV-1 DNA and plasma RNA) is confirmed with sensitive methods, but replication-competent virus is not detected. The child has weak HIV-specific antibody and T cell responses. Furthermore, we determine his HLA and KIR genotypes. This case aids in understanding post-treatment control and may help design of future intervention strategies. Some perinatally HIV infected children who have received early antiretroviral therapy (ART) show long-term sustained virological control after ART cessation. Here the authors describe a case who, at age 9.5 years, shows normal CD4:CD8 T cell ratios and has no detectable levels of replication-competent virus.
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16
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Okoye AA, Hansen SG, Vaidya M, Fukazawa Y, Park H, Duell DM, Lum R, Hughes CM, Ventura AB, Ainslie E, Ford JC, Morrow D, Gilbride RM, Legasse AW, Hesselgesser J, Geleziunas R, Li Y, Oswald K, Shoemaker R, Fast R, Bosche WJ, Borate BR, Edlefsen PT, Axthelm MK, Picker LJ, Lifson JD. Early antiretroviral therapy limits SIV reservoir establishment to delay or prevent post-treatment viral rebound. Nat Med 2018; 24:1430-1440. [PMID: 30082858 PMCID: PMC6389357 DOI: 10.1038/s41591-018-0130-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Prophylactic vaccination of rhesus macaques with rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) elicits immune responses that stringently control highly pathogenic SIV infection, with subsequent apparent clearance of the infection, in ~50% of vaccinees. In contrast, here, we show that therapeutic RhCMV/SIV vaccination of rhesus macaques previously infected with SIV and given continuous combination antiretroviral therapy (cART) beginning 4-9 d post-SIV infection does not mediate measurable SIV reservoir clearance during over 600 d of follow-up on cART relative to RhCMV/control vaccination. However, none of the six animals started on cART on day four or five, across both RhCMV/SIV- and RhCMV/control-vaccinated groups, those rhesus macaques with SIV reservoirs most closely resembling those of prophylactically RhCMV/SIV-vaccinated and protected animals early in their course, showed post-cART viral rebound with up to nine months of follow-up. Moreover, at necropsy, these rhesus macaques showed little to no evidence of replication-competent SIV. These results suggest that the early SIV reservoir is limited in durability and that effective blockade of viral replication and spread in this critical time window by either pharmacologic or immunologic suppression may result in reduction, and potentially loss, of rebound-competent virus over a period of ~two years.
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Affiliation(s)
- Afam A Okoye
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Mukta Vaidya
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Yoshinori Fukazawa
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Haesun Park
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Derick M Duell
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Richard Lum
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Emily Ainslie
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Julia C Ford
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - David Morrow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Alfred W Legasse
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | | | | | - Yuan Li
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Randy Fast
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William J Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bhavesh R Borate
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul T Edlefsen
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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17
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Genetically Intact but Functionally Impaired HIV-1 Env Glycoproteins in the T-Cell Reservoir. J Virol 2018; 92:JVI.01684-17. [PMID: 29187544 DOI: 10.1128/jvi.01684-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/20/2017] [Indexed: 01/16/2023] Open
Abstract
HIV-infected subjects under antiretroviral treatment (ART) harbor a persistent viral reservoir in resting CD4+ T cells, which accounts for the resurgence of HIV replication after ART interruption. A large majority of HIV reservoir genomes are genetically defective, but even among intact proviruses few seem able to generate infectious virus. To understand this phenomenon, we examined the function and expression of HIV envelope glycoproteins reactivated from the reservoir of four HIV-infected subjects under suppressive ART. We studied full-length genetically intact env sequences from both replicative viruses and cell-associated mRNAs. We found that these Env proteins varied extensively in fusogenicity and infectivity, with strongest functional defects found in Envs from cell-associated mRNAs. Env functional impairments were essentially explained by defects in Env protein expression. Our results support the idea that defects in HIV Env expression, preventing cytopathic or immune HIV clearance, contribute to the persistence of the HIV T-cell reservoir in vivoIMPORTANCE In most individuals, evolution of HIV infection is efficiently controlled on the long-term by combination antiviral therapies. These treatments, however, fail to eradicate HIV from the infected subjects, a failure that results both in resurgence of virus replication and in resumption of HIV pathogenicity when the treatment is stopped. HIV resurgence, in these instances, is widely assumed to emerge from a reservoir of silent virus integrated in the genomes of a small number of T lymphocytes. The silent HIV reservoir is mostly composed of heavily deleted or mutated HIV DNA. Moreover, among the seemingly intact remaining HIV, only very few are actually able to efficiently propagate in tissue culture. In this study, we find that intact HIV in the reservoir often carry strong defects in their capacity to promote fusion to neighboring cells and infection of target cells, a defect related to the function and expression of the HIV envelope glycoprotein. Impaired envelope glycoprotein expression and function could explain why cells harboring these viruses tend to remain undetected and unharmed in the reservoir.
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18
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Khoury G, Darcis G, Lee MY, Bouchat S, Van Driessche B, Purcell DFJ, Van Lint C. The Molecular Biology of HIV Latency. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1075:187-212. [PMID: 30030794 DOI: 10.1007/978-981-13-0484-2_8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
HIV remains incurable due to the existence of a reservoir of cells that harbor intact integrated genomes of the virus in the absence of viral replication. This population of infected cells remains invisible to the immune system and is not targeted by the drugs used in the current antiretroviral therapies (cART). Reversal of latency by the use of inhibitors of chromatin-remodeling enzymes has been studied extensively in an attempt to purge this reservoir of latent HIV but has thus far not shown any success in clinical trials. The full complexity of latent HIV infection has still not been appreciated, and the gaps in knowledge prevent development of adequate small-molecule compounds that can effectively perturb this reservoir. In this review, we will examine the role of epigenetic silencing of HIV transcription, posttranscriptional regulation, and mRNA processing in promoting HIV-1 latency.
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Affiliation(s)
- Georges Khoury
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Gilles Darcis
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Michelle Y Lee
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sophie Bouchat
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Benoit Van Driessche
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium.
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19
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Antiviral Activity of Bictegravir and Cabotegravir against Integrase Inhibitor-Resistant SIVmac239 and HIV-1. Antimicrob Agents Chemother 2017; 61:AAC.01695-17. [PMID: 28923862 DOI: 10.1128/aac.01695-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/08/2017] [Indexed: 01/26/2023] Open
Abstract
Animal models are essential to study novel antiretroviral drugs, resistance-associated mutations (RAMs), and treatment strategies. Bictegravir (BIC) is a novel potent integrase strand transfer inhibitor (INSTI) that has shown promising results against HIV-1 infection in vitro and in vivo and against clinical isolates with resistance against INSTIs. BIC has a higher genetic barrier to the development of resistance than two clinically approved INSTIs, termed raltegravir and elvitegravir. Another clinically approved INSTI, dolutegravir (DTG) also possesses a high genetic barrier to resistance, while a fourth compound, termed cabotegravir (CAB), is currently in late phases of clinical development. Here we report the susceptibilities of simian immunodeficiency virus (SIV) and HIV-1 integrase (IN) mutants containing various RAMs to BIC, CAB, and DTG. BIC potently inhibited SIV and HIV-1 in single cycle infection with 50% effective concentrations (EC50s) in the low nM range. In single cycle SIV infections, none of the E92Q, T97A, Y143R, or N155H substitutions had a significant effect on susceptibility to BIC (≤4-fold increase in EC50), whereas G118R and R263K conferred ∼14-fold and ∼6-fold increases in EC50, respectively. In both single and multiple rounds of HIV-1 infections, BIC remained active against the Y143R, N155H, R263K, R263K/M50I, and R263K/E138K mutants (≤4-fold increase in EC50). In multiple rounds of infection, the G140S/Q148H combination of substitutions decreased HIV-1 susceptibility to BIC 4.8-fold compared to 16.8- and 7.4-fold for CAB and DTG, respectively. BIC possesses an excellent resistance profile in regard to HIV and SIV and could be useful in nonhuman primate models of HIV infection.
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20
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Longitudinal sequencing of HIV-1 infected patients with low-level viremia for years while on ART shows no indications for genetic evolution of the virus. Virology 2017; 510:185-193. [PMID: 28750322 DOI: 10.1016/j.virol.2017.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022]
Abstract
HIV-infected patients on antiretroviral therapy (ART) may present low-level viremia (LLV) above the detection level of current viral load assays. In many cases LLV is persistent but does not result in overt treatment failure or selection of drug resistant viral variants. To elucidate whether LLV reflects active virus replication, we extensively sequenced pol and env genes of the viral populations present before and during LLV in 18 patients and searched for indications of genetic evolution. Maximum likelihood phylogenetic trees were inspected for temporal structure both visually and by linear regression analysis of root-to-tip and pairwise distances. Viral coreceptor tropism was assessed at different time points before and during LLV. In none of the patients consistent indications for genetic evolution were found over a median period of 4.8 years of LLV. As such these findings could not provide evidence that active virus replication is the main driver of LLV.
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21
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Lythgoe KA, Gardner A, Pybus OG, Grove J. Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections. Trends Microbiol 2017; 25:336-348. [PMID: 28377208 PMCID: PMC5405858 DOI: 10.1016/j.tim.2017.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 12/24/2022]
Abstract
With extremely short generation times and high mutability, many viruses can rapidly evolve and adapt to changing environments. This ability is generally beneficial to viruses as it allows them to evade host immune responses, evolve new behaviours, and exploit ecological niches. However, natural selection typically generates adaptation in response to the immediate selection pressures that a virus experiences in its current host. Consequently, we argue that some viruses, particularly those characterised by long durations of infection and ongoing replication, may be susceptible to short-sighted evolution, whereby a virus' adaptation to its current host will be detrimental to its onward transmission within the host population. Here we outline the concept of short-sighted viral evolution and provide examples of how it may negatively impact viral transmission among hosts. We also propose that viruses that are vulnerable to short-sighted evolution may exhibit strategies that minimise its effects. We speculate on the various mechanisms by which this may be achieved, including viral life history strategies that result in low rates of within-host evolution, or the establishment of a 'germline' lineage of viruses that avoids short-sighted evolution. These concepts provide a new perspective on the way in which some viruses have been able to establish and maintain global pandemics.
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Affiliation(s)
| | - Andy Gardner
- School of Biology, University of St Andrews, St Andrews, KY16 9TH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Joe Grove
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, WC1E 6BT, UK
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22
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Abstract
OBJECTIVE To review the recent literatures related to the factors associated with the size of the HIV reservoir and their clinical significance. DATA SOURCES Literatures related to the size of HIV DNA was collected from PubMed published from 1999 to June 2016. STUDY SELECTION All relevant articles on the HIV DNA and reservoir were collected and reviewed, with no limitation of study design. RESULTS The composition and development of the HIV-1 DNA reservoir in either treated or untreated patients is determined by integrated mechanism comprising viral characteristics, immune system, and treatment strategies. The HIV DNA reservoir is a combination of latency and activity. The residual viremia from the stochastic activation of the reservoir acts as the fuse, continuing to stimulate the immune system to maintain the activated microenvironment for the rebound of competent virus once treatment with antiretroviral therapy is discontinued. CONCLUSION The size of the HIV-1 DNA pool and its composition has great significance in clinical treatment and disease progression.
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Affiliation(s)
- Ni-Dan Wang
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Tai-Sheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
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23
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Abstract
To complete its life cycle, HIV-1 enters the nucleus of the host cell as reverse-transcribed viral DNA. The nucleus is a complex environment, in which chromatin is organized to support different structural and functional aspects of cell physiology. As such, it represents a challenge for an incoming viral genome, which needs to be integrated into cellular DNA to ensure productive infection. Integration of the viral genome into host DNA depends on the enzymatic activity of HIV-1 integrase and involves different cellular factors that influence the selection of integration sites. The selection of integration site has functional consequences for viral transcription, which usually follows the integration event. However, in resting CD4+ T cells, the viral genome can be silenced for long periods of time, which leads to the generation of a latent reservoir of quiescent integrated HIV-1 DNA. Integration represents the only nuclear event in the viral life cycle that can be pharmacologically targeted with current therapies, and the aspects that connect HIV-1 nuclear entry to HIV-1 integration and viral transcription are only beginning to be elucidated.
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24
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Bivalkar-Mehla S, Mehla R, Chauhan A. Chimeric peptide-mediated siRNA transduction to inhibit HIV-1 infection. J Drug Target 2016; 25:307-319. [PMID: 27800697 DOI: 10.1080/1061186x.2016.1245311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Persistent human immunodeficiency virus 1 (HIV-1) infection provokes immune activation and depletes CD4+ lymphocytes, leading to acquired immunodeficiency syndrome. Uninterrupted administration of combination antiretroviral therapy (cART) in HIV-infected patients suppresses viral replication to below the detectable level and partially restores the immune system. However, cART-unresponsive residual HIV-1 infection and elusive transcriptionally silent but reactivatable viral reservoirs maintain a permanent viral DNA blue print. The virus rebounds within a few weeks after interruption of suppressive therapy. Adjunct gene therapy to control viral replication by ribonucleic acid interference (RNAi) is a post-transcriptional gene silencing strategy that could suppress residual HIV-1 burden and overcome viral resistance. Small interfering ribonucleic acids (siRNAs) are efficient transcriptional inhibitors, but need delivery systems to reach inside target cells. We investigated the potential of chimeric peptide (FP-PTD) to deliver specific siRNAs to HIV-1-susceptible and permissive cells. Chimeric FP-PTD peptide was designed with an RNA binding domain (PTD) to bind siRNA and a cell fusion peptide domain (FP) to enter cells. FP-PTD-siRNA complex entered and inhibited HIV-1 replication in susceptible cells, and could be a candidate for in vivo testing.
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Affiliation(s)
- Shalmali Bivalkar-Mehla
- a Department of Pathology, Microbiology and Immunology , University of South Carolina School of Medicine , Columbia , SC , USA
| | - Rajeev Mehla
- a Department of Pathology, Microbiology and Immunology , University of South Carolina School of Medicine , Columbia , SC , USA
| | - Ashok Chauhan
- a Department of Pathology, Microbiology and Immunology , University of South Carolina School of Medicine , Columbia , SC , USA
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25
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Melkova Z, Shankaran P, Madlenakova M, Bodor J. Current views on HIV-1 latency, persistence, and cure. Folia Microbiol (Praha) 2016; 62:73-87. [PMID: 27709447 DOI: 10.1007/s12223-016-0474-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/20/2016] [Indexed: 01/01/2023]
Abstract
HIV-1 infection cannot be cured as it persists in latently infected cells that are targeted neither by the immune system nor by available therapeutic approaches. Consequently, a lifelong therapy suppressing only the actively replicating virus is necessary. The latent reservoir has been defined and characterized in various experimental models and in human patients, allowing research and development of approaches targeting individual steps critical for HIV-1 latency establishment, maintenance, and reactivation. However, additional mechanisms and processes driving the remaining low-level HIV-1 replication in the presence of the suppressive therapy still remain to be identified and targeted. Current approaches toward HIV-1 cure involve namely attempts to reactivate and purge HIV latently infected cells (so-called "shock and kill" strategy), as well as approaches involving gene therapy and/or gene editing and stem cell transplantation aiming at generation of cells resistant to HIV-1. This review summarizes current views and concepts underlying different approaches aiming at functional or sterilizing cure of HIV-1 infection.
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Affiliation(s)
- Zora Melkova
- Department of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studnickova 7, 128 00, Prague 2, Czech Republic. .,BIOCEV, Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec, Průmyslová 595, 252 50, Vestec, Czech Republic.
| | - Prakash Shankaran
- Department of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studnickova 7, 128 00, Prague 2, Czech Republic
| | - Michaela Madlenakova
- Department of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studnickova 7, 128 00, Prague 2, Czech Republic.,BIOCEV, Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Josef Bodor
- BIOCEV, Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec, Průmyslová 595, 252 50, Vestec, Czech Republic
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26
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Defective proviruses rapidly accumulate during acute HIV-1 infection. Nat Med 2016; 22:1043-9. [PMID: 27500724 PMCID: PMC5014606 DOI: 10.1038/nm.4156] [Citation(s) in RCA: 548] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 06/28/2016] [Indexed: 12/12/2022]
Abstract
Although antiretroviral therapy (ART) suppresses viral replication to clinically undetectable levels, HIV-1 persists in CD4+ T cells in a latent form not targeted by the immune system or ART1–5. This latent reservoir is a major barrier to cure. Many individuals initiate ART during chronic infection, and in this setting, most proviruses are defective6. However, the dynamics of the accumulation and persistence of defective proviruses during acute HIV-1 infection are largely unknown. Here we show that defective proviruses accumulate rapidly within the first few weeks of infection to make up over 93% of all proviruses, regardless of how early ART is initiated. Using an unbiased method to amplify near full-length proviral genomes from HIV-1 infected adults treated at different stages of infection, we demonstrate that early ART initiation limits the size of the reservoir but does not profoundly impact the proviral landscape. This analysis allows us to revise our understanding of the composition of proviral populations and estimate the true reservoir size in individuals treated early vs. late in infection. Additionally, we demonstrate that common assays for measuring the reservoir do not correlate with reservoir size. These findings reveal hurdles that must be overcome to successfully analyze future HIV-1 cure strategies.
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27
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Boritz EA, Darko S, Swaszek L, Wolf G, Wells D, Wu X, Henry AR, Laboune F, Hu J, Ambrozak D, Hughes MS, Hoh R, Casazza JP, Vostal A, Bunis D, Nganou-Makamdop K, Lee JS, Migueles SA, Koup RA, Connors M, Moir S, Schacker T, Maldarelli F, Hughes SH, Deeks SG, Douek DC. Multiple Origins of Virus Persistence during Natural Control of HIV Infection. Cell 2016; 166:1004-1015. [PMID: 27453467 DOI: 10.1016/j.cell.2016.06.039] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/09/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
Abstract
Targeted HIV cure strategies require definition of the mechanisms that maintain the virus. Here, we tracked HIV replication and the persistence of infected CD4 T cells in individuals with natural virologic control by sequencing viruses, T cell receptor genes, HIV integration sites, and cellular transcriptomes. Our results revealed three mechanisms of HIV persistence operating within distinct anatomic and functional compartments. In lymph node, we detected viruses with genetic and transcriptional attributes of active replication in both T follicular helper (TFH) cells and non-TFH memory cells. In blood, we detected inducible proviruses of archival origin among highly differentiated, clonally expanded cells. Linking the lymph node and blood was a small population of circulating cells harboring inducible proviruses of recent origin. Thus, HIV replication in lymphoid tissue, clonal expansion of infected cells, and recirculation of recently infected cells act together to maintain the virus in HIV controllers despite effective antiviral immunity.
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Affiliation(s)
- Eli A Boritz
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luke Swaszek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Gideon Wolf
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - David Wells
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Farida Laboune
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jianfei Hu
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - David Ambrozak
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Marybeth S Hughes
- Thoracic and Gastrointestinal Oncology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Joseph P Casazza
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alexander Vostal
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Daniel Bunis
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - James S Lee
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Mark Connors
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Susan Moir
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Timothy Schacker
- Program in HIV Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
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