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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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2
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Rausch JW, Parvez S, Pathak S, Capoferri AA, Kearney MF. HIV Expression in Infected T Cell Clones. Viruses 2024; 16:108. [PMID: 38257808 PMCID: PMC10820123 DOI: 10.3390/v16010108] [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: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among persistence determinants, as it allows infected cells to evade the cytopathic effects of virion production and killing by cytotoxic T lymphocytes (CTL) and other immune factors. HIV-1 persistence is also governed by cellular proliferation, an innate and essential capacity of CD4+ T cells that both sustains cell populations over time and enables a robust directed response to immunological threats. However, when HIV-1 infects CD4+ T cells, this capacity for proliferation can enable surreptitious HIV-1 propagation without the deleterious effects of viral gene expression in latently infected cells. Over time on ART, the HIV-1 reservoir is shaped by both persistence determinants, with selective forces most often favoring clonally expanded infected cell populations harboring transcriptionally quiescent proviruses. Moreover, if HIV latency is incomplete or sporadically reversed in clonal infected cell populations that are replenished faster than they are depleted, such populations could both persist indefinitely and contribute to low-level persistent viremia during ART and viremic rebound if treatment is withdrawn. In this review, select genetic, epigenetic, cellular, and immunological determinants of viral transcriptional suppression and clonal expansion of HIV-1 reservoir T cells, interdependencies among these determinants, and implications for HIV-1 persistence will be presented and discussed.
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Affiliation(s)
- Jason W. Rausch
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.P.); (S.P.); (A.A.C.); (M.F.K.)
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3
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Wu F, Simonetti FR. Learning from Persistent Viremia: Mechanisms and Implications for Clinical Care and HIV-1 Cure. Curr HIV/AIDS Rep 2023; 20:428-439. [PMID: 37955826 PMCID: PMC10719122 DOI: 10.1007/s11904-023-00674-w] [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] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
PURPOSE OF REVIEW In this review, we discuss what persistent viremia has taught us about the biology of the HIV-1 reservoir during antiretroviral therapy (ART). We will also discuss the implications of this phenomenon for HIV-1 cure research and its clinical management. RECENT FINDINGS While residual viremia (RV, 1-3 HIV-1 RNA copies/ml) can be detected in most of people on ART, some individuals experience non-suppressible viremia (NSV, > 20-50 copies/mL) despite optimal adherence. When issues of drug resistance and pharmacokinetics are ruled out, this persistent virus in plasma is the reflection of virus production from clonally expanded CD4+ T cells carrying proviruses. Recent work has shown that a fraction of the proviruses source of NSV are not infectious, due to defects in the 5'-Leader sequence. However, additional viruses and host determinants of NSV are not fully understood. The study of NSV is of prime importance because it represents a challenge for the clinical care of people on ART, and it sheds light on virus-host interactions that could advance HIV-1 remission research.
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Affiliation(s)
- Fengting Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA
| | - Francesco R Simonetti
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA.
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Reeves DB, Bacchus-Souffan C, Fitch M, Abdel-Mohsen M, Hoh R, Ahn H, Stone M, Hecht F, Martin J, Deeks SG, Hellerstein MK, McCune JM, Schiffer JT, Hunt PW. Estimating the contribution of CD4 T cell subset proliferation and differentiation to HIV persistence. Nat Commun 2023; 14:6145. [PMID: 37783718 PMCID: PMC10545742 DOI: 10.1038/s41467-023-41521-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
Persistence of HIV in people living with HIV (PWH) on suppressive antiretroviral therapy (ART) has been linked to physiological mechanisms of CD4+ T cells. Here, in the same 37 male PWH on ART we measure longitudinal kinetics of HIV DNA and cell turnover rates in five CD4 cell subsets: naïve (TN), stem-cell- (TSCM), central- (TCM), transitional- (TTM), and effector-memory (TEM). HIV decreases in TTM and TEM but not in less-differentiated subsets. Cell turnover is ~10 times faster than HIV clearance in memory subsets, implying that cellular proliferation consistently creates HIV DNA. The optimal mathematical model for these integrated data sets posits HIV DNA also passages between CD4 cell subsets via cellular differentiation. Estimates are heterogeneous, but in an average participant's year ~10 (in TN and TSCM) and ~104 (in TCM, TTM, TEM) proviruses are generated by proliferation while ~103 proviruses passage via cell differentiation (per million CD4). In simulations, therapies blocking proliferation and/or enhancing differentiation could reduce HIV DNA by 1-2 logs over 3 years. In summary, HIV exploits cellular proliferation and differentiation to persist during ART but clears faster in more proliferative/differentiated CD4 cell subsets and the same physiological mechanisms sustaining HIV might be temporarily modified to reduce it.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
- Department of Global Health, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA.
| | | | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | | | - Rebecca Hoh
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Mars Stone
- Vitalant Research Institute, 360 Spear St Suite 200, San Francisco, CA, 94105, USA
| | - Frederick Hecht
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Jeffrey Martin
- Epidemiology & Biostatistics, University of California San Francisco School of Medicine, 550 16th Street, San Francisco, CA, 94158, USA
| | - Steven G Deeks
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Marc K Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | - Joseph M McCune
- HIV Frontiers, Global Health Accelerator, Bill & Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98109, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
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Chvatal-Medina M, Lopez-Guzman C, Diaz FJ, Gallego S, Rugeles MT, Taborda NA. Molecular mechanisms by which the HIV-1 latent reservoir is established and therapeutic strategies for its elimination. Arch Virol 2023; 168:218. [PMID: 37530901 DOI: 10.1007/s00705-023-05800-y] [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: 11/23/2022] [Accepted: 04/12/2023] [Indexed: 08/03/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) reservoir, composed of cells harboring the latent, integrated virus, is not eliminated by antiretroviral therapy. It therefore represents a significant barrier to curing the infection. The biology of HIV-1 reservoirs, the mechanisms of their persistence, and effective strategies for their eradication are not entirely understood. Here, we review the molecular mechanisms by which HIV-1 reservoirs develop, the cells and compartments where the latent virus resides, and advancements in curative therapeutic strategies. We first introduce statistics and relevant data on HIV-1 infection, aspects of pathogenesis, the role of antiretroviral therapy, and the general features of the latent HIV reservoir. Then, the article is built on three main pillars: The molecular mechanisms related to latency, the different strategies for targeting the reservoir to obtain a cure, and the current progress in immunotherapy to counteract said reservoirs.
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Affiliation(s)
- Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Carolina Lopez-Guzman
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Francisco J Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Salomon Gallego
- Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Natalia A Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
- Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia.
- Universidad Cooperativa de Colombia, Campus Medellin, Envigado, Colombia.
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6
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Abstract
Specialized subpopulations of CD4+ T cells survey major histocompatibility complex class II-peptide complexes to control phagosomal infections, help B cells, regulate tissue homeostasis and repair or perform immune regulation. Memory CD4+ T cells are positioned throughout the body and not only protect the tissues from reinfection and cancer, but also participate in allergy, autoimmunity, graft rejection and chronic inflammation. Here we provide updates on our understanding of the longevity, functional heterogeneity, differentiation, plasticity, migration and human immunodeficiency virus reservoirs as well as key technological advances that are facilitating the characterization of memory CD4+ T cell biology.
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Affiliation(s)
- Marco Künzli
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - David Masopust
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.
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Ajibola G, Maswabi K, Hughes MD, Bennett K, Holme MP, Capparelli EV, Jean-Philippe P, Moyo S, Mohammed T, Batlang O, Sakoi M, Ricci L, Lockman S, Makhema J, Kuritzkes DR, Lichterfeld M, Shapiro RL. Brief Report: Long-Term Clinical, Immunologic, and Virologic Outcomes Among Early-Treated Children With HIV in Botswana: A Nonrandomized Controlled Clinical Trial. J Acquir Immune Defic Syndr 2023; 92:393-398. [PMID: 36729692 PMCID: PMC10006291 DOI: 10.1097/qai.0000000000003147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/29/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Early antiretroviral treatment (ART) improves outcomes in children, but few studies have comprehensively evaluated the impact of ART started from the first week of life. METHODS Children diagnosed with HIV within 96 hours of life were enrolled into the Early Infant Treatment Study in Botswana and followed on ART for 96 weeks. Nevirapine, zidovudine, and lamivudine were initiated; nevirapine was switched to lopinavir/ritonavir between weeks 2-5 in accordance with gestational age. Clinical and laboratory evaluations occurred at weeks 1, 2, 4, 8, 12, 24, 36, 48, 60, 72, 84, and 96. FINDINGS Forty children initiated ART at a median of 2 (IQR 2, 3) days of life; 38 (95%) completed follow-up through 96 weeks, and 2 (5%) died between 12 and 24 weeks. ART was well tolerated; 9 children (24%) experienced a grade 3 or 4 hematologic event, and 2 (5%) required treatment modification for anemia. The median 96-week CD4 count was 1625 (IQR 1179, 2493) cells/mm 3 with only 5/38 (13%) having absolute counts <1000 cells/mm 3 . Although 23 (61%) had at least one visit with HIV-1 RNA ≥40 copies/mL at or after 24 weeks, 28 (74%) had HIV-1 RNA <40 copies/mL at the 96-week visit. Median cell-associated HIV-1 DNA at 84/96-week PBMCs was 1.9 (IQR 1.0, 2.6) log 10 copies/10 6 cells. Pre-ART reservoir size at birth was predictive of the viral reservoir at 84/96 weeks. INTERPRETATION Initiation of ART in the first week of life led to favorable clinical outcomes, preserved CD4 cell counts, and low viral reservoir through 96 weeks of life.
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Affiliation(s)
| | - Kenneth Maswabi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Michael D. Hughes
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kara Bennett
- Bennett Statistical Consulting, Inc., Ballston Lake, NY, USA
| | - Molly Pretorius Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Oganne Batlang
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Maureen Sakoi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Lucia Ricci
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Mathias Lichterfeld
- Brigham and Women’s Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Roger L. Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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8
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Boulay A, Trabanelli S, Boireau S, Boyer-Clavel M, Nisole S, Romero P, Jandus C, Beignon AS, Arhel NJ. Assessing the Impact of Persistent HIV Infection on Innate Lymphoid Cells Using In Vitro Models. Immunohorizons 2023; 7:243-255. [PMID: 37000496 PMCID: PMC10563434 DOI: 10.4049/immunohorizons.2300007] [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: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 04/01/2023] Open
Abstract
Pathogens that persist in their host induce immune dysfunctions even in the absence of detectable replication. To better understand the phenotypic and functional changes that persistent infections induce in sentinel innate immune cells, we developed human PBMC-based HIV models of persistent infection. Autologous nonactivated PBMCs were cocultured with chronically infected, acutely infected, or uninfected cells and were then analyzed by unsupervised high-dimensional flow cytometry. Using this approach, we identified prevalent patterns of innate immune dysfunctions associated with persistent HIV infections that at least in part mirror immune dysfunctions observed in patients. In one or more models of chronic infection, bystander CD16+ NK cells expressing markers of activation, such as CD94, CD45RO, CD62L, CD69, CD25, and immune checkpoints PD1, Tim3, TIGIT, NKG2A and Lag3, were significantly reduced. Conversely, helper ILC subsets expressing PDL1/PDL2 were significantly enriched in chronic infection compared with either uninfected or acute infection, suggesting that chronic HIV-1 infection was associated with an inhibitory environment for bystander ILC and NK subsets. The cell-based models of persistent infection that we describe here provide versatile tools to explore the molecular mechanisms of these immune dysfunctions and unveil the contribution of innate immunity in sustaining pathogen persistence.
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Affiliation(s)
- Aude Boulay
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Sara Trabanelli
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
| | - Stéphanie Boireau
- Montpellier Ressources Imagerie, Biocampus, Université de Montpellier, CNRS, Montpellier, France
| | - Myriam Boyer-Clavel
- Montpellier Ressources Imagerie, Biocampus, Université de Montpellier, CNRS, Montpellier, France
| | - Sébastien Nisole
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Pedro Romero
- Department of Oncology, University of Lausanne, Épalinges, Switzerland
| | - Camilla Jandus
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
| | - Anne-Sophie Beignon
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Nathalie J. Arhel
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
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Gillespie SL, Chinen J, Paul ME. Human Immunodeficiency Virus Infection and Acquired Immunodeficiency Syndrome. Clin Immunol 2023. [DOI: 10.1016/b978-0-7020-8165-1.00041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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10
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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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11
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Packard TA, Schwarzer R, Herzig E, Rao D, Luo X, Egedal JH, Hsiao F, Widera M, Hultquist JF, Grimmett ZW, Messer RJ, Krogan NJ, Deeks SG, Roan NR, Dittmer U, Hasenkrug KJ, Greene WC. CCL2: a Chemokine Potentially Promoting Early Seeding of the Latent HIV Reservoir. mBio 2022; 13:e0189122. [PMID: 36073812 PMCID: PMC9600577 DOI: 10.1128/mbio.01891-22] [Citation(s) in RCA: 6] [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: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/20/2022] Open
Abstract
HIV infects long-lived CD4 memory T cells, establishing a latent viral reservoir that necessitates lifelong antiretroviral therapy (ART). How this reservoir is formed so quickly after infection remains unclear. We now show the innate inflammatory response to HIV infection results in CCL2 chemokine release, leading to recruitment of cells expressing the CCR2 receptor, including a subset of central memory CD4 T cells. Supporting a role for the CCL2/CCR2 axis in rapid reservoir formation, we find (i) treatment of humanized mice with anti-CCL2 antibodies during early HIV infection decreases reservoir seeding and preserves CCR2/5+ cells and (ii) CCR2/5+ cells from the blood of HIV-infected individuals on long-term ART contain significantly more integrated provirus than CCR2/5-negative memory or naive cells. Together, these studies support a model where the host's innate inflammatory response to HIV infection, including CCL2 production, leads to the recruitment of CCR2/5+ central memory CD4 T cells to zones of virus-associated inflammation, likely contributing to rapid formation of the latent HIV reservoir. IMPORTANCE There are currently over 35 million people living with HIV worldwide, and we still have no vaccine or scalable cure. One of the difficulties with HIV is its ability to rapidly establish a viral reservoir in lymphoid tissues that allows it to elude antivirals and the immune system. Thus, it is important to understand how HIV accomplishes this so we can develop preventive strategies. Our current results show that an early inflammatory response to HIV infection includes production of the chemokine CCL2, which recruits a unique subset of CCR2/5+ CD4+ T cells that become infected and form a significant reservoir for latent infection. Furthermore, we show that blockade of CCL2 in humanized mice significantly reduces persistent HIV infection. This information is relevant to the development of therapeutics to prevent and/or treat chronic HIV infections.
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Affiliation(s)
| | - Roland Schwarzer
- J. David Gladstone Institutes, San Francisco, California, USA
- Institute for Translational HIV Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Eytan Herzig
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Deepashri Rao
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Xiaoyu Luo
- J. David Gladstone Institutes, San Francisco, California, USA
| | | | - Feng Hsiao
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Judd F. Hultquist
- J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | | | - Ronald J. Messer
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Nevan J. Krogan
- J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Steven G. Deeks
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Nadia R. Roan
- J. David Gladstone Institutes, San Francisco, California, USA
- Department of Urology, University of California San Francisco, San Francisco, California, USA
| | - Ulf Dittmer
- Institute for Translational HIV Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Warner C. Greene
- J. David Gladstone Institutes, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
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12
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Baiyegunhi OO, Mann J, Khaba T, Nkosi T, Mbatha A, Ogunshola F, Chasara C, Ismail N, Ngubane T, Jajbhay I, Pansegrouw J, Dong KL, Walker BD, Ndung'u T, Ndhlovu ZM. CD8 lymphocytes mitigate HIV-1 persistence in lymph node follicular helper T cells during hyperacute-treated infection. Nat Commun 2022; 13:4041. [PMID: 35831418 PMCID: PMC9279299 DOI: 10.1038/s41467-022-31692-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
HIV persistence in tissue sites despite ART is a major barrier to HIV cure. Detailed studies of HIV-infected cells and immune responses in native lymph node tissue environment is critical for gaining insight into immune mechanisms impacting HIV persistence and clearance in tissue sanctuary sites. We compared HIV persistence and HIV-specific T cell responses in lymph node biopsies obtained from 14 individuals who initiated therapy in Fiebig stages I/II, 5 persons treated in Fiebig stages III-V and 17 late treated individuals who initiated ART in Fiebig VI and beyond. Using multicolor immunofluorescence staining and in situ hybridization, we detect HIV RNA and/or protein in 12 of 14 Fiebig I/II treated persons on suppressive therapy for 1 to 55 months, and in late treated persons with persistent antigens. CXCR3+ T follicular helper cells harbor the greatest amounts of gag mRNA transcripts. Notably, HIV-specific CD8+ T cells responses are associated with lower HIV antigen burden, suggesting that these responses may contribute to HIV suppression in lymph nodes during therapy. These results reveal HIV persistence despite the initiation of ART in hyperacute infection and highlight the contribution of virus-specific responses to HIV suppression in tissue sanctuaries during suppressive ART.
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Affiliation(s)
- Omolara O Baiyegunhi
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Trevor Khaba
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thandeka Nkosi
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Anele Mbatha
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Funsho Ogunshola
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
| | | | - Nasreen Ismail
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thandekile Ngubane
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
| | - Bruce D Walker
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
- Institute for Medical Sciences and Engineering and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, UK
| | - Zaza M Ndhlovu
- Africa Health Research Institute (AHRI), Durban, South Africa.
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA.
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13
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Rudd H, Toborek M. Pitfalls of Antiretroviral Therapy: Current Status and Long-Term CNS Toxicity. Biomolecules 2022; 12:biom12070894. [PMID: 35883450 PMCID: PMC9312798 DOI: 10.3390/biom12070894] [Citation(s) in RCA: 1] [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: 05/11/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
HIV can traverse the BBB using a Trojan horse-like mechanism. Hidden within infected immune cells, HIV can infiltrate the highly safeguarded CNS and propagate disease. Once integrated within the host genome, HIV becomes a stable provirus, which can remain dormant, evade detection by the immune system or antiretroviral therapy (ART), and result in rebound viraemia. As ART targets actively replicating HIV, has low BBB penetrance, and exposes patients to long-term toxicity, further investigation into novel therapeutic approaches is required. Viral proteins can be produced by latent HIV, which may play a synergistic role alongside ART in promoting neuroinflammatory pathophysiology. It is believed that the ability to specifically target these proviral reservoirs would be a vital driving force towards a cure for HIV infection. A novel drug design platform, using the in-tandem administration of several therapeutic approaches, can be used to precisely target the various components of HIV infection, ultimately leading to the eradication of active and latent HIV and a functional cure for HIV. The aim of this review is to explore the pitfalls of ART and potential novel therapeutic alternatives.
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Affiliation(s)
- Harrison Rudd
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Michal Toborek
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
- Institute of Physiotherapy and Health Sciences, The Jerzy Kukuczka Academy of Physical Education, 40-065 Katowice, Poland
- Correspondence: ; Tel.: +1-(305)-243-0230
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14
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Galvão-Lima LJ, Zambuzi FA, Soares LS, Fontanari C, Meireles AFG, Brauer VS, Faccioli LH, Gama L, Figueiredo LTM, Bou-Habib DC, Frantz FG. HIV-1 Gag and Vpr impair the inflammasome activation and contribute to the establishment of chronic infection in human primary macrophages. Mol Immunol 2022; 148:68-80. [PMID: 35659727 DOI: 10.1016/j.molimm.2022.04.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 02/07/2023]
Abstract
The successful establishment of HIV-1 infection is related to inflammasome blocking or inactivation, which can result in the viral evasion of the immune responses and formation of reservoirs in several tissues. In this sense, we aimed to evaluate the viral and cellular mechanisms activated during HIV-1 infection in human primary macrophages that allow an effective viral replication in these cells. We found that resting HIV-1-infected macrophages, but not those activated in classical or alternative patterns, released IL-1β and other pro-inflammatory cytokines, and showed increased CXCL10 expression, without changes in the NLRP3, AIM2 or RIG-I inflammasome pathways. Also, similar levels of Casp-1, phosphorylated NF-κB (p65) and NLRP3 proteins were found in uninfected and HIV-1-infected macrophages. Likewise, no alterations were detected in ASC specks released in the culture supernatant after HIV-1 infection, suggesting that macrophages remain viable after infection. Using in silico prediction studies, we found that the HIV-1 proteins Gag and Vpr interact with several host proteins. Comparable levels of trans-LTB4 were found in the supernatants of uninfected and HIV-1-infected macrophages, whereas ROS production was impaired in infected cells, which was not reversed after the PMA stimulus. Immunofluorescence analysis showed structural alterations in the mitochondrial architecture and an increase of BIM in the cytoplasm of infected cells. Our data suggest that HIV-1 proteins Gag and Vpr, through interacting with cellular proteins in the early steps of infection, preclude the inflammasome activation and the development of effective immune responses, thus allowing the establishment of the infection.
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Affiliation(s)
- Leonardo J Galvão-Lima
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil; Laboratory of Technological Innovation in Health (LAIS), Hospital Universitário Onofre Lopes, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil
| | - Fabiana A Zambuzi
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Luana S Soares
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Caroline Fontanari
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Aline F Galvão Meireles
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Verônica S Brauer
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Lúcia H Faccioli
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Lúcio Gama
- Retrovirus Lab, Johns Hopkins University - School of Medicine, Baltimore, MD, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Luiz T M Figueiredo
- Virology Research Center, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Dumith Chequer Bou-Habib
- Laboratory on Thymus Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
| | - Fabiani G Frantz
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil.
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15
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Therapeutic efficacy of an Ad26/MVA vaccine with SIV gp140 protein and vesatolimod in ART-suppressed rhesus macaques. NPJ Vaccines 2022; 7:53. [PMID: 35585080 PMCID: PMC9117189 DOI: 10.1038/s41541-022-00477-x] [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: 12/05/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Developing an intervention that results in virologic control following discontinuation of antiretroviral therapy (ART) is a major objective of HIV-1 cure research. In this study, we investigated the therapeutic efficacy of a vaccine consisting of adenovirus serotype 26 (Ad26) and modified vaccinia Ankara (MVA) with or without an SIV Envelope (Env) gp140 protein with alum adjuvant in combination with the TLR7 agonist vesatolimod (GS-9620) in 36 ART-suppressed, SIVmac251-infected rhesus macaques. Ad26/MVA therapeutic vaccination led to robust humoral and cellular immune responses, and the Env protein boost increased antibody responses. Following discontinuation of ART, virologic control was observed in 5/12 animals in each vaccine group, compared with 0/12 animals in the sham control group. These data demonstrate therapeutic efficacy of Ad26/MVA vaccination with vesatolimod but no clear additional benefit of adding an Env protein boost. SIV-specific cellular immune responses correlated with virologic control. Our findings show partial efficacy of therapeutic vaccination following ART discontinuation in SIV-infected rhesus macaques.
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16
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York J, Gowrishankar K, Micklethwaite K, Palmer S, Cunningham AL, Nasr N. Evolving Strategies to Eliminate the CD4 T Cells HIV Viral Reservoir via CAR T Cell Immunotherapy. Front Immunol 2022; 13:873701. [PMID: 35572509 PMCID: PMC9098815 DOI: 10.3389/fimmu.2022.873701] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Although the advent of ART has significantly reduced the morbidity and mortality associated with HIV infection, the stable pool of HIV in latently infected cells requires lifelong treatment adherence, with the cessation of ART resulting in rapid reactivation of the virus and productive HIV infection. Therefore, these few cells containing replication-competent HIV, known as the latent HIV reservoir, act as the main barrier to immune clearance and HIV cure. While several strategies involving HIV silencing or its reactivation in latently infected cells for elimination by immune responses have been explored, exciting cell based immune therapies involving genetically engineered T cells expressing synthetic chimeric receptors (CAR T cells) are highly appealing and promising. CAR T cells, in contrast to endogenous cytotoxic T cells, can function independently of MHC to target HIV-infected cells, are efficacious and have demonstrated acceptable safety profiles and long-term persistence in peripheral blood. In this review, we present a comprehensive picture of the current efforts to target the HIV latent reservoir, with a focus on CAR T cell therapies. We highlight the current challenges and advances in this field, while discussing the importance of novel CAR designs in the efforts to find a HIV cure.
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Affiliation(s)
- Jarrod York
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Kavitha Gowrishankar
- Centre for Cancer Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney Children’s Hospitals Network, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Kenneth Micklethwaite
- Centre for Cancer Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- NSW Health Pathology Blood Transplant and Cell Therapies Laboratory – Institute of Clinical Pathology and Medical Research (ICPMR) Westmead, Sydney, NSW, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
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17
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Zayas JP, Mamede JI. HIV Infection and Spread between Th17 Cells. Viruses 2022; 14:v14020404. [PMID: 35215997 PMCID: PMC8874668 DOI: 10.3390/v14020404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
HIV mainly targets CD4+ T cells, from which Th17 cells represent a major cell type, permissive, and are capable of supporting intracellular replication at mucosal sites. Th17 cells possess well-described dual roles, while being central to maintaining gut integrity, these may induce inflammation and contribute to autoimmune disorders; however, Th17 cells’ antiviral function in HIV infection is not completely understood. Th17 cells are star players to HIV-1 pathogenesis and a potential target to prevent or decrease HIV transmission. HIV-1 can be spread among permissive cells via direct cell-to-cell and/or cell-free infection. The debate on which mode of transmission is more efficient is still ongoing without a concrete conclusion yet. Most assessments of virus transmission analyzing either cell-to-cell or cell-free modes use in vitro systems; however, the actual interactions and conditions in vivo are not fully understood. The fact that infected breast milk, semen, and vaginal secretions contain a mix of both cell-free viral particles and infected cells presents an argument for the probability of HIV taking advantage of both modes of transmission to spread. Here, we review important insights and recent findings about the role of Th17 cells during HIV pathogenesis in mucosal surfaces, and the mechanisms of HIV-1 infection spread among T cells in tissues.
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18
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Huang AS, Ramos V, Oliveira TY, Gaebler C, Jankovic M, Nussenzweig MC, Cohn LB. Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence. J Exp Med 2021; 218:e20211427. [PMID: 34636876 PMCID: PMC8515646 DOI: 10.1084/jem.20211427] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/17/2021] [Accepted: 09/27/2021] [Indexed: 01/26/2023] Open
Abstract
Latent intact HIV-1 proviruses persist in a small subset of long-lived CD4+ T cells that can undergo clonal expansion in vivo. Expanded clones of CD4+ T cells dominate latent reservoirs in individuals on long-term antiretroviral therapy (ART) and represent a major barrier to HIV-1 cure. To determine how integration landscape might contribute to latency, we analyzed integration sites of near full length HIV-1 genomes from individuals on long-term ART, focusing on individuals whose reservoirs are highly clonal. We find that intact proviruses in expanded CD4+ T cell clones are preferentially integrated within Krüppel-associated box (KRAB) domain-containing zinc finger (ZNF) genes. ZNF genes are associated with heterochromatin in memory CD4+ T cells; nevertheless, they are expressed in these cells under steady-state conditions. In contrast to genes carrying unique integrations, ZNF genes carrying clonal intact integrations are down-regulated upon cellular activation. Together, the data suggest selected genomic sites, including ZNF genes, can be especially permissive for maintaining HIV-1 latency during memory CD4+ T cell expansion.
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Affiliation(s)
- Amy S. Huang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Thiago Y. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
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19
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Zhang Z, Trypsteen W, Blaauw M, Chu X, Rutsaert S, Vandekerckhove L, van der Heijden W, Dos Santos JC, Xu CJ, Swertz MA, van der Ven A, Li Y. IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis. BMC Med 2021; 19:282. [PMID: 34781942 PMCID: PMC8594146 DOI: 10.1186/s12916-021-02156-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/07/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Combination antiretroviral treatment (cART) cannot eradicate HIV-1 from the body due to the establishment of persisting viral reservoirs which are not affected by therapy and reinitiate new rounds of HIV-1 replication after treatment interruption. These HIV-1 reservoirs mainly comprise long-lived resting memory CD4+ T cells and are established early after infection. There is a high variation in the size of these viral reservoirs among virally suppressed individuals. Identification of host factors that contribute to or can explain this observed variation could open avenues for new HIV-1 treatment strategies. METHODS In this study, we conducted a genome-wide quantitative trait locus (QTL) analysis to probe functionally relevant genetic variants linked to levels of cell-associated (CA) HIV-1 DNA, CA HIV-1 RNA, and RNA:DNA ratio in CD4+ T cells isolated from blood from a cohort of 207 (Caucasian) people living with HIV-1 (PLHIV) on long-term suppressive antiretroviral treatment (median = 6.6 years). CA HIV-1 DNA and CA HIV-1 RNA levels were measured with corresponding droplet digital PCR (ddPCR) assays, and genotype information of 522,455 single-nucleotide variants was retrieved via the Infinium Global Screening array platform. RESULTS The analysis resulted in one significant association with CA HIV-1 DNA (rs2613996, P < 5 × 10-8) and two suggestive associations with RNA:DNA ratio (rs7113204 and rs7817589, P < 5 × 10-7). Then, we prioritized PTDSS2, IRF7, RNH1, and DEAF1 as potential HIV-1 reservoir modifiers and validated that higher expressions of IRF7 and RNH1 were accompanied by rs7113204-G. Moreover, RNA:DNA ratio, indicating relative HIV-1 transcription activity, was lower in PLHIV carrying this variant. CONCLUSIONS The presented data suggests that the amount of CA HIV-1 DNA and RNA:DNA ratio can be influenced through PTDSS2, RNH1, and IRF7 that were anchored by our genome-wide association analysis. Further, these observations reveal potential host genetic factors affecting the size and transcriptional activity of HIV-1 reservoirs and could indicate new targets for HIV-1 therapeutic strategies.
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Affiliation(s)
- Zhenhua Zhang
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands.,Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Genomics Coordination Center, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Marc Blaauw
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Xiaojing Chu
- Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wouter van der Heijden
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Jéssica Cristina Dos Santos
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Genomics Coordination Center, University Medical Center Groningen, 9700RB, Groningen, the Netherlands
| | - Andre van der Ven
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands.
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands. .,Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands. .,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany. .,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
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20
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Rahman SA, Yagnik B, Bally AP, Morrow KN, Wang S, Vanderford TH, Freeman GJ, Ahmed R, Amara RR. PD-1 blockade and vaccination provide therapeutic benefit against SIV by inducing broad and functional CD8 + T cells in lymphoid tissue. Sci Immunol 2021; 6:eabh3034. [PMID: 34516743 DOI: 10.1126/sciimmunol.abh3034] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Sheikh Abdul Rahman
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Bhrugu Yagnik
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Alexander P Bally
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Kristen N Morrow
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Shelly Wang
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gordon J Freeman
- Department of Medical Oncology and Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Rafi Ahmed
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Rama Rao Amara
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
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21
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Fiorino S, Tateo F, Biase DD, Gallo CG, Orlandi PE, Corazza I, Budriesi R, Micucci M, Visani M, Loggi E, Hong W, Pica R, Lari F, Zippi M. SARS-CoV-2: lessons from both the history of medicine and from the biological behavior of other well-known viruses. Future Microbiol 2021; 16:1105-1133. [PMID: 34468163 PMCID: PMC8412036 DOI: 10.2217/fmb-2021-0064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is the etiological agent of the current pandemic worldwide and its associated disease COVID-19. In this review, we have analyzed SARS-CoV-2 characteristics and those ones of other well-known RNA viruses viz. HIV, HCV and Influenza viruses, collecting their historical data, clinical manifestations and pathogenetic mechanisms. The aim of the work is obtaining useful insights and lessons for a better understanding of SARS-CoV-2. These pathogens present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne, whereas HIV and HCV are bloodborne. However, these viruses exhibit some potential similar clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2.
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Affiliation(s)
- Sirio Fiorino
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Fabio Tateo
- Institute of Geosciences & Earth Resources, CNR, c/o Department of Geosciences, Padova University, 35127, Italy
| | - Dario De Biase
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Claudio G Gallo
- Fisiolaserterapico Emiliano, Castel San Pietro Terme, Bologna, 40024, Italy
| | | | - Ivan Corazza
- Department of Experimental, Diagnostic & Specialty Medicine, University of Bologna, Bologna, 40126, Italy
| | - Roberta Budriesi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Matteo Micucci
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Michela Visani
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Loggi
- Hepatology Unit, Department of Medical & Surgical Sciences, University of Bologna, Bologna, 40126, Italy
| | - Wandong Hong
- Department of Gastroenterology & Hepatology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang, 325035, PR China
| | - Roberta Pica
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
| | - Federico Lari
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Maddalena Zippi
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
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22
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UHRF1 Suppresses HIV-1 Transcription and Promotes HIV-1 Latency by Competing with p-TEFb for Ubiquitination-Proteasomal Degradation of Tat. mBio 2021; 12:e0162521. [PMID: 34465029 PMCID: PMC8406157 DOI: 10.1128/mbio.01625-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
HIV-1 remains incurable due to viral reservoirs, which lead to durably latent HIV infection. Identifying novel host factors and deciphering the molecular mechanisms involved in the establishment and maintenance of latency are critical to discover new targets for the development of novel anti-HIV agents. Here, we show that ubiquitin-like with PHD and RING finger domain 1 (UHRF1) modulates HIV-1 5'-long terminal repeat (LTR)-driven transcription of the viral genome as a novel HIV-1 restriction factor. Correspondingly, UHRF1 depletion reversed the latency of HIV-1 proviruses. Mechanistically, UHRF1 competed with positive transcription factor b (p-TEFb) for the binding to the cysteine-rich motifs of HIV-1 Tat via its TTD, PHD, and RING finger domains. Furthermore, UHRF1 mediated K48-linked ubiquitination and proteasomal degradation of Tat in RING-dependent ways, leading to the disruption of Tat/cyclin T1/CDK9 complex and consequential impediment of transcription elongation. In summary, our findings revealed that UHRF1 is an important mediator of HIV-1 latency by controlling Tat-mediated transcriptional activation, providing novel insights on host-pathogen interaction for modulating HIV-1 latency, beneficial for the development of anti-AIDS therapies. IMPORTANCE HIV-1 latency is systematically modulated by host factors and viral proteins. In our work, we identified a critical role of host factor ubiquitin-like with PHD and RING finger domain 1 (UHRF1) in HIV-1 latency via the modulation of the viral protein Tat stability. By disrupting the Tat/cyclin T1/CDK9 complex, UHRF1 promotes the suppression of HIV-1 transcription and maintenance of HIV-1 latency. Our findings provide novel insights in controlling Tat expression via host-pathogen interaction for modulating HIV-1 latency. Based on our results, modulating UHRF1 expression or activity by specific inhibitors is a potential therapeutic strategy for latency reversal in HIV-1 patients.
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23
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Insights from Clonal Expansion and HIV Persistence in Perinatal Infections. mBio 2021; 12:e0098321. [PMID: 34425702 PMCID: PMC8406253 DOI: 10.1128/mbio.00983-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The latent HIV reservoir forms early in the course of infection and is maintained for life despite effective antiretroviral treatment (ART), including early treatment. Perinatal HIV infection presents a unique opportunity to limit seeding of the reservoir through early ART. However, a greater understanding of the persistence of the integrated proviruses is needed for targeting the residual proviruses that form barriers to cure. A study was performed by Bale and Katusiime et al. (M. J. Bale, M. G. Katusiime, D. Wells, X. Wu, et al., mBio 12:e00568-21, 2021, https://doi.org/10.1128/mBio.00568-21) using in-depth integration site analysis in 11 children before ART and after up to nine years of ART. They have identified early development of long-lived proviruses, although the replication competence is unknown. A small fraction of cells bearing integrated proviruses clonally expand early during infection and persist. Integration in the oncogenes STAT5B and BACH2 were also found; these findings confirm the early development of clonal proliferation in perinatal HIV infection despite early effective ART, with a propensity for oncogenes.
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24
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Xu X, Petersen S, Rodriguez C, Yi G. VISTA facilitates phagocytic clearance of HIV infected CEM-SS T cells. Heliyon 2021; 7:e07496. [PMID: 34401556 PMCID: PMC8353305 DOI: 10.1016/j.heliyon.2021.e07496] [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: 10/22/2020] [Revised: 12/03/2020] [Accepted: 07/02/2021] [Indexed: 11/02/2022] Open
Abstract
Phagocytosis is a critical component of the innate immune response to viral infection, resulting in the clearance of infected cells while minimizing the exposure of uninfected cells. On the other hand, phagocytosis of HIV-infected T cells may cause phagocytes, such as macrophages and dendritic cells, to be infected, thus leading to HIV cell-to-cell transmission. V domain immunoglobulin suppressor of T cell activation (VISTA, gene Vsir, aliases Gi24, Dies-1, PD-1H, and DD1α) has been identified as an immune checkpoint molecule that possesses dual activities when expressed on APCs and T cells. Our study found that VISTA might play a significant role during the immune response to HIV infection via apoptosis upregulation and subsequent phagocytosis of infected CEM-SS T cells. HIV-induced apoptosis and monocytic cell engulfment were tested utilizing CEM-SS T cells as target cells and the monocytic cell line THP-1 as phagocytic cells. Cells were infected with a GFP-labeled HIV strain, NL4-3. HIV-infected CEM-SS T cells displayed greater apoptotic activity (approximately 18.0%) than mock-infected controls. Additionally, phagocytosis of HIV-infected CEM-SS T cells was increased approximately 4-fold. Expression of VISTA on infected CEM-SS T cells was detected in 16.7% of cells, which correlated with the increased phagocytosis observed. When an antagonistic antibody against VISTA was used, the number of phagocytosed cells was reduced by a factor of 2, which was replicated utilizing human stem cell-derived dendritic cells. Phagocytosis was also confirmed by the upregulation of IL-1β expression, which was 5-fold higher in infected cells than in control cells. We also found that VISTA overexpression on both phagocytes and HIV-infected CEM-SS T cells facilitated phagocytosis. Our study suggests that VISTA may act as a direct ligand in the phagocytosis of HIV-infected T cells.
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Affiliation(s)
- Xuequn Xu
- Center of Emphasis in Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, United States
| | - Sean Petersen
- Center of Emphasis in Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, United States
| | - Cynthia Rodriguez
- Center of Emphasis in Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, United States
| | - Guohua Yi
- Center of Emphasis in Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, United States.,Department of Pulmonary Immunology, The University of Texas Health Science Center at Tyler, United States
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25
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Atkins A, Chung CH, Allen AG, Dampier W, Gurrola TE, Sariyer IK, Nonnemacher MR, Wigdahl B. Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy. Front Genome Ed 2021; 3:673022. [PMID: 34713260 PMCID: PMC8525399 DOI: 10.3389/fgeed.2021.673022] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022] Open
Abstract
As genome-editing nucleases move toward broader clinical applications, the need to define the limits of their specificity and efficiency increases. A variety of approaches for nuclease cleavage detection have been developed, allowing a full-genome survey of the targeting landscape and the detection of a variety of repair outcomes for nuclease-induced double-strand breaks. Each approach has advantages and disadvantages relating to the means of target-site capture, target enrichment mechanism, cellular environment, false discovery, and validation of bona fide off-target cleavage sites in cells. This review examines the strengths, limitations, and origins of the different classes of off-target cleavage detection systems including anchored primer enrichment (GUIDE-seq), in situ detection (BLISS), in vitro selection libraries (CIRCLE-seq), chromatin immunoprecipitation (ChIP) (DISCOVER-Seq), translocation sequencing (LAM PCR HTGTS), and in vitro genomic DNA digestion (Digenome-seq and SITE-Seq). Emphasis is placed on the specific modifications that give rise to the enhanced performance of contemporary techniques over their predecessors and the comparative performance of techniques for different applications. The clinical relevance of these techniques is discussed in the context of assessing the safety of novel CRISPR/Cas9 HIV-1 curative strategies. With the recent success of HIV-1 and SIV-1 viral suppression in humanized mice and non-human primates, respectively, using CRISPR/Cas9, rigorous exploration of potential off-target effects is of critical importance. Such analyses would benefit from the application of the techniques discussed in this review.
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Affiliation(s)
- Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore E. Gurrola
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States,*Correspondence: Brian Wigdahl
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26
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Rausch JW, Le Grice SFJ. Characterizing the Latent HIV-1 Reservoir in Patients with Viremia Suppressed on cART: Progress, Challenges, and Opportunities. Curr HIV Res 2021; 18:99-113. [PMID: 31889490 PMCID: PMC7475929 DOI: 10.2174/1570162x18666191231105438] [Citation(s) in RCA: 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: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Modern combination antiretroviral therapy (cART) can bring HIV-1 in blood plasma to level undetectable by standard tests, prevent the onset of acquired immune deficiency syndrome (AIDS), and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, cART is not curative, as within a few weeks of treatment cessation, HIV viremia in most patients rebounds to pre-cART levels. The primary source of this rebound, and the principal barrier to a cure, is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of resting memory CD4+ T cells. In this review, prevailing models for how the latent reservoir is established and maintained, residual viremia and viremic rebound upon withdrawal of cART, and the types and characteristics of cells harboring latent HIV-1 will be discussed. Selected technologies currently being used to advance our understanding of HIV latency will also be presented, as will a perspective on which areas of advancement are most essential for producing the next generation of HIV-1 therapeutics.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
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27
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Abeynaike S, Paust S. Humanized Mice for the Evaluation of Novel HIV-1 Therapies. Front Immunol 2021; 12:636775. [PMID: 33868262 PMCID: PMC8047330 DOI: 10.3389/fimmu.2021.636775] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
With the discovery of antiretroviral therapy, HIV-1 infection has transitioned into a manageable but chronic illness, which requires lifelong treatment. Nevertheless, complete eradication of the virus has still eluded us. This is partly due to the virus’s ability to remain in a dormant state in tissue reservoirs, ‘hidden’ from the host’s immune system. Also, the high mutation rate of HIV-1 results in escape mutations in response to many therapeutics. Regardless, the development of novel cures for HIV-1 continues to move forward with a range of approaches from immunotherapy to gene editing. However, to evaluate in vivo pathogenesis and the efficacy and safety of therapeutic approaches, a suitable animal model is necessary. To this end, the humanized mouse was developed by McCune in 1988 and has continued to be improved on over the past 30 years. Here, we review the variety of humanized mouse models that have been utilized through the years and describe their specific contribution in translating HIV-1 cure strategies to the clinic.
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Affiliation(s)
- Shawn Abeynaike
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,The Skaggs Graduate Program in Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, United States
| | - Silke Paust
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,The Skaggs Graduate Program in Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, United States
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28
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Janssens J, Bruggemans A, Christ F, Debyser Z. Towards a Functional Cure of HIV-1: Insight Into the Chromatin Landscape of the Provirus. Front Microbiol 2021; 12:636642. [PMID: 33868195 PMCID: PMC8044952 DOI: 10.3389/fmicb.2021.636642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Despite potent combination antiretroviral therapy, HIV-1 infection persists due to irreversible integration of the virus in long-living cells of the immune system. The main focus of HIV-1 cure strategies has been on HIV-1 eradication, yet without great success so far. Therefore, HIV-1 remission or a functional cure, whereby the virus is silenced rather than eradicated, is considered as an alternative strategy. Elite controllers, individuals who spontaneously control HIV-1, may point us the way toward a functional HIV-1 cure. In order to achieve such a cure, a profound understanding of the mechanisms controlling HIV-1 expression and silencing is needed. In recent years, evidence has grown that the site of integration as well as the chromatin landscape surrounding the integration site affects the transcriptional state of the provirus. Still, at present, the impact of integration site selection on the establishment and maintenance of the HIV-1 reservoirs remains poorly understood. The discovery of LEDGF/p75 as a binding partner of HIV-1 integrase has led to a better understanding of integration site selection. LEDGF/p75 is one of the important determinants of integration site selection and targets integration toward active genes. In this review, we will provide an overview of the most important determinants of integration site selection. Secondly, we will discuss the chromatin landscape at the integration site and its implications on HIV-1 gene expression and silencing. Finally, we will discuss how interventions that affect integration site selection or modifications of the chromatin could yield a functional cure of HIV-1 infection.
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Affiliation(s)
- Julie Janssens
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Anne Bruggemans
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
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29
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Scott TA, O’Meally D, Grepo NA, Soemardy C, Lazar DC, Zheng Y, Weinberg MS, Planelles V, Morris KV. Broadly active zinc finger protein-guided transcriptional activation of HIV-1. Mol Ther Methods Clin Dev 2021; 20:18-29. [PMID: 33335944 PMCID: PMC7726486 DOI: 10.1016/j.omtm.2020.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) causes a persistent viral infection resulting in the demise of immune regulatory cells. Clearance of HIV-1 infection results in integration of proviral DNA into the genome of host cells, which provides a means for evasion and long-term persistence. A therapeutic compound that specifically targets and sustainably activates a latent HIV-1 provirus could be transformative and is the goal for the "shock-and-kill" approach to a functional cure for HIV-1. Substantial progress has been made toward the development of recombinant proteins that target specific genomic loci for gene activation, repression, or inactivation by directed mutations. However, most of these modalities are too large or too complex for efficient therapeutic application. We describe here the development and testing of a novel recombinant zinc finger protein transactivator, ZFP-362-VPR, which specifically and potently enhances proviral HIV-1 transcription both in established latency models and activity across different viral clades. Additionally, ZFP-362-VPR-activated HIV-1 reporter gene expression in a well-established primary human CD4+ T cell latency model and off-target pathways were determined by transcriptome analyses. This study provides clear proof of concept for the application of a novel, therapeutically relevant, protein transactivator to purge cellular reservoirs of HIV-1.
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Affiliation(s)
- Tristan A. Scott
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Denis O’Meally
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Nicole Anne Grepo
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Daniel C. Lazar
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yue Zheng
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 92037, USA
| | - Marc S. Weinberg
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicente Planelles
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 92037, USA
| | - Kevin V. Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
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30
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Lu Y, Singh H, Singh A, Dar RD. A transient heritable memory regulates HIV reactivation from latency. iScience 2021; 24:102291. [PMID: 33889814 PMCID: PMC8050369 DOI: 10.1016/j.isci.2021.102291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/04/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
Reactivation of human immunodeficiency virus 1 (HIV-1) from latently infected T cells is a critical barrier to cure patients. It remains unknown whether reactivation of individual latent cells occurs stochastically in response to latency reversal agents (LRAs) or is a deterministic outcome of an underlying cell state. To characterize these single-cell responses, we leverage the classical Luria-Delbrück fluctuation test where single cells are isolated from a clonal population and exposed to LRAs after colony expansion. Data show considerable colony-to-colony fluctuations with the fraction of reactivating cells following a skewed distribution. Modeling systematic measurements of fluctuations over time uncovers a transient heritable memory that regulates HIV-1 reactivation, where single cells are in an LRA-responsive state for a few weeks before switching back to an irresponsive state. These results have enormous implications for designing therapies to purge the latent reservoir and further utilize fluctuation-based assays to uncover hidden transient cellular states underlying phenotypic heterogeneity.
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Affiliation(s)
- Yiyang Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Harpal Singh
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
- Corresponding author
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
- Corresponding author
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31
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Mohamed H, Clemen R, Freund E, Lackmann JW, Wende K, Connors J, Haddad EK, Dampier W, Wigdahl B, Miller V, Bekeschus S, Krebs FC. Non-thermal plasma modulates cellular markers associated with immunogenicity in a model of latent HIV-1 infection. PLoS One 2021; 16:e0247125. [PMID: 33647028 PMCID: PMC7920340 DOI: 10.1371/journal.pone.0247125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/02/2021] [Indexed: 12/25/2022] Open
Abstract
Effective control of infection by human immunodeficiency virus type 1 (HIV-1), the causative agent of the acquired immunodeficiency syndrome (AIDS), requires continuous and life-long use of anti-retroviral therapy (ART) by people living with HIV-1 (PLWH). In the absence of ART, HIV-1 reemergence from latently infected cells is ineffectively suppressed due to suboptimal innate and cytotoxic T lymphocyte responses. However, ART-free control of HIV-1 infection may be possible if the inherent immunological deficiencies can be reversed or restored. Herein we present a novel approach for modulating the immune response to HIV-1 that involves the use of non-thermal plasma (NTP), which is an ionized gas containing various reactive oxygen and nitrogen species (RONS). J-Lat cells were used as a model of latent HIV-1 infection to assess the effects of NTP application on viral latency and the expression of pro-phagocytic and pro-chemotactic damage-associated molecular patterns (DAMPs). Exposure of J-Lat cells to NTP resulted in stimulation of HIV-1 gene expression, indicating a role in latency reversal, a necessary first step in inducing adaptive immune responses to viral antigens. This was accompanied by the release of pro-inflammatory cytokines and chemokines including interleukin-1β (IL-1β) and interferon-γ (IFN-γ); the display of pro-phagocytic markers calreticulin (CRT), heat shock proteins (HSP) 70 and 90; and a correlated increase in macrophage phagocytosis of NTP-exposed J-Lat cells. In addition, modulation of surface molecules that promote or inhibit antigen presentation was also observed, along with an altered array of displayed peptides on MHC I, further suggesting methods by which NTP may modify recognition and targeting of cells in latent HIV-1 infection. These studies represent early progress toward an effective NTP-based ex vivo immunotherapy to resolve the dysfunctions of the immune system that enable HIV-1 persistence in PLWH.
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Affiliation(s)
- Hager Mohamed
- Department of Microbiology and Immunology, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ramona Clemen
- Centre for Innovation Competence (ZIK) plasmatis, Leibniz Institute for Plasma Science and Technology Greifswald (INP), Greifswald, Germany
| | - Eric Freund
- Centre for Innovation Competence (ZIK) plasmatis, Leibniz Institute for Plasma Science and Technology Greifswald (INP), Greifswald, Germany
| | - Jan-Wilm Lackmann
- Centre for Innovation Competence (ZIK) plasmatis, Leibniz Institute for Plasma Science and Technology Greifswald (INP), Greifswald, Germany.,CECAD proteomics facility, University of Cologne, Cologne, Germany
| | - Kristian Wende
- Centre for Innovation Competence (ZIK) plasmatis, Leibniz Institute for Plasma Science and Technology Greifswald (INP), Greifswald, Germany
| | - Jennifer Connors
- Department of Microbiology and Immunology, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Elias K Haddad
- Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Will Dampier
- Department of Microbiology and Immunology, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Vandana Miller
- Department of Microbiology and Immunology, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sander Bekeschus
- Centre for Innovation Competence (ZIK) plasmatis, Leibniz Institute for Plasma Science and Technology Greifswald (INP), Greifswald, Germany
| | - Fred C Krebs
- Department of Microbiology and Immunology, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
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Wolf G, Singh NJ. Modular Approaches to Understand the Immunobiology of Human Immunodeficiency Virus Latency. Viral Immunol 2021; 34:365-375. [PMID: 33600238 DOI: 10.1089/vim.2020.0171] [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: 11/12/2022] Open
Abstract
Despite advances in slowing the progression of acquired immunodeficiency syndrome (AIDS), there is no viable cure for human immunodeficiency virus (HIV). The challenge toward a cure is mainly the formation and maintenance of a latent reservoir of cells that harbor the virus in both replication-competent and replication-defective states. This small niche of quiescent cells has been identified to reside primarily in quiescent and memory CD4+ T cells, but parameters that could reliably distinguish an infected T cell from an uninfected one, if any, are not clear. In addition, the migratory properties and specific anatomical reservoirs of latent T cells are difficult to measure at a high resolution in humans. A functional cure of HIV would require targeting this population using innovative new clinical strategies. One constraint toward the empirical development of such approaches is the absence of a native small animal model for AIDS. Since HIV does not efficiently infect murine cells, probing molecular-genetic questions involving latently infected T cells homing to deep tissue sites, interacting with stroma and persisting through different treatment regimens, is challenging. The goal of this article is to discuss how examining the dynamics of T cells in mouse models can provide a framework for effectively studying these questions, even without infecting mice with HIV. The inflammatory and cytokine milieu found in early human HIV infections are being increasingly understood as a result of clinical measurements. Mouse studies that recreate this milieu can potentially be used to subsequently map the fate of T cells activated in this context as well as their migratory routes. In essence, such a framework could allow complementary studies in mice to enhance our understanding of aspects of the biology of HIV latency. This can be the basis of a modular approach to small animal HIV modeling, amenable to preclinical curative strategy development.
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Affiliation(s)
- Gideon Wolf
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nevil J Singh
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Adams P, Fievez V, Schober R, Amand M, Iserentant G, Rutsaert S, Dessilly G, Vanham G, Hedin F, Cosma A, Moutschen M, Vandekerckhove L, Seguin-Devaux C. CD32 +CD4 + memory T cells are enriched for total HIV-1 DNA in tissues from humanized mice. iScience 2021; 24:101881. [PMID: 33364576 PMCID: PMC7753142 DOI: 10.1016/j.isci.2020.101881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/04/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022] Open
Abstract
CD32 has raised conflicting results as a putative marker of the HIV-1 reservoir. We measured CD32 expression in tissues from viremic and virally suppressed humanized mice treated relatively early or late after HIV-1 infection with combined antiretroviral therapy. CD32 was expressed in a small fraction of the memory CD4+ T-cell subsets from different tissues in viremic and aviremic mice, regardless of treatment initiation time. CD32+ memory CD4+ T cells were enriched in cell-associated (CA) HIV-1 DNA but not in CA HIV-1 RNA as compared to the CD32-CD4+ fraction. Using multidimensional reduction analysis, several memory CD4+CD32+ T-cell clusters were identified expressing HLA-DR, TIGIT, or PD-1. Importantly, although tissue-resident CD32+CD4+ memory cells were enriched with translation-competent reservoirs, most of it was detected in memory CD32-CD4+ T cells. Our findings support that CD32 labels highly activated/exhausted memory CD4+ T-cell subsets that contain only a small proportion of the translation-competent reservoir.
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Affiliation(s)
- Philipp Adams
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
- Department of Biomedical and Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp 2000, Belgium
| | - Virginie Fievez
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Rafaëla Schober
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Mathieu Amand
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Gilles Iserentant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent 9000, Belgium
| | - Géraldine Dessilly
- AIDS Reference Laboratory, Catholic University of Louvain, Brussels 1348, Belgium
| | - Guido Vanham
- Department of Biomedical and Clinical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp 2000, Belgium
| | - Fanny Hedin
- Quantitative Biology Unit, National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Antonio Cosma
- Quantitative Biology Unit, National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Michel Moutschen
- Department of Infectious Diseases, University of Liège, CHU de Liège, Liège 4000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University, Ghent 9000, Belgium
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
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Ferreira RC, Prodger JL, Redd AD, Poon AFY. Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir. Virus Evol 2021; 7:veaa104. [PMID: 33505711 PMCID: PMC7816690 DOI: 10.1093/ve/veaa104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Among people living with human immunodeficiency virus type 1 (HIV-1), the long-term persistence of a population of cells carrying transcriptionally silent integrated viral DNA (provirus) remains the primary barrier to developing an effective cure. Ongoing cell division via proliferation is generally considered to be the driving force behind the persistence of this latent HIV-1 reservoir. The contribution of this mechanism (clonal expansion) is supported by the observation that proviral sequences sampled from the reservoir are often identical. This outcome is quantified as the ‘clonality’ of the sample population, e.g. the fraction of provirus sequences observed more than once. However, clonality as a quantitative measure is inconsistently defined and its statistical properties are not well understood. In this Reflections article, we use mathematical and phylogenetic frameworks to formally examine the inherent problems of using clonality to characterize the dynamics and proviral composition of the reservoir. We describe how clonality is not adequate for this task due to the inherent complexity of how infected cells are ‘labeled’ by proviral sequences—the outcome of a sampling process from the evolutionary history of active viral replication before treatment—as well as variation in cell birth and death rates among lineages and over time. Lastly, we outline potential directions in statistical and phylogenetic research to address these issues.
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Affiliation(s)
- Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, 1151 Richmond Street London, ON, Canada
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, 1151 Richmond Street London, ON, Canada
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5640 Fishers Lane Rockville, MD 20852, USA.,Department of Medicine, Johns Hopkins School of Medicine, 600 N. Wolfe Street Baltimore, MD 21205-2196, USA
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, 1151 Richmond Street London, ON, Canada
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35
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Moranguinho I, Valente ST. Block-And-Lock: New Horizons for a Cure for HIV-1. Viruses 2020; 12:v12121443. [PMID: 33334019 PMCID: PMC7765451 DOI: 10.3390/v12121443] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
HIV-1/AIDS remains a global public health problem. The world health organization (WHO) reported at the end of 2019 that 38 million people were living with HIV-1 worldwide, of which only 67% were accessing antiretroviral therapy (ART). Despite great success in the clinical management of HIV-1 infection, ART does not eliminate the virus from the host genome. Instead, HIV-1 remains latent as a viral reservoir in any tissue containing resting memory CD4+ T cells. The elimination of these residual proviruses that can reseed full-blown infection upon treatment interruption remains the major barrier towards curing HIV-1. Novel approaches have recently been developed to excise or disrupt the virus from the host cells (e.g., gene editing with the CRISPR-Cas system) to permanently shut off transcription of the virus (block-and-lock and RNA interference strategies), or to reactivate the virus from cell reservoirs so that it can be eliminated by the immune system or cytopathic effects (shock-and-kill strategy). Here, we will review each of these approaches, with the major focus placed on the block-and-lock strategy.
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36
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van Dorp CH, Conway JM, Barouch DH, Whitney JB, Perelson AS. Models of SIV rebound after treatment interruption that involve multiple reactivation events. PLoS Comput Biol 2020; 16:e1008241. [PMID: 33001979 PMCID: PMC7529301 DOI: 10.1371/journal.pcbi.1008241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023] Open
Abstract
In order to assess the efficacy of novel HIV-1 treatments leading to a functional cure, the time to viral rebound is frequently used as a surrogate endpoint. The longer the time to viral rebound, the more efficacious the therapy. In support of such an approach, mathematical models serve as a connection between the size of the latent reservoir and the time to HIV-1 rebound after treatment interruption. The simplest of such models assumes that a single successful latent cell reactivation event leads to observable viremia after a period of exponential viral growth. Here we consider a generalization developed by Pinkevych et al. and Hill et al. of this simple model in which multiple reactivation events can occur, each contributing to the exponential growth of the viral load. We formalize and improve the previous derivation of the dynamics predicted by this model, and use the model to estimate relevant biological parameters from SIV rebound data. We confirm a previously described effect of very early antiretroviral therapy (ART) initiation on the rate of recrudescence and the viral load growth rate after treatment interruption. We find that every day ART initiation is delayed results in a 39% increase in the recrudescence rate (95% credible interval: [18%, 62%]), and a 11% decrease of the viral growth rate (95% credible interval: [4%, 20%]). We show that when viral rebound occurs early relative to the viral load doubling time, a model with multiple successful reactivation events fits the data better than a model with only a single successful reactivation event.
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Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - James B. Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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37
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Ernst MPT, Broeders M, Herrero-Hernandez P, Oussoren E, van der Ploeg AT, Pijnappel WWMP. Ready for Repair? Gene Editing Enters the Clinic for the Treatment of Human Disease. Mol Ther Methods Clin Dev 2020; 18:532-557. [PMID: 32775490 PMCID: PMC7393410 DOI: 10.1016/j.omtm.2020.06.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present an overview of clinical trials involving gene editing using clustered interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), or zinc finger nucleases (ZFNs) and discuss the underlying mechanisms. In cancer immunotherapy, gene editing is applied ex vivo in T cells, transgenic T cell receptor (tTCR)-T cells, or chimeric antigen receptor (CAR)-T cells to improve adoptive cell therapy for multiple cancer types. This involves knockouts of immune checkpoint regulators such as PD-1, components of the endogenous TCR and histocompatibility leukocyte antigen (HLA) complex to generate universal allogeneic CAR-T cells, and CD7 to prevent self-destruction in adoptive cell therapy. In cervix carcinoma caused by human papillomavirus (HPV), E6 and E7 genes are disrupted using topically applied gene editing machinery. In HIV infection, the CCR5 co-receptor is disrupted ex vivo to generate HIV-resistant T cells, CAR-T cells, or hematopoietic stem cells. In β-thalassemia and sickle cell disease, hematopoietic stem cells are engineered ex vivo to induce the production of fetal hemoglobin. AAV-mediated in vivo gene editing is applied to exploit the liver for systemic production of therapeutic proteins in hemophilia and mucopolysaccharidoses, and in the eye to restore splicing of the CEP920 gene in Leber's congenital amaurosis. Close consideration of safety aspects and education of stakeholders will be essential for a successful implementation of gene editing technology in the clinic.
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Affiliation(s)
- Martijn P T Ernst
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Mike Broeders
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Pablo Herrero-Hernandez
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Esmee Oussoren
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Ans T van der Ploeg
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - W W M Pim Pijnappel
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
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38
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Gianella S, Chaillon A, Chun TW, Sneller MC, Ignacio C, Vargas-Meneses MV, Caballero G, Ellis RJ, Kovacs C, Benko E, Huibner S, Kaul R. HIV RNA Rebound in Seminal Plasma after Antiretroviral Treatment Interruption. J Virol 2020; 94:e00415-20. [PMID: 32434884 PMCID: PMC7375368 DOI: 10.1128/jvi.00415-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
If strategies currently in development succeed in eradicating HIV reservoirs in peripheral blood and lymphoid tissues, residual sources of virus may remain in anatomic compartments. Paired blood and semen samples were collected from 12 individuals enrolled in a randomized, double-blind, placebo-controlled therapeutic vaccine clinical trial in people with HIV (PWH) who began antiretroviral therapy (ART) during acute or early infection (ClinicalTrials registration no. NCT01859325). After the week 56 visit (postintervention), all participants interrupted ART. At the first available time points after viral rebound, we sequenced HIV-1 env (C2-V3), gag (p24), and pol (reverse transcriptase) regions amplified from cell-free HIV RNA in blood and seminal plasma using the MiSeq Illumina platform. Comprehensive sequence and phylogenetic analyses were performed to evaluate viral population structure, compartmentalization, and viral diversity in blood and seminal plasma. Compared to that in blood, HIV RNA rebound in semen occurred significantly later (median of 66 versus 42 days post-ART interruption, P < 0.01) and reached lower levels (median 164 versus 16,090 copies/ml, P < 0.01). Three of five participants with available sequencing data presented compartmentalized viral rebound between blood and semen in one HIV coding region. Despite early ART initiation, HIV RNA molecular diversity was higher in semen than in blood in all three coding regions for most participants. Higher HIV RNA molecular diversity in the genital tract (compared to that in blood plasma) and evidence of compartmentalization illustrate the distinct evolutionary dynamics between these two compartments after ART interruption. Future research should evaluate whether the genital compartment might contribute to viral rebound in some PWH interrupting ART.IMPORTANCE To cure HIV, we likely need to target the reservoirs in all anatomic compartments. Here, we used sophisticated statistical and phylogenetic methods to analyze blood and semen samples collected from 12 persons with HIV who began antiretroviral therapy (ART) during very early HIV infection and who interrupted their ART as part of a clinical trial. First, we found that HIV RNA rebound in semen occurred significantly later and reached lower levels than in blood. Second, we found that the virus in semen was genetically different in some participants compared to that in blood. Finally, we found increased HIV RNA molecular diversity in semen compared to that in blood in almost all study participants. These data suggest that the HIV RNA populations emerging from the genital compartment after ART interruption might not be the same as those emerging from blood plasma. Future research should evaluate whether the genital compartment might contribute to viral rebound in some people with HIV (PWH) interrupting ART.
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Affiliation(s)
- Sara Gianella
- University of California, San Diego, La Jolla, California, USA
| | | | - Tae-Wook Chun
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Michael C Sneller
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | | | | | - Gemma Caballero
- University of California, San Diego, La Jolla, California, USA
| | - Ronald J Ellis
- University of California, San Diego, La Jolla, California, USA
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Sanja Huibner
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rupert Kaul
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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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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40
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Extremely low viral reservoir in treated chronically HIV-1-infected individuals. EBioMedicine 2020; 57:102830. [PMID: 32580136 PMCID: PMC7317241 DOI: 10.1016/j.ebiom.2020.102830] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Small viral reservoirs are found predominantly in HIV-1 controllers and individuals treated during acute/early HIV-1 infection. However, other HIV+ individuals could naturally also harbour low viral reservoirs. METHODS We screened 451 HIV-1-infected treated-individuals with suppressed plasma viremia for at least 3 years and stored cryopreserved peripheral blood mononuclear cells (PBMCs). Total HIV-DNA was analysed in PBMCs with ddPCR. Individuals with <50 HIV-DNA copies/106 PBMCs constitute the 'Low Viral Reservoir Treated' cohort (LoViReT). Longitudinal samples were obtained from 12 chronically treated LoViReT and compared to 13 controls (>50 HIV-DNA copies/106 PBMCs) to analyse total HIV-DNA, T-cell and NK-cell populations, HIV-1 specific antibodies, and plasma inflammation markers. FINDINGS We found that 9.3% of the individuals screened had <50 HIV-DNA copies/106 PBMCs. At least 66% initiated cART during the chronic phase of HIV-1 infection (cp-LoViReT). Cp-LoViReT harboured lower levels of HIV-DNA before cART and after treatment introduction the decays were greater compared to controls. They displayed a marked decline in quantity and avidity in HIV-specific antibodies after initiation of cART. Cp-LoViReT had fewer CD8+ TTM and TEMRA in the absence of cART, and higher CD8+ TN after 18 months on therapy. INTERPRETATION Treated chronically HIV-1-infected LoViReT represent a new phenotype of individuals characterized by an intrinsically reduced viral reservoir, less impaired CD8+ T-cell compartment before cART, and low circulating HIV-1 antigens despite being treated in the chronic phase of infection. The identification of this unique group of individuals is of great interest for the design of future eradication studies. FUNDING MSD Spain.
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41
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Chen C, Lu X, Wu N. RNA sequencing of CD4 T-cells reveals the relationships between lncRNA-mRNA co-expression in elite controller vs. HIV-positive infected patients. PeerJ 2020; 8:e8911. [PMID: 32341894 PMCID: PMC7182024 DOI: 10.7717/peerj.8911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/15/2020] [Indexed: 12/27/2022] Open
Abstract
Background Elite controller refers to a patient with human immunodeficiency virus infection with an undetected viral load in the absence of highly active antiretroviral therapy. Studies on gene expression and regulation in these individuals are limited but significant, and have helped researchers and clinicians to understand the interrelationships between HIV and its host. Methods We collected CD4 T-cell samples from two elite controllers (ECs), two HIV-positive infected patients (HPs), and two healthy controls (HCs) to perform second-generation transcriptome sequencing. Using the Cufflinks software, we calculated the Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) and identified differentially expressed (DE) mRNAs and long non-coding RNAs (lncRNAs), with corrected P value < 0.05 (based on a false discovery rate (FDR) < 0.05). We then constructed a protein-protein interaction network using cytoHubba and a long non-coding RNA-mRNA co-expression network based on the Pearson correlation coefficient. Results In total, 1109 linear correlations of DE lncRNAs targeting DE mRNAs were found and several interesting interactions were identified as being associated with viral infections and immune responses within the networks based on these correlations. Among these lncRNA-mRNA relationships, hub mRNAs including HDAC6, MAPK8, MAPK9, ATM and their corresponding annotated co-expressed lncRNAs presented strong correlations with the MAPK-NF-kappa B pathway, which plays a role in the reactivation and replication of the virus. Conclusions Using RNA-sequencing, we systematically analyzed the expression profiles of lncRNAs and mRNAs from CD4+ T cells from ECs, HPs, and HCs, and constructed a co-expression network based on the relationships among DE transcripts and database annotations. This was the first study to examine gene transcription in elite controllers and to study their functional relationships. Our results provide a reference for subsequent functional verification at the molecular or cellular level.
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Affiliation(s)
- Chaoyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangyun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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42
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Wang W, Xiong L, Wang P, Wang F, Ma Q. Major vault protein plays important roles in viral infection. IUBMB Life 2020; 72:624-631. [PMID: 31769934 PMCID: PMC7165711 DOI: 10.1002/iub.2200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022]
Abstract
Viral replication and related protein expression inside the host cells, and host antiviral immune responses can lead to the occurrence of diverse diseases. With the outbreak of viral infection, a large number of newly diagnosed and died patients infected with various viruses are still reported every year. Viral infection has already been one of the major global public health issues and lead to huge economic and social burdens. Studying of viral pathogenesis is a very important way to find methods for prevention, diagnosis, and cure of viral infection; more evidence has confirmed that major vault protein (MVP) is closely associated with viral infection and pathogenesis, and this review is intended to provide a broad relationship between viruses and MVP to stimulate the interest of related researchers.
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Affiliation(s)
- Wei Wang
- Department of Clinical Laboratory, Puai Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Liang Xiong
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Pengyun Wang
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Fubing Wang
- Department of Laboratory MedicineZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Qingfeng Ma
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Arca-Suarez J, Corrales-Cuevas M, Pascual-Pérez S, Trujillo-Soto T, Fernández-Gutiérrez Del Álamo C, Cuesta-Sancho S, Rodríguez-Iglesias M, Girón-González JA. HIV antibodies level as a marker of HIV persistence: the role of hepatitis C virus coinfection. Eur J Clin Microbiol Infect Dis 2020; 39:1503-1512. [PMID: 32232689 DOI: 10.1007/s10096-020-03875-y] [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: 01/01/2020] [Accepted: 03/23/2020] [Indexed: 12/24/2022]
Abstract
Human immunodeficiency virus (HIV) antibodies have been proposed as a measure of the size of the HIV reservoir. The aim of our study is to quantify the anti-HIV antibodies level in a cohort of people living with HIV (PLWH), stratified based on the presence of continuous undetectable HIV viral load and the co-existence of hepatitis C virus infection. A sample of 229 HIV-monoinfected (n = 114) or HIV/HCV-coinfected [either with resolved HCV infection (n = 75) or active HCV coinfection (n = 40)] patients, followed up a median of 34 (IQR 20-44) months, was studied. Anti-HIV index was obtained as the 1:800 dilution of HIV antibodies. CD4+ T cell count, time with undetectable HIV viral load, annual increase of CD4+ T cell count, anti-HCV therapy, and diagnosis of cirrhosis were analyzed. Patients with a continued suppressed HIV viral load had significant lower anti-HIV index compared with those with virologic failure during the follow-up. Significant higher CD4+ T cell increase was observed in those with a lower anti-HIV index. HIV-monoinfected patients showed an anti-HIV index significantly lower than patients with HCV coinfection. Resolved HCV infection after interferon-based therapy, but not with direct acting antivirals, was associated with a lower anti-HIV index. HIV/HCV-coinfected patients showed higher HIV antibodies level when compared with HIV-monoinfected individuals. A decrease in anti-HIV index in HIV/HCV-coinfected patients was detected when a sustained virological HCV response was obtained after interferon-based therapy, in possible relation with the direct or indirect effect of interferon on PLWH CD4 T cells.
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Affiliation(s)
- Jorge Arca-Suarez
- Servicio de Microbiología, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Manuel Corrales-Cuevas
- Servicio de Medicina Interna, Unidad de Enfermedades Infecciosas, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Susana Pascual-Pérez
- Servicio de Medicina Interna, Unidad de Enfermedades Infecciosas, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Teresa Trujillo-Soto
- Servicio de Microbiología, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Clotilde Fernández-Gutiérrez Del Álamo
- Servicio de Microbiología, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Sara Cuesta-Sancho
- Servicio de Medicina Interna, Unidad de Enfermedades Infecciosas, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Manuel Rodríguez-Iglesias
- Servicio de Microbiología, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - José-Antonio Girón-González
- Servicio de Medicina Interna, Unidad de Enfermedades Infecciosas, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Instituto para la Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain.
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Abstract
PURPOSE OF REVIEW To provide a summary of the recent data examining infected CD4+ T cell dynamics during ART and implications for cure strategies. RECENT FINDINGS HIV-1 cure is a worldwide unmet medical need. Although combination antiretroviral therapies effectively suppress HIV-1 replication in vivo, viral rebound occurs shortly after therapy cessation. The major barrier to HIV-1 cure is a pool of latently infected CD4+ T cells, called the latent reservoir, which is established early during infection, has a long half-life in vivo, and is not eliminated by treatment. It was thought that the stability of the reservoir came from long-lived latently infected CD4+ T cells, but more recent data suggests that the reservoir is dynamic, such that there is an equilibrium in which proliferation of HIV-1-infected cells is offset by an equivalent loss of cells harboring HIV-1 DNA. SUMMARY We review the evidence to support this dynamic model of persistence, mechanisms by which infected cells expand and are eliminated, and discuss the impact of a dynamic reservoir on the future of HIV-1 cure studies.
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Dash PK, Kevadiya BD, Su H, Banoub MG, Gendelman HE. Pathways towards human immunodeficiency virus elimination. EBioMedicine 2020; 53:102667. [PMID: 32114397 PMCID: PMC7047153 DOI: 10.1016/j.ebiom.2020.102667] [Citation(s) in RCA: 8] [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: 11/29/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/17/2022] Open
Abstract
Antiretroviral therapy (ART) suppresses human immunodeficiency virus (HIV) infection. Research seeking to transform viral suppression into elimination has generated novel immune, chemical and molecular antiviral agents. However, none, to date, have excised latent integrated proviral DNA or removed infected cells from infected persons. These efforts included, but are not limited to, broadly neutralizing antibodies, "shock" and "kill" latency-reversing agents, innate immune regulators, and sequential long-acting antiretroviral nanoformulated prodrugs and CRISPR-Cas9 gene editing. While, the latter, enabled the complete excision of latent HIV-1 from the host genome success was so far limited. We contend that improvements in antiretroviral delivery, potency, agent specificity, or combinatorial therapies can provide a pathway towards complete HIV elimination.
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Affiliation(s)
- Prasanta K Dash
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Hang Su
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Mary G Banoub
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA.
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Dhummakupt A, Rubens JH, Anderson T, Powell L, Nonyane BA, Siems LV, Collinson-Streng A, Nilles T, Jones RB, Tepper V, Agwu A, Persaud D. Differences in inducibility of the latent HIV reservoir in perinatal and adult infection. JCI Insight 2020; 5:134105. [PMID: 31999647 DOI: 10.1172/jci.insight.134105] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
The HIV latent reservoir in resting memory CD4+ T cells precludes cure. Therapeutics to reactivate and eliminate this reservoir are in clinical trials in adults, but not yet in pediatric populations. We determined, ex vivo, the inducibility of the latent reservoir in perinatal infection as compared with adult infections using the Tat/rev induced limiting dilution assay (TILDA), in which a single round (12 hours) of CD4+ T cell stimulation with PMA/ionomycin maximally activates T cells and leads to proviral expression with multiply spliced HIV RNA production. Markers of immune activation and exhaustion were measured to assess interactions with inducibility. Although rates of T cell activation with PMA/ionomycin were similar, the latent reservoir in perinatal infection was slower to reactivate and of lower magnitude compared with adult infection, independent of proviral load. An enhanced TILDA with the addition of phytohemagglutin and a duration of 18 hours augmented proviral expression in perinatal but not adult infection. The baseline HLA-DR+CD4+ T cell level was significantly lower in perinatal compared with adult infections, but not correlated with induced reservoir size. These data support the hypothesis that there are differences in kinetics of latency reversal and baseline immune activation in perinatal compared with adult infections, with implications for latency reversal strategies toward reservoir clearance and remission.
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Affiliation(s)
- Adit Dhummakupt
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Jessica H Rubens
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Thuy Anderson
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Laura Powell
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Bareng As Nonyane
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lilly V Siems
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | | | - Tricia Nilles
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Vicki Tepper
- Department of Pediatrics, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Allison Agwu
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Deborah Persaud
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
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47
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P-TEFb as A Promising Therapeutic Target. Molecules 2020; 25:molecules25040838. [PMID: 32075058 PMCID: PMC7070488 DOI: 10.3390/molecules25040838] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) was first identified as a general factor that stimulates transcription elongation by RNA polymerase II (RNAPII), but soon afterwards it turned out to be an essential cellular co-factor of human immunodeficiency virus (HIV) transcription mediated by viral Tat proteins. Studies on the mechanisms of Tat-dependent HIV transcription have led to radical advances in our knowledge regarding the mechanism of eukaryotic transcription, including the discoveries that P-TEFb-mediated elongation control of cellular transcription is a main regulatory step of gene expression in eukaryotes, and deregulation of P-TEFb activity plays critical roles in many human diseases and conditions in addition to HIV/AIDS. P-TEFb is now recognized as an attractive and promising therapeutic target for inflammation/autoimmune diseases, cardiac hypertrophy, cancer, infectious diseases, etc. In this review article, I will summarize our knowledge about basic P-TEFb functions, the regulatory mechanism of P-TEFb-dependent transcription, P-TEFb’s involvement in biological processes and diseases, and current approaches to manipulating P-TEFb functions for the treatment of these diseases.
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48
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Kwon KJ, Timmons AE, Sengupta S, Simonetti FR, Zhang H, Hoh R, Deeks SG, Siliciano JD, Siliciano RF. Different human resting memory CD4 + T cell subsets show similar low inducibility of latent HIV-1 proviruses. Sci Transl Med 2020; 12:eaax6795. [PMID: 31996465 PMCID: PMC7875249 DOI: 10.1126/scitranslmed.aax6795] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]
Abstract
The latent reservoir of HIV-1 in resting CD4+ T cells is a major barrier to cure. It is unclear whether the latent reservoir resides principally in particular subsets of CD4+ T cells, a finding that would have implications for understanding its stability and developing curative therapies. Recent work has shown that proliferation of HIV-1-infected CD4+ T cells is a major factor in the generation and persistence of the latent reservoir and that latently infected T cells that have clonally expanded in vivo can proliferate in vitro without producing virions. In certain CD4+ memory T cell subsets, the provirus may be in a deeper state of latency, allowing the cell to proliferate without producing viral proteins, thus permitting escape from immune clearance. To evaluate this possibility, we used a multiple stimulation viral outgrowth assay to culture resting naïve, central memory (TCM), transitional memory (TTM), and effector memory (TEM) CD4+ T cells from 10 HIV-1-infected individuals on antiretroviral therapy. On average, only 1.7% of intact proviruses across all T cell subsets were induced to transcribe viral genes and release replication-competent virus after stimulation of the cells. We found no consistent enrichment of intact or inducible proviruses in any T cell subset. Furthermore, we observed notable plasticity among the canonical memory T cell subsets after activation in vitro and saw substantial person-to-person variability in the inducibility of infectious virus release. This finding complicates the vision for a targeted approach for HIV-1 cure based on T cell memory subsets.
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Affiliation(s)
- Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Timmons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hao Zhang
- Flow Cytometry and Immunology Core, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA
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49
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Impact of Antiretroviral Therapy Duration on HIV-1 Infection of T Cells within Anatomic Sites. J Virol 2020; 94:JVI.01270-19. [PMID: 31723024 PMCID: PMC7000983 DOI: 10.1128/jvi.01270-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/02/2019] [Indexed: 12/23/2022] Open
Abstract
Understanding the impact of antiretroviral therapy (ART) duration on HIV-infected cells is critical for developing successful curative strategies. To address this issue, we conducted a cross-sectional/inter-participant genetic characterization of HIV-1 RNA from pre- and on-therapy plasmas and HIV-1 DNA from CD4+ T cell subsets derived from peripheral blood (PB), lymph node (LN), and gut tissues of 26 participants after 3 to 17.8 years of ART. Our studies revealed in four acute/early participants who had paired PB and LN samples a substantial reduction in the proportion of HIV-infected cells per year on therapy within the LN. Extrapolation to all 12 acute/early participants estimated a much smaller reduction in the proportion of HIV-1-infected cells within LNs per year on therapy that was similar to that in the participants treated during chronic infection. LN-derived effector memory T (TEM) cells contained HIV-1 DNA that was genetically identical to viral sequences derived from pre- and on-therapy plasma samples. The proportion of identical HIV-1 DNA sequences increased within PB-derived TEM cells. However, the infection frequency of TEM cells in PB was stable, indicating that cellular proliferation that compensates for T cell loss over time contributes to HIV-1 persistence. This study suggests that ART reduces HIV-infected T cells and that clonal expansion of HIV-infected cells maintains viral persistence. Importantly, LN-derived TEM cells are a probable source of HIV-1 genomes capable of producing infectious HIV-1 and should be targeted by future curative strategies.IMPORTANCE HIV-1 persists as an integrated genome in CD4+ memory T cells during effective therapy, and cessation of current treatments results in resumption of viral replication. To date, the impact of antiretroviral therapy duration on HIV-infected CD4+ T cells and the mechanisms of viral persistence in different anatomic sites is not clearly elucidated. In the current study, we found that treatment duration was associated with a reduction in HIV-infected T cells. Our genetic analyses revealed that CD4+ effector memory T (TEM) cells derived from the lymph node appeared to contain provirus that was genetically identical to plasma-derived virions. Moreover, we found that cellular proliferation counterbalanced the decay of HIV-infected cells throughout therapy. The contribution of cellular proliferation to viral persistence is particularly significant in TEM cells. Our study emphasizes the importance of HIV-1 intervention and provides new insights into the location of memory T cells infected with HIV-1 DNA, which is capable of contributing to viremia.
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50
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Ko EJ, Robert-Guroff M. Dendritic Cells in HIV/SIV Prophylactic and Therapeutic Vaccination. Viruses 2019; 12:v12010024. [PMID: 31878130 PMCID: PMC7019216 DOI: 10.3390/v12010024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Dendritic cells (DCs) are involved in human and simian immunodeficiency virus (HIV and SIV) pathogenesis but also play a critical role in orchestrating innate and adaptive vaccine-specific immune responses. Effective HIV/SIV vaccines require strong antigen-specific CD4 T cell responses, cytotoxic activity of CD8 T cells, and neutralizing/non-neutralizing antibody production at mucosal and systemic sites. To develop a protective HIV/SIV vaccine, vaccine regimens including DCs themselves, protein, DNA, mRNA, virus vectors, and various combinations have been evaluated in different animal and human models. Recent studies have shown that DCs enhanced prophylactic HIV/SIV vaccine efficacy by producing pro-inflammatory cytokines, improving T cell responses, and recruiting effector cells to target tissues. DCs are also targets for therapeutic HIV/SIV vaccines due to their ability to reverse latency, present antigen, and augment T and B cell immunity. Here, we review the complex interactions of DCs over the course of HIV/SIV prophylactic and therapeutic immunizations, providing new insights into development of advanced DC-targeted HIV/SIV vaccines.
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Affiliation(s)
- Eun-Ju Ko
- College of Veterinary Medicine, Jeju National University, Jeju 63243, Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Korea
- Correspondence: (E.-J.K.); (M.R.-G.)
| | - Marjorie Robert-Guroff
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Correspondence: (E.-J.K.); (M.R.-G.)
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