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Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso M, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA. Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.27.24304867. [PMID: 38585951 PMCID: PMC10996734 DOI: 10.1101/2024.03.27.24304867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Antiretroviral therapy (ART) is not a cure. Upon ART cessation, virus rapidly rebounds from latently-infected cells ("the HIV reservoir"). The reservoir is largely stabilized at the time of ART initiation and then decays slowly. Here, leveraging >500 longitudinal samples from 67 people with HIV (PWH) treated during acute infection, we developed a novel mathematical model to predict reservoir decay using the intact proviral DNA assay (IPDA) from peripheral CD4+ T cells. Nonlinear generalized additive models adjusted for initial CD4+ T count, pre-ART viral load, and timing of ART initiation demonstrated rapid biphasic decay of intact DNA (week 0-5: t1/2 ~0.71 months; week 5-24: t1/2 ~3.9 months) that extended out to 1 year of ART, with similar trends for defective DNA. Predicted reservoir decay were faster for participants individuals with earlier timing of ART initiation, higher initial CD4+ T cell count, and lower pre-ART viral load. These estimates are ~5-fold faster than prior reservoir decay estimates among chronic-treated PWH. Thus, these data add to our limited understanding of host viral control at the earliest stages of HIV reservoir stabilization, potentially informing future HIV cure efforts aimed at diverse, global population of PWH initiating ART at varying stages of disease.
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Affiliation(s)
- Alton Barbehenn
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Lei Shi
- Department of Biostatistics, University of California Berkeley, Berkeley, CA 94110, USA
| | - Junzhe Shao
- Department of Biostatistics, University of California Berkeley, Berkeley, CA 94110, USA
| | - Rebecca Hoh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Heather M. Hartig
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Vivian Pae
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Sannidhi Sarvadhavabhatla
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Sophia Donaire
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Caroline Sheikhzadeh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Jeffrey Milush
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | | | | | | | - Michael Peluso
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Jeffrey Martin
- Department of Biostatistics & Epidemiology, University of California San Francisco, CA 94158, USA
| | - Frederick Hecht
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Christopher Pilcher
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Stephanie E. Cohen
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
- San Francisco Department of Public Health, San Francisco, CA 94102, USA
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, CA 94102, USA
| | - Diane Havlir
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Monica Gandhi
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Timothy J. Henrich
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Hiroyu Hatano
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Jingshen Wang
- Department of Biostatistics, University of California Berkeley, Berkeley, CA 94110, USA
| | - Steven G. Deeks
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Sulggi A. Lee
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA 94110, USA
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Koofhethile CK, Gao C, Chang C, Lian X, Shapiro R, Yu XG, Lichterfeld M, Kanki PJ. The HIV-2 proviral landscape is dominated by defective proviruses. AIDS 2024; 38:309-316. [PMID: 37916471 PMCID: PMC10842655 DOI: 10.1097/qad.0000000000003776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Compared with HIV-1 infection, HIV-2 infection is associated with a slower progression to AIDS. Understanding the persistence of HIV-2 infection might inform the mechanisms responsible for differences in the pathogenicity of HIV-2 versus HIV-1. METHODS In this study, we analyzed the genetic composition of the proviral reservoir in archived blood samples collected from 13 untreated HIV-2-infected adults from Senegal. We used single-genome, near-full-length individual proviral sequencing (FLIP-Seq) to assess the relative frequency of intact and defective proviruses. RESULTS Ten out of 13 (77%) study participants demonstrated virologic suppression (<90 HIV RNA copies/ml) while the remaining 3 (23%) had detectable HIV RNA. We obtained 363 proviral sequences from peripheral blood mononuclear cells (PBMCs) from the 13 study participants. Within these sequences, 342 (94%) defective proviruses were detected. Twenty-one (6%) intact proviruses were detected from three study participants, with one study participant displaying a large clone consisting of 16 genome-intact sequences. CONCLUSION This data suggests that similar to HIV-1 infection, the proviral landscape of HIV-2 is dominated by defective proviruses.
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Affiliation(s)
- Catherine K. Koofhethile
- Harvard T.H. Chan School of Public Health, Boston
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | | | | | | | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
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Oliveira MF, Pankow A, Vollbrecht T, Kumar NM, Cabalero G, Ignacio C, Zhao M, Vitomirov A, Gouaux B, Nakawawa M, Murrell B, Ellis RJ, Gianella S. Evaluation of Archival HIV DNA in Brain and Lymphoid Tissues. J Virol 2023; 97:e0054323. [PMID: 37184401 PMCID: PMC10308944 DOI: 10.1128/jvi.00543-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
HIV reservoirs persist in anatomic compartments despite antiretroviral therapy (ART). Characterizing archival HIV DNA in the central nervous system (CNS) and other tissues is crucial to inform cure strategies. We evaluated paired autopsy brain-frontal cortex (FC), occipital cortex (OCC), and basal ganglia (BG)-and peripheral lymphoid tissues from 63 people with HIV. Participants passed away while virally suppressed on ART at the last visit and without evidence of CNS opportunistic disease. We quantified total HIV DNA in all participants and obtained full-length HIV-envelope (FL HIV-env) sequences from a subset of 14 participants. We detected HIV DNA (gag) in most brain (65.1%) and all lymphoid tissues. Lymphoid tissues had higher HIV DNA levels than the brain (P < 0.01). Levels of HIV gag between BG and FC were similar (P > 0.2), while OCC had the lowest levels (P = 0.01). Females had higher HIV DNA levels in tissues than males (gag, P = 0.03; 2-LTR, P = 0.05), suggesting possible sex-associated mechanisms for HIV reservoir persistence. Most FL HIV-env sequences (n = 143) were intact, while 42 were defective. Clonal sequences were found in 8 out of 14 participants, and 1 participant had clonal defective sequences in the brain and spleen, suggestive of cell migration. From 10 donors with paired brain and lymphoid sequences, we observed evidence of compartmentalized sequences in 2 donors. Our data further the idea that the brain is a site for archival HIV DNA during ART where compartmentalized provirus may occur in a subset of people. Future studies assessing FL HIV-provirus and replication competence are needed to further evaluate the HIV reservoirs in tissues. IMPORTANCE HIV infection of the brain is associated with adverse neuropsychiatric outcomes, despite efficient antiretroviral treatment. HIV may persist in reservoirs in the brain and other tissues, which can seed virus replication if treatment is interrupted, representing a major challenge to cure HIV. We evaluated reservoirs and genetic features in postmortem brain and lymphoid tissues from people with HIV who passed away during suppressed HIV replication. We found a differential distribution of HIV reservoirs across brain regions which was lower than that in lymphoid tissues. We observed that most HIV reservoirs in tissues had intact envelope sequences, suggesting they could potentially generate replicative viruses. We found that women had higher HIV reservoir levels in brain and lymphoid tissues than men, suggesting possible sex-based mechanisms of maintenance of HIV reservoirs in tissues, warranting further investigation. Characterizing the archival HIV DNA in tissues is important to inform future HIV cure strategies.
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Affiliation(s)
- Michelli F. Oliveira
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Vollbrecht
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Veterans Affairs San Diego Healthcare System, San Diego, California, USA
| | - Nikesh M. Kumar
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gemma Cabalero
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Caroline Ignacio
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Mitchell Zhao
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Andrej Vitomirov
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Ben Gouaux
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Masato Nakawawa
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Ben Murrell
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Ronald J. Ellis
- Department of Neurosciences and Psychiatry, University of California San Diego, La Jolla, California, USA
| | - Sara Gianella
- Department of Medicine, University of California San Diego, La Jolla, California, 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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5
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Geretti AM, Blanco JL, Marcelin AG, Perno CF, Stellbrink HJ, Turner D, Zengin T. HIV DNA Sequencing to Detect Archived Antiretroviral Drug Resistance. Infect Dis Ther 2022; 11:1793-1803. [PMID: 35915392 DOI: 10.1007/s40121-022-00676-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Proviral HIV DNA integrated within CD4 T-cells maintains an archive of viral variants that replicate during the course of the infection, including variants with reduced drug susceptibility. We considered studies that investigated archived drug resistance, with a focus on virologically suppressed patients and highlighted interpretative caveats and gaps in knowledge. RESULTS Either Sanger or deep sequencing can be used to investigate resistance-associated mutations (RAMs) in HIV DNA recovered from peripheral blood. Neither technique is free of limitations. Furthermore, evidence regarding the establishment, maintenance, expression and clinical significance of archived drug-resistant variants is conflicting. This in part reflects the complexity of the HIV proviral landscape and its dynamics during therapy. Clinically, detection of RAMs in cellular HIV DNA has a variable impact on treatment outcomes, modulated by the drugs affected, treatment duration and additional determinants of virological failure, including those leading to suboptimal drug exposure. CONCLUSIONS Sequencing cellular HIV DNA can provide helpful complementary information in treatment-experienced patients with suppressed plasma HIV RNA who require a change of regimen. However, care should be taken when interpreting the results. Presence of RAMs is not necessarily a barrier to treatment success. Conversely, even the most sensitive sequencing techniques will fail to provide a comprehensive view of the HIV DNA archive. To inform treatment decisions appropriately, the overall clinical and treatment history of a patient must always be considered alongside the results of resistance testing. Prospective controlled studies are needed to validate the utility of drug resistance testing using cellular HIV DNA.
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Affiliation(s)
- Anna Maria Geretti
- Department of Infectious Diseases, Fondazione PTV and University of Rome Tor Vergata, Viale Oxford 81, 00133, Rome, Italy. .,School of Immunology & Microbial Sciences, King's College London, London, UK.
| | - Jose Luis Blanco
- Infectious Diseases Department, Hospital Clinic of Barcelona, Barcelona, Spain.,Infectious Diseases & AIDS Unit Hospital Clinic Barcelona, University of Barcelona, Barcelona, Spain
| | - Anne Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Virologie, 75013, Paris, France
| | - Carlo Federico Perno
- Multimodal Medicine Research Area, Children Hospital IRCCS Bambino Gesù, Rome, Italy
| | | | - Dan Turner
- Crusaid Kobler AIDS Center, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tuba Zengin
- Global Medical Affairs HIV, Gilead Sciences, London, UK
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Heterogeneity of Latency Establishment in the Different Human CD4
+
T Cell Subsets Stimulated with IL-15. J Virol 2022; 96:e0037922. [PMID: 35499323 PMCID: PMC9131862 DOI: 10.1128/jvi.00379-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
HIV integrates into the host genome, creating a viral reservoir of latently infected cells that persists despite effective antiretroviral treatment. CD4-positive (CD4+) T cells are the main contributors to the HIV reservoir. CD4+ T cells are a heterogeneous population, and the mechanisms of latency establishment in the different subsets, as well as their contribution to the reservoir, are still unclear. In this study, we analyzed HIV latency establishment in different CD4+ T cell subsets stimulated with interleukin 15 (IL-15), a cytokine that increases both susceptibility to infection and reactivation from latency. Using a dual-reporter virus that allows discrimination between latent and productive infection at the single-cell level, we found that IL-15-treated primary human CD4+ T naive and CD4+ T stem cell memory (TSCM) cells are less susceptible to HIV infection than CD4+ central memory (TCM), effector memory (TEM), and transitional memory (TTM) cells but are also more likely to harbor transcriptionally silent provirus. The propensity of these subsets to harbor latent provirus compared to the more differentiated memory subsets was independent of differential expression of pTEFb components. Microscopy analysis of NF-κB suggested that CD4+ T naive cells express smaller amounts of nuclear NF-κB than the other subsets, partially explaining the inefficient long terminal repeat (LTR)-driven transcription. On the other hand, CD4+ TSCM cells display similar levels of nuclear NF-κB to CD4+ TCM, CD4+ TEM, and CD4+ TTM cells, indicating the availability of transcription initiation and elongation factors is not solely responsible for the inefficient HIV gene expression in the CD4+ TSCM subset. IMPORTANCE The formation of a latent reservoir is the main barrier to HIV cure. Here, we investigated how HIV latency is established in different CD4+ T cell subsets in the presence of IL-15, a cytokine that has been shown to efficiently induce latency reversal. We observed that, even in the presence of IL-15, the less differentiated subsets display lower levels of productive HIV infection than the more differentiated subsets. These differences were not related to different expression of pTEFb, and modest differences in NF-κB were observed for CD4+ T naive cells only, implying the involvement of other mechanisms. Understanding the molecular basis of latency establishment in different CD4+ T cell subsets might be important for tailoring specific strategies to reactivate HIV transcription in all the CD4+ T subsets that compose the latent reservoir.
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Immune Responses and Viral Persistence in Simian/Human Immunodeficiency Virus SHIV.C.CH848-Infected Rhesus Macaques. J Virol 2021; 95:JVI.02198-20. [PMID: 33568508 PMCID: PMC8104099 DOI: 10.1128/jvi.02198-20] [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] [Received: 11/18/2020] [Accepted: 02/01/2021] [Indexed: 01/16/2023] Open
Abstract
SHIVs have been extensively used in a nonhuman primate (NHP) model for HIV research. In this study, we investigated viral reservoirs in tissues and immune responses in an NHP model inoculated with newly generated transmitted/founder HIV-1 clade C-based SHIV.C.CH848. Chimeric simian/human immunodeficiency viruses (SHIVs) are widely used in nonhuman primate models to recapitulate human immunodeficiency virus (HIV) infection in humans, yet most SHIVs fail to establish persistent viral infection. We investigated immunological and virological events in rhesus macaques infected with the newly developed SHIV.C.CH848 (SHIVC) and treated with combined antiretroviral therapy (cART). Similar to HIV/simian immunodeficiency virus (SIV) infection, SHIV.C.CH848 infection established viral reservoirs in CD4+ T cells and myeloid cells, accompanied by productive infection and depletion of CD4+ T cells in systemic and lymphoid tissues throughout SHIV infection. Despite 6 months of cART-suppressed viral replication, integrated proviral DNA levels remained stable, especially in CD4+ T cells, and the viral rebound was also observed after ART interruption. Autologous neutralizing antibodies to the parental HIV-1 strain CH848 were detected, with limited viral evolution at 5 months postinfection. In comparison, heterogenous neutralizing antibodies in SHIV.C.CH848-infected macaques were not detected except for 1 (1 of 10) animal at 2 years postinfection. These findings suggest that SHIV.C.CH848, a novel class of transmitted/founder SHIVs, can establish sustained viremia and viral reservoirs in rhesus macaques with clinical immunodeficiency consequences, providing a valuable SHIV model for HIV research. IMPORTANCE SHIVs have been extensively used in a nonhuman primate (NHP) model for HIV research. In this study, we investigated viral reservoirs in tissues and immune responses in an NHP model inoculated with newly generated transmitted/founder HIV-1 clade C-based SHIV.C.CH848. The data show that transmitted founder (T/F) SHIVC infection of macaques more closely recapitulates the virological and clinical features of HIV infection, including persistent viremia and viral rebound once antiretroviral therapy is discontinued. These results suggest this CCR5-tropic, SHIVC strain is valuable for testing responses to HIV vaccines and therapeutics.
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8
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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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Increased Proviral DNA in Circulating Cells Correlates with Plasma Viral Rebound in Simian Immunodeficiency Virus-Infected Rhesus Macaques after Antiretroviral Therapy Interruption. J Virol 2021; 95:JVI.02064-20. [PMID: 33408173 PMCID: PMC8094949 DOI: 10.1128/jvi.02064-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/18/2020] [Indexed: 12/30/2022] Open
Abstract
Viral reservoirs are involved in persistent HIV infection, and a small number of mosaic latent cellular reservoirs promote viral rebound upon analytical treatment interruption, which is the major obstacle to a cure. However, early indicators that can predict resurgence of viremia after treatment interruption may aid treatment decisions in people living with HIV. The human immunodeficiency virus (HIV) reservoir is responsible for persistent viral infection, and a small number of mosaic latent cellular reservoirs promote viral rebound upon antiretroviral therapy interruption, which is the major obstacle to a cure. However, markers that determine effective therapy and viral rebound posttreatment interruption remain unclear. In this study, we comprehensively and longitudinally tracked dynamic decay of cell-associated viral RNA/DNA in systemic and lymphoid tissues in simian immunodeficiency virus (SIV)-infected rhesus macaques on prolonged combined antiretroviral therapy (cART) and evaluated predictors of viral rebound after treatment cessation. The results showed that suppressive ART substantially reduced plasma SIV RNA, cell-associated unspliced, and multiply spliced SIV RNA to undetectable levels, yet viral DNA remained detectable in systemic tissues and lymphoid compartments throughout cART. Intriguingly, a rapid increase of integrated proviral DNA in peripheral mononuclear cells was detected once treatment was withdrawn, accompanied by the emergence of detectable plasma viral load. Notably, the increase of peripheral proviral DNA after treatment interruption correlated with the emergence and degree of viral rebound. These findings suggest that measuring total viral DNA in SIV infection may be a relatively simple surrogate marker of reservoir size and may predict viral rebound after treatment interruption and inform treatment strategies. IMPORTANCE Viral reservoirs are involved in persistent HIV infection, and a small number of mosaic latent cellular reservoirs promote viral rebound upon analytical treatment interruption, which is the major obstacle to a cure. However, early indicators that can predict resurgence of viremia after treatment interruption may aid treatment decisions in people living with HIV. Utilizing the rhesus macaque model, we demonstrated that increased proviral DNA in peripheral cells after treatment interruption, rather than levels of proviral DNA, was a useful marker to predict the emergence and degree of viral rebound after treatment interruption, providing a rapid approach for monitoring HIV rebound and informing decisions.
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10
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Wang X, Xu H. Residual Proviral Reservoirs: A High Risk for HIV Persistence and Driving Forces for Viral Rebound after Analytical Treatment Interruption. Viruses 2021; 13:335. [PMID: 33670027 PMCID: PMC7926539 DOI: 10.3390/v13020335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Antiretroviral therapy (ART) has dramatically suppressed human immunodeficiency virus (HIV) replication and become undetectable viremia. However, a small number of residual replication-competent HIV proviruses can still persist in a latent state even with lifelong ART, fueling viral rebound in HIV-infected patient subjects after treatment interruption. Therefore, the proviral reservoirs distributed in tissues in the body represent a major obstacle to a cure for HIV infection. Given unavailable HIV vaccine and a failure to eradicate HIV proviral reservoirs by current treatment, it is crucial to develop new therapeutic strategies to eliminate proviral reservoirs for ART-free HIV remission (functional cure), including a sterilizing cure (eradication of HIV reservoirs). This review highlights recent advances in the establishment and persistence of HIV proviral reservoirs, their detection, and potential eradication strategies.
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Affiliation(s)
| | - Huanbin Xu
- Tulane National Primate Research Center, Division of Comparative Pathology, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA 70433, USA;
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11
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Ajibola G, Garcia-Broncano P, Maswabi K, Bennett K, Hughes MD, Moyo S, Mohammed T, Jean-Philippe P, Sakoi M, Batlang O, Lockman S, Makhema J, Kuritzkes DR, Lichterfeld M, Shapiro RL. Viral Reservoir in Early-Treated HIV-Infected Children and Markers for Sustained Viral Suppression. Clin Infect Dis 2021; 73:e997-e1003. [PMID: 33605999 PMCID: PMC8366827 DOI: 10.1093/cid/ciab143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The impact of very early infant treatment on HIV reservoir, and markers for treatment success, require study. METHODS The Early Infant Treatment Study (EIT) enrolled 40 children living with HIV started on antiretroviral treatment (ART) at <7 days of age and 23 who had started treatment between 30-365 days to serve as controls. Quantitative HIV DNA was evaluated every 1-3 months in PBMCs. 84-week repeat qualitative whole blood DNA PCR and dual enzyme EIA were performed. RESULTS Median quantitative cell-associated DNA after at least 84 weeks was significantly lower among the first 27 EIT children tested than among 10 controls (40.8 vs. 981.4 copies/million cells; p<0.001) and correlated with pre-ART DNA. Median DNA after 84 weeks did not differ significantly by negative or positive serostatus at 84 weeks (p=0.94), and appeared unaffected by periods of unsuppressed plasma RNA from 24-84 weeks (p=0.70). However, negative 84-week serostatus was 67% predictive for sustained RNA suppression and positive serostatus was 100% predictive for viremia. Loss of qualitative DNA positivity at 84 weeks was 73% predictive for sustained suppression and persistent positivity was 77% predictive for viremia. CONCLUSIONS Lower viral reservoir was associated with starting ART at <1 week. Negative serostatus and qualitative DNA were useful markers of sustained viral suppression from 24-84 weeks.
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Affiliation(s)
| | | | - Kenneth Maswabi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Kara Bennett
- Bennett Statistical Consulting Inc, Ballston Lake, NY, USA
| | - Michael D Hughes
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Patrick Jean-Philippe
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Maureen Sakoi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Oganne Batlang
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias Lichterfeld
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 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, Massachusetts, USA
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12
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Cornu TI, Mussolino C, Müller MC, Wehr C, Kern WV, Cathomen T. HIV Gene Therapy: An Update. Hum Gene Ther 2021; 32:52-65. [PMID: 33349126 DOI: 10.1089/hum.2020.159] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Progress in antiretroviral therapy has considerably reduced mortality and notably improved the quality of life of individuals infected with HIV since the pandemic began some 40 years ago. However, drug resistance, treatment-associated toxicity, adherence to medication, and the need for lifelong therapy have remained major challenges. While the development of an HIV vaccine has remained elusive, considerable progress in developing innovative cell and gene therapies to treat HIV infection has been made. This includes immune cell therapies, such as chimeric antigen receptor T cells to target HIV infected cells, as well as gene therapies and genome editing strategies to render the patient's immune system resistant to HIV. Nonetheless, all of these attempts to achieve a functional cure in HIV patients have failed thus far. This review introduces the clinical as well as the technical challenges of treating HIV infection, and summarizes the most promising cell and gene therapy concepts that have aspired to bring about functional cure for people living with HIV. It further discusses socioeconomic aspects as well as future directions for developing cell and gene therapies with a potential to be an effective one-time treatment with minimal toxicity.
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Affiliation(s)
- Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias C Müller
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Infectious Diseases, Department of Medicine II, Medical Center-University of Freiburg, Freiburg, Germany.,Department of Infection Medicine, Medical Care Center, MVZ Clotten, Freiburg, Germany
| | - Claudia Wehr
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center-University of Freiburg, Freiburg, Germany
| | - Winfried V Kern
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Infectious Diseases, Department of Medicine II, Medical Center-University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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13
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Abstract
Currently, the incidence of HIV infection exceeds the death rate from HIV, and as a result, the prevalence of individuals living with the infection continues to increase. A critical limitation preventing the development of curative strategies is the lack of knowledge regarding mechanisms that allow HIV-infected cells to persist in individuals during combination antiviral therapy (ART). In this issue of the JCI, Chaillon and coworkers assessed HIV-infected cells from various anatomic compartments obtained through a rapid autopsy program of individuals undergoing long-term ART. This study, made possible with strong community collaboration, provides new insights on the potential locations of reservoirs of HIV-infected cells that persist during therapy.
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14
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Singh R. Single-Cell Sequencing in Human Genital Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:203-220. [PMID: 32949402 DOI: 10.1007/978-981-15-4494-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Human genital infections are one of the most concerning issues worldwide and can be categorized into sexually transmitted, urinary tract and vaginal infections. These infections, if left untreated, can disseminate to the other parts of the body and cause more complicated illnesses such as pelvic inflammatory disease, urethritis, and anogenital cancers. The effective treatment against these infections is further complicated by the emergence of antimicrobial resistance in the genital infection causing pathogens. Furthermore, the development and applications of single-cell sequencing technologies have open new possibilities to study the drug resistant clones, cell to cell variations, the discovery of acquired drug resistance mutations, transcriptional diversity of a pathogen across different infection stages, to identify rare cell types and investigate different cellular states of genital infection causing pathogens, and to develop novel therapeutical strategies. In this chapter, I will provide a complete review of the applications of single-cell sequencing in human genital infections before discussing their limitations and challenges.
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Affiliation(s)
- Reema Singh
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada. .,Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK, Canada.
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15
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Abstract
Human immunodeficiency virus 1 (HIV-1) replicates through the integration of its viral DNA into the genome of human immune target cells. Chronically infected individuals thus carry a genomic burden of virus-derived sequences that persists through antiretroviral therapy. This burden consists of a small fraction of intact, but transcriptionally silenced, i.e. latent, viral genomes and a dominant fraction of defective sequences. Remarkably, all viral-derived sequences are subject to interaction with host cellular physiology at various levels. In this review, we focus on epigenetic aspects of this interaction. We provide a comprehensive overview of how epigenetic mechanisms contribute to establishment and maintenance of HIV-1 gene repression during latency. We furthermore summarize findings indicating that HIV-1 infection leads to changes in the epigenome of target and bystander immune cells. Finally, we discuss how an improved understanding of epigenetic features and mechanisms involved in HIV-1 infection could be exploited for clinical use.
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16
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T cells with high PD-1 expression are associated with lower HIV-specific immune responses despite long-term antiretroviral therapy. AIDS 2020; 34:15-24. [PMID: 31634201 DOI: 10.1097/qad.0000000000002406] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVE We evaluated frequencies of T cells with high PD-1 expression (PD-1) before and after long-term effective antiretroviral therapy (ART), and determined if frequencies on-ART correlated positively with measures of HIV persistence and negatively with HIV-specific responses. METHODS We enrolled individuals who started ART during chronic infection and had durable suppression of viremia for at least 4 years (N = 99). We assessed PD-1 T-cell frequencies at timepoints pre-ART and on-ART using flow cytometry, and evaluated how frequencies on-ART are associated with measures of HIV persistence, HIV-specific immune responses, and immune activation levels. RESULTS Pre-ART, PD-1 CD4 T cells correlated positively with viremia and negatively with CD4 T-cell count. At year 1 on-ART, %PD-1 CD4 T cells decreased but then remained stable at 4 and 6-15 years on-ART, whereas %PD-1 CD8 T cells on-ART remained similar to pre-ART. PD-1 CD4 T cells correlated positively with HIV DNA pre-ART and on-ART, and with CD4 T-cell activation on-ART. PD-1 CD4 T cells negatively correlated with HIV Gag-specific and Env-specific T-cell responses but not with CMV-specific or EBV-specific responses. PD-1 CD8 T cells trended towards a negative correlation with responses to Gag and Env, but not to CMV and EBV. CONCLUSION PD-1 T cells persist in blood despite prolonged suppression on ART, correlate with HIV DNA levels, and are associated with lower HIV-specific T-cell responses but not CMV-specific or EBV-specific responses, suggesting that these cells are HIV-specific. The findings support evaluating PD-1 blockade strategies for their effect on HIV persistence and HIV-specific immunity.
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17
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Bozzi G, Simonetti FR, Watters SA, Anderson EM, Gouzoulis M, Kearney MF, Rote P, Lange C, Shao W, Gorelick R, Fullmer B, Kumar S, Wank S, Hewitt S, Kleiner DE, Hattori J, Bale MJ, Hill S, Bell J, Rehm C, Grossman Z, Yarchoan R, Uldrick T, Maldarelli F. No evidence of ongoing HIV replication or compartmentalization in tissues during combination antiretroviral therapy: Implications for HIV eradication. SCIENCE ADVANCES 2019; 5:eaav2045. [PMID: 31579817 PMCID: PMC6760922 DOI: 10.1126/sciadv.aav2045] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/29/2019] [Indexed: 05/28/2023]
Abstract
HIV persistence during combination antiretroviral therapy (cART) is the principal obstacle to cure. Mechanisms responsible for persistence remain uncertain; infections may be maintained by persistence and clonal expansion of infected cells or by ongoing replication in anatomic locations with poor antiretroviral penetration. These mechanisms require different strategies for eradication, and determining their contributions to HIV persistence is essential. We used phylogenetic approaches to investigate, at the DNA level, HIV populations in blood, lymphoid, and other infected tissues obtained at colonoscopy or autopsy in individuals who were on cART for 8 to 16 years. We found no evidence of ongoing replication or compartmentalization of HIV; we did detect clonal expansion of infected cells that were present before cART. Long-term persistence, and not ongoing replication, is primarily responsible for maintaining HIV. HIV-infected cells present when cART is initiated represent the only identifiable source of persistence and is the appropriate focus for eradication.
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Affiliation(s)
- G. Bozzi
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
- Department of Biomedical and Clinical Sciences, L. Sacco Hospital, University of Milan, Milan, Italy
| | - F. R. Simonetti
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
- Department of Biomedical and Clinical Sciences, L. Sacco Hospital, University of Milan, Milan, Italy
| | - S. A. Watters
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
- Department of Infection and Immunity, University College London, London, UK
| | - E. M. Anderson
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - M. Gouzoulis
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - M. F. Kearney
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - P. Rote
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - C. Lange
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - W. Shao
- Advanced Biomedical Computing Center, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - R. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - B. Fullmer
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - S. Kumar
- Digestive Diseases Branch, NIDDK, NIH, Bethesda, MD, USA
| | - S. Wank
- Digestive Diseases Branch, NIDDK, NIH, Bethesda, MD, USA
| | - S. Hewitt
- Laboratory of Pathology, NCI, NIH, Bethesda, MD, USA
| | - D. E. Kleiner
- Laboratory of Pathology, NCI, NIH, Bethesda, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - J. Hattori
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - M. J. Bale
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - S. Hill
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - J. Bell
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - C. Rehm
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Z. Grossman
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
| | - R. Yarchoan
- HIV and AIDS Malignancy Branch, NCI, NIH, Bethesda, MD, USA
| | - T. Uldrick
- HIV and AIDS Malignancy Branch, NCI, NIH, Bethesda, MD, USA
| | - F. Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, USA
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18
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Colomb F, Giron LB, Trbojevic-Akmacic I, Lauc G, Abdel-Mohsen M. Breaking the Glyco-Code of HIV Persistence and Immunopathogenesis. Curr HIV/AIDS Rep 2019; 16:151-168. [PMID: 30707400 PMCID: PMC6441623 DOI: 10.1007/s11904-019-00433-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Glycoimmunology is an emerging field focused on understanding how immune responses are mediated by glycans (carbohydrates) and their interaction with glycan-binding proteins called lectins. How glycans influence immunological functions is increasingly well understood. In a parallel way, in the HIV field, it is increasingly understood how the host immune system controls HIV persistence and immunopathogenesis. However, what has mostly been overlooked, despite its potential for therapeutic applications, is the role that the host glycosylation machinery plays in modulating the persistence and immunopathogenesis of HIV. Here, we will survey four areas in which the links between glycan-lectin interactions and immunology and between immunology and HIV are well described. For each area, we will describe these links and then delineate the opportunities for the HIV field in investigating potential interactions between glycoimmunology and HIV persistence/immunopathogenesis. RECENT FINDINGS Recent studies show that the human glycome (the repertoire of human glycan structures) plays critical roles in driving or modulating several cellular processes and immunological functions that are central to maintaining HIV infection. Understanding the links between glycoimmunology and HIV infection may create a new paradigm for discovering novel glycan-based therapies that can lead to eradication, functional cure, or improved tolerance of lifelong infection.
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Affiliation(s)
- Florent Colomb
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, USA
| | - Leila B Giron
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, USA
| | | | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovacica 1, Zagreb, Croatia
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19
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Cellular HIV Reservoirs and Viral Rebound from the Lymphoid Compartments of 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (EFdA)-Suppressed Humanized Mice. Viruses 2019; 11:v11030256. [PMID: 30871222 PMCID: PMC6466357 DOI: 10.3390/v11030256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 12/28/2022] Open
Abstract
Although antiretroviral therapy (ART) greatly suppresses HIV replication, lymphoid tissues remain a sanctuary site where the virus may replicate. Tracking the earliest steps of HIV spread from these cellular reservoirs after drug cessation is pivotal for elucidating how infection can be prevented. In this study, we developed an in vivo model of HIV persistence in which viral replication in the lymphoid compartments of humanized mice was inhibited by the HIV reverse transcriptase inhibitor 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) to very low levels, which recapitulated ART-suppression in HIV-infected individuals. Using a combination of RNAscope in situ hybridization (ISH) and immunohistochemistry (IHC), we quantitatively investigated the distribution of HIV in the lymphoid tissues of humanized mice during active infection, EFdA suppression, and after drug cessation. The lymphoid compartments of EFdA-suppressed humanized mice harbored very rare transcription/translation-competent HIV reservoirs that enable viral rebound. Our data provided the visualization and direct measurement of the early steps of HIV reservoir expansion within anatomically intact lymphoid tissues soon after EFdA cessation and suggest a strategy to enhance therapeutic approaches aimed at eliminating the HIV reservoir.
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20
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Okoye AA, Hansen SG, Vaidya M, Fukazawa Y, Park H, Duell DM, Lum R, Hughes CM, Ventura AB, Ainslie E, Ford JC, Morrow D, Gilbride RM, Legasse AW, Hesselgesser J, Geleziunas R, Li Y, Oswald K, Shoemaker R, Fast R, Bosche WJ, Borate BR, Edlefsen PT, Axthelm MK, Picker LJ, Lifson JD. Early antiretroviral therapy limits SIV reservoir establishment to delay or prevent post-treatment viral rebound. Nat Med 2018; 24:1430-1440. [PMID: 30082858 PMCID: PMC6389357 DOI: 10.1038/s41591-018-0130-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Prophylactic vaccination of rhesus macaques with rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) elicits immune responses that stringently control highly pathogenic SIV infection, with subsequent apparent clearance of the infection, in ~50% of vaccinees. In contrast, here, we show that therapeutic RhCMV/SIV vaccination of rhesus macaques previously infected with SIV and given continuous combination antiretroviral therapy (cART) beginning 4-9 d post-SIV infection does not mediate measurable SIV reservoir clearance during over 600 d of follow-up on cART relative to RhCMV/control vaccination. However, none of the six animals started on cART on day four or five, across both RhCMV/SIV- and RhCMV/control-vaccinated groups, those rhesus macaques with SIV reservoirs most closely resembling those of prophylactically RhCMV/SIV-vaccinated and protected animals early in their course, showed post-cART viral rebound with up to nine months of follow-up. Moreover, at necropsy, these rhesus macaques showed little to no evidence of replication-competent SIV. These results suggest that the early SIV reservoir is limited in durability and that effective blockade of viral replication and spread in this critical time window by either pharmacologic or immunologic suppression may result in reduction, and potentially loss, of rebound-competent virus over a period of ~two years.
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Affiliation(s)
- Afam A Okoye
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Mukta Vaidya
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Yoshinori Fukazawa
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Haesun Park
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Derick M Duell
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Richard Lum
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Emily Ainslie
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Julia C Ford
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - David Morrow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Alfred W Legasse
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | | | | | - Yuan Li
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Randy Fast
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William J Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bhavesh R Borate
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul T Edlefsen
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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21
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Abstract
PURPOSE OF REVIEW To provide an overview of recent research of how HIV integration relates to productive and latent infection and implications for cure strategies. RECENT FINDINGS How and where HIV integrates provides new insights into how HIV persists on antiretroviral therapy (ART). Clonal expansion of infected cells with the same integration site demonstrates that T-cell proliferation is an important factor in HIV persistence, however, the driver of proliferation remains unclear. Clones with identical integration sites harbouring defective provirus can accumulate in HIV-infected individuals on ART and defective proviruses can express RNA and produce protein. HIV integration sites differ in clonally expanded and nonexpanded cells and in latently and productively infected cells and this influences basal and inducible transcription. There is a growing number of cellular proteins that can alter the pattern of integration to favour latency. Understanding these pathways may identify new interventions to eliminate latently infected cells. SUMMARY Using advances in analysing HIV integration sites, T-cell proliferation of latently infected cells is thought to play a major role in HIV persistence. Clonal expansion has been demonstrated with both defective and intact viruses. Production of viral RNA and protein from defective viruses may play a role in driving chronic immune activation. The site of integration may determine the likelihood of proliferation and the degree of basal and induced transcription. Finally, host factors and gene expression at the time of infection may determine the integration site. Together these new insights may lead to novel approaches to elimination of latently infected cells.
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Affiliation(s)
- Jori Symons
- The Peter Doherty nstitute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria
| | - Paul U Cameron
- The Peter Doherty nstitute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Sharon R Lewin
- The Peter Doherty nstitute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
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