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Fombellida-Lopez C, Berkhout B, Darcis G, Pasternak AO. Persistent HIV-1 transcription during ART: time to reassess its significance? Curr Opin HIV AIDS 2024; 19:124-132. [PMID: 38502547 PMCID: PMC10990031 DOI: 10.1097/coh.0000000000000849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), HIV-1 reservoirs persist and reignite viral replication if therapy is interrupted. Persistence of the viral reservoir in people with HIV-1 (PWH) is the main obstacle to an HIV-1 cure. The reservoirs are not transcriptionally silent, and viral transcripts can be detected in most ART-treated individuals. Here, we review the recent progress in the characterization of persistent HIV-1 transcription during ART. RECENT FINDINGS Evidence from several studies indicates that, although cell-associated unspliced (US) HIV-1 RNA is abundantly expressed in ART-treated PWH, intact full-length US transcripts are rare and most US RNA is derived from defective proviruses. The transcription- and translation-competent defective proviruses, previously considered irrelevant, are increasingly being linked to residual HIV-1 pathogenesis under suppressive ART. Recent data suggest a continuous crosstalk between the residual HIV-1 activity under ART and the immune system. Persistent HIV-1 transcription on ART, despite being mostly derived from defective proviruses, predicts viral rebound upon therapy interruption, suggesting its role as an indicator of the strength of the host antiviral immune response that is shaping the viral rebound. SUMMARY In light of the recent findings, the significance of persistent HIV-1 transcription during ART for the long-term health of PWH and the cure research should be reassessed.
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Affiliation(s)
- Céline Fombellida-Lopez
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gilles Darcis
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
- Department of General Internal Medicine and Infectious Diseases, University Hospital of Liège, Liège, Belgium
| | - Alexander O. Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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2
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Emert-Sedlak LA, Tice CM, Shi H, Alvarado JJ, Shu ST, Reitz AB, Smithgall TE. PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication. Cell Chem Biol 2024; 31:658-668.e14. [PMID: 38508197 PMCID: PMC11031313 DOI: 10.1016/j.chembiol.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
The HIV-1 Nef accessory factor enhances the viral life cycle in vivo, promotes immune escape of HIV-infected cells, and represents an attractive antiretroviral drug target. However, Nef lacks enzymatic activity and an active site, complicating traditional occupancy-based drug development. Here we describe the development of proteolysis targeting chimeras (PROTACs) for the targeted degradation of Nef. Nef-binding compounds, based on an existing hydroxypyrazole core, were coupled to ligands for ubiquitin E3 ligases via flexible linkers. The resulting bivalent PROTACs induced formation of a ternary complex between Nef and the cereblon E3 ubiquitin ligase thalidomide-binding domain in vitro and triggered Nef degradation in a T cell expression system. Nef-directed PROTACs efficiently rescued Nef-mediated MHC-I and CD4 downregulation in T cells and suppressed HIV-1 replication in donor PBMCs. Targeted degradation is anticipated to reverse all HIV-1 Nef functions and may help restore adaptive immune responses against HIV-1 reservoir cells in vivo.
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Affiliation(s)
- Lori A Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Colin M Tice
- Fox Chase Therapeutics Discovery, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Allen B Reitz
- Fox Chase Therapeutics Discovery, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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Kufera JT, Armstrong C, Wu F, Singhal A, Zhang H, Lai J, Wilkins HN, Simonetti FR, Siliciano JD, Siliciano RF. CD4+ T cells with latent HIV-1 have reduced proliferative responses to T cell receptor stimulation. J Exp Med 2024; 221:e20231511. [PMID: 38270554 PMCID: PMC10818065 DOI: 10.1084/jem.20231511] [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: 08/24/2023] [Revised: 11/04/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy as a barrier to cure. The antigen-driven proliferation of infected cells is a major mechanism of reservoir persistence. However, activation through the T cell antigen receptor (TCR) can induce latent proviruses, leading to viral cytopathic effects and immune clearance. In single-cell studies, we show that, relative to uninfected cells or cells with a defective provirus, CD4+ T cells with an intact provirus have a profound proliferative defect in response to TCR stimulation. Virion production was observed in only 16.5% of cultures with an intact provirus, but proliferation was reduced even when no virion production was detected. Proliferation was inversely correlated with in vivo clone size. These results may reflect the effects of previous in vivo proliferation and do not support attempts to reduce the reservoir with antiproliferative agents, which may have greater effects on normal T cell responses.
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Affiliation(s)
- Joshua T. Kufera
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ciara Armstrong
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anushka Singhal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah N. Wilkins
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 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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Tassaneetrithep B, Phuphuakrat A, Pasomsub E, Bhukhai K, Wongkummool W, Priengprom T, Khamaikawin W, Chaisavaneeyakorn S, Anurathapan U, Apiwattanakul N, Hongeng S. HIV-1 proviral DNA in purified peripheral blood CD34 + stem and progenitor cells in individuals with long-term HAART; paving the way to HIV gene therapy. Heliyon 2024; 10:e26613. [PMID: 38434025 PMCID: PMC10906414 DOI: 10.1016/j.heliyon.2024.e26613] [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: 08/04/2023] [Revised: 02/03/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
Human immunodeficiency virus (HIV)-1 infection is an important public health problem worldwide. After primary HIV-1 infection, transcribed HIV-1 DNA is integrated into the host genome, serving as a reservoir of the virus and hindering a definite cure. Although highly active antiretroviral therapy suppresses active viral replication, resulting in undetectable levels of HIV RNA in the blood, a viral rebound can be detected after a few weeks of treatment interruption. This supports the concept that there is a stable HIV-1 reservoir in people living with HIV-1. Recently, a few individuals with HIV infection were reported to be probably cured by hematopoietic stem transplantation (HSCT). The underlying mechanism for this success involved transfusion of uninfected hematopoietic stem and progenitor cells (HSPCs) from CCR5-mutated donors who were naturally resistant to HIV infection. Thus, gene editing technology to provide HIV-resistant HSPC has promise in the treatment of HIV infections by HSCT. In this study, we aimed to find HIV-infected individuals likely to achieve a definite cure via gene editing HSCT. We screened for total HIV proviral DNA by Alu PCR in peripheral blood mononuclear cells (PBMCs) of 20 HIV-infected individuals with prolonged viral suppression. We assessed the amount of intact proviral DNA via a modified intact proviral DNA assay (IPDA) in purified peripheral CD34+ HSPCs. PBMCs from all 20 individuals were positive for the gag gene in Alu PCR, and peripheral CD34+ HSPCs were IPDA-negative for six individuals. Our results suggested that these six HIV-infected individuals could be candidates for further studies into the ability of gene editing HSCT to lead to a definite HIV cure.
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Affiliation(s)
- Boonrat Tassaneetrithep
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Kanit Bhukhai
- Department of Physiology, Faculty of Science, Mahidol University, Thailand
| | | | - Thongkoon Priengprom
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Wannisa Khamaikawin
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Thailand
| | | | - Usanarat Anurathapan
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Nopporn Apiwattanakul
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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Buchholtz NVEJ, Nühn MM, de Jong TCM, Stienstra TAT, Reddy K, Ndung'u T, Ndhlovu ZM, Fisher K, Palmer S, Wensing AMJ, Symons J, Nijhuis M. Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C. Virol J 2024; 21:36. [PMID: 38297379 PMCID: PMC10832250 DOI: 10.1186/s12985-024-02300-6] [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: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
INTRODUCTION HIV reservoir quantification is essential for evaluation of HIV curative strategies and may provide valuable insights about reservoir dynamics during antiretroviral therapy. The Intact Proviral DNA Assay (IPDA) provides the unique opportunity to quantify the intact and defective reservoir. The current IPDA is optimized for HIV-1 subtype B, the dominant subtype in resource-rich settings. However, subtype C is dominant in Sub-Saharan Africa, jointly accounting for around 60% of the pandemic. We developed an assay capable of quantifying intact and defective proviral HIV-1 DNA of subtype B and C. METHODS Primer and probe sequences were strategically positioned at conserved regions in psi and env and adapted to subtype B&C. In silico analysis of 752 subtype B and 697 subtype C near-full length genome sequences (nFGS) was performed to predict the specificity and sensitivity. Gblocks were used to determine the limit of blank (LoB), limit of detection (LoD), and different annealing temperatures were tested to address impact of sequence variability. RESULTS The in silico analysis showed that the HIV-1 B&C IPDA correctly identified 100% of the intact subtype B, and 86% of the subtype C sequences. In contrast, the original IPDA identified 86% and 12% of these subtype B and C sequences as intact. Furthermore, the HIV-1 B&C IPDA correctly identified hypermutated (87% and 88%) and other defective sequences (73% and 66%) for subtype B and C with comparable specificity as the original IPDA for subtype B (59% and 63%). Subtype B cis-acting sequences were more frequently identified as intact by the HIV-1 B&C IPDA compared to the original IPDA (39% and 2%). The LoB for intact proviral DNA copies was 0, and the LoD for intact proviral DNA copies was 6 (> 95% certainty) at 60 °C. Quantification of 2-6 copies can be performed with > 80% certainty. Lowering the annealing temperature to 55 °C slightly lowered the specificity but prevented exclusion of samples with single mutations in the primer/probe region. CONCLUSIONS We developed a robust and sensitive assay for the quantification of intact and defective HIV-1 subtype B and C proviral DNA, making this a suitable tool to monitor the impact of (large-scale) curative interventions.
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Affiliation(s)
- N V E J Buchholtz
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M M Nühn
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T C M de Jong
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T A T Stienstra
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - K Reddy
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - T 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
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA, 01238, USA
- Division of Infection and Immunity, University College London, London, UK
| | - Z M Ndhlovu
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - K Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - S Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - A M J Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
- ha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J Symons
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands.
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
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Cannon L, Fehrman S, Pinzone M, Weissman S, O'Doherty U. Machine Learning Bolsters Evidence That D1, Nef, and Tat Influence HIV Reservoir Dynamics. Pathog Immun 2024; 8:37-58. [PMID: 38292079 PMCID: PMC10827039 DOI: 10.20411/pai.v8i2.621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024] Open
Abstract
Background The primary hurdle to curing HIV is due to the establishment of a reservoir early in infection. In an effort to find new treatment strategies, we and others have focused on understanding the selection pressures exerted on the reservoir by studying how proviral sequences change over time. Methods To gain insights into the dynamics of the HIV reservoir we analyzed longitudinal near full-length sequences from 7 people living with HIV between 1 and 20 years following the initiation of antiretroviral treatment. We used this data to employ Bayesian mixed effects models to characterize the decay of the reservoir using single-phase and multiphasic decay models based on near full-length sequencing. In addition, we developed a machine-learning approach utilizing logistic regression to identify elements within the HIV genome most associated with proviral decay and persistence. By systematically analyzing proviruses that are deleted for a specific element, we gain insights into their role in reservoir contraction and expansion. Results Our analyses indicate that biphasic decay models of intact reservoir dynamics were better than single-phase models with a stronger statistical fit. Based on the biphasic decay pattern of the intact reservoir, we estimated the half-lives of the first and second phases of decay to be 18.2 (17.3 to 19.2, 95%CI) and 433 (227 to 6400, 95%CI) months, respectively.In contrast, the dynamics of defective proviruses differed favoring neither model definitively, with an estimated half-life of 87.3 (78.1 to 98.8, 95% CI) months during the first phase of the biphasic model. Machine-learning analysis of HIV genomes at the nucleotide level revealed that the presence of the splice donor site D1 was the principal genomic element associated with contraction. This role of D1 was then validated in an in vitro system. Using the same approach, we additionally found supporting evidence that HIV nef may confer a protective advantage for latently infected T cells while tat was associated with clonal expansion. Conclusions The nature of intact reservoir decay suggests that the long-lived HIV reservoir contains at least 2 distinct compartments. The first compartment decays faster than the second compartment. Our machine-learning analysis of HIV proviral sequences reveals specific genomic elements are associated with contraction while others are associated with persistence and expansion. Together, these opposing forces shape the reservoir over time.
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Affiliation(s)
- LaMont Cannon
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia
| | - Sophia Fehrman
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia
| | - Marilia Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sam Weissman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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8
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Peterson JJ, Lewis CA, Burgos SD, Manickam A, Xu Y, Rowley AA, Clutton G, Richardson B, Zou F, Simon JM, Margolis DM, Goonetilleke N, Browne EP. A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV-infected cells. Cell Chem Biol 2023; 30:1617-1633.e9. [PMID: 38134881 PMCID: PMC10754471 DOI: 10.1016/j.chembiol.2023.11.009] [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: 05/16/2022] [Revised: 08/23/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
A long-lived latent reservoir of HIV-1-infected CD4 T cells persists with antiretroviral therapy and prevents cure. We report that the emergence of latently infected primary CD4 T cells requires the activity of histone deacetylase enzymes HDAC1/2 and HDAC3. Data from targeted HDAC molecules, an HDAC3-directed PROTAC, and CRISPR-Cas9 knockout experiments converge on a model where either HDAC1/2 or HDAC3 targeting can prevent latency, whereas all three enzymes must be targeted to achieve latency reversal. Furthermore, HDACi treatment targets features of memory T cells that are linked to proviral latency and persistence. Latency prevention is associated with increased H3K9ac at the proviral LTR promoter region and decreased H3K9me3, suggesting that this epigenetic switch is a key proviral silencing mechanism that depends on HDAC activity. These findings support further mechanistic work on latency initiation and eventual clinical studies of HDAC inhibitors to interfere with latency initiation.
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Affiliation(s)
- Jackson J Peterson
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Catherine A Lewis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Samuel D Burgos
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Ashokkumar Manickam
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Yinyan Xu
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Allison A Rowley
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Genevieve Clutton
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Brian Richardson
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Fei Zou
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Jeremy M Simon
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC 27514, USA; UNC Neuroscience Center, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA; Department of Medicine, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Edward P Browne
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA.
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Cossarini F, Aberg JA, Chen BK, Mehandru S. Viral Persistence in the Gut-Associated Lymphoid Tissue and Barriers to HIV Cure. AIDS Res Hum Retroviruses 2023; 40:54-65. [PMID: 37450338 PMCID: PMC10790554 DOI: 10.1089/aid.2022.0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
More than 40 years after the first reported cases of what then became known as acquired immunodeficiency syndrome (AIDS), tremendous progress has been achieved in transforming the disease from almost universally fatal to a chronic manageable condition. Nonetheless, the efforts to find a preventative vaccine or a cure for the underlying infection with Human Immunodeficiency Virus (HIV) remain largely unsuccessful. Many challenges intrinsic to the virus characteristics and host response need to be overcome for either goal to be achieved. This article will review the obstacles to an effective HIV cure, specifically the steps involved in the generation of HIV latency, focusing on the role of the gut-associated lymphoid tissue, which has received less attention compared with the peripheral blood, despite being the largest repository of lymphoid tissue in the human body, and a large site for HIV persistence.
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Affiliation(s)
- Francesca Cossarini
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
| | - Judith A. Aberg
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
- Division of Gastroenterology, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
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10
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Więcek K, Chen HC. Understanding latent HIV-1 reservoirs through host genomics approaches. iScience 2023; 26:108342. [PMID: 38026212 PMCID: PMC10665824 DOI: 10.1016/j.isci.2023.108342] [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] [Indexed: 12/01/2023] Open
Abstract
Genetically intact HIV-1 proviruses are a major concern with regard to curing infection because they cause viral rebound after the cessation of antiretroviral therapy. However, intact proviruses are not prevalent in HIV-1 reservoirs. As such, it is essential to precisely determine the position of these proviruses before putting forward a better antiretroviral cure. Recently, a revised HIV-1 deeply latent reservoir concept has been proposed, stating that the progress of the establishment of HIV-1 reservoirs is influenced by immune-mediated selection during the course of infection. This selection force leads to the persistence of genetically intact proviruses as those with the best fit to avoid clearance. This hypothesis refreshes our understanding of HIV-1 latent reservoirs. For this reason, we reviewed current studies relevant to this theme and provide our perspectives to reinforce the overall understanding of HIV-1 latency in the context of the host genome.
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Affiliation(s)
- Kamil Więcek
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
| | - Heng-Chang Chen
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. mBio 2023; 14:e0241723. [PMID: 37971267 PMCID: PMC10746175 DOI: 10.1128/mbio.02417-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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12
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Pasternak AO, Tsukamoto T, Berkhout B. 'Zombie' proviruses in the spotlight: exploring the dark side of HIV persistence. AIDS 2023; 37:2239-2241. [PMID: 37877277 DOI: 10.1097/qad.0000000000003721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tetsuo Tsukamoto
- Department of Health Informatics, Niigata University of Health and Welfare, Niigata, Japan
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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13
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Singh K, Natarajan V, Dewar R, Rupert A, Badralmaa Y, Zhai T, Winchester N, Scrimieri F, Smith M, Davis I, Lallemand P, Giglietti A, Hensien J, Buerkert T, Goshu B, Rehm CA, Hu Z, Lane HC, Imamichi H. Long-term persistence of transcriptionally active 'defective' HIV-1 proviruses: implications for persistent immune activation during antiretroviral therapy. AIDS 2023; 37:2119-2130. [PMID: 37555786 PMCID: PMC10615727 DOI: 10.1097/qad.0000000000003667] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/10/2023]
Abstract
OBJECTIVES People with HIV-1 (PWH) on effective antiretroviral therapy (ART) continue to exhibit chronic systemic inflammation, immune activation, and persistent elevations in markers of HIV-1 infection [including HIV-DNA, cell-associated HIV-RNA (CA HIV-RNA), and antibodies to HIV-1 proteins] despite prolonged suppression of plasma HIV-RNA levels less than 50 copies/ml. Here, we investigated the hypothesis that nonreplicating but transcriptionally and translationally competent 'defective' HIV-1 proviruses may be one of drivers of these phenomena. DESIGN A combined cohort of 23 viremic and virologically suppressed individuals on ART were studied. METHODS HIV-DNA, CA HIV-RNA, western blot score (measure of anti-HIV-1 antibodies as a surrogate for viral protein expression in vivo ), and key biomarkers of inflammation and coagulation (IL-6, hsCRP, TNF-alpha, tissue factor, and D-dimer) were measured in peripheral blood and analyzed using a combined cross-sectional and longitudinal approaches. Sequences of HIV-DNA and CA HIV-RNA obtained via 5'-LTR-to-3'-LTR PCR and single-genome sequencing were also analyzed. RESULTS We observed similar long-term persistence of multiple, unique, transcriptionally active 'defective' HIV-1 provirus clones (average: 11 years., range: 4-20 years) and antibody responses against HIV-1 viral proteins among all ART-treated participants evaluated. A direct correlation was observed between the magnitude of HIV-1 western blot score and the levels of transcription of 'defective' HIV-1 proviruses ( r = 0.73, P < 0.01). Additional correlations were noted between total CD8 + T-cell counts and HIV-DNA ( r = 0.52, P = 0.01) or CA HIV-RNA ( r = 0.65, P < 0.01). CONCLUSION These findings suggest a novel interplay between transcription and translation of 'defective' HIV-1 proviruses and the persistent immune activation seen in the setting of treated chronic HIV-1 infection.
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Affiliation(s)
- Kanal Singh
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Ven Natarajan
- Frederick National Laboratory for Cancer Research, Frederick
| | - Robin Dewar
- Frederick National Laboratory for Cancer Research, Frederick
| | - Adam Rupert
- Frederick National Laboratory for Cancer Research, Frederick
| | - Yuden Badralmaa
- Frederick National Laboratory for Cancer Research, Frederick
| | - Tracey Zhai
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Nicole Winchester
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | | | - Mindy Smith
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Ivery Davis
- Frederick National Laboratory for Cancer Research, Frederick
| | | | - Aude Giglietti
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Jack Hensien
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Thomas Buerkert
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Bruktawit Goshu
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Catherine A. Rehm
- Clinical Research Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH
| | - Zonghui Hu
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - H. Clifford Lane
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Hiromi Imamichi
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
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14
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Lamers SL, Fogel GB, Liu ES, Nolan DJ, Rose R, McGrath MS. HIV-1 subtypes maintain distinctive physicochemical signatures in Nef domains associated with immunoregulation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105514. [PMID: 37832752 PMCID: PMC10842591 DOI: 10.1016/j.meegid.2023.105514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND HIV subtype is associated with varied rates of disease progression. The HIV accessory protein, Nef, continues to be present during antiretroviral therapy (ART) where it has numerous immunoregulatory effects. In this study, we analyzed Nef sequences from HIV subtypes A1, B, C, and D using a machine learning approach that integrates functional amino acid information to identify if unique physicochemical features are associated with Nef functional/structural domains in a subtype-specific manner. METHODS 2253 sequences representing subtypes A1, B, C, and D were aligned and domains with known functional properties were scored based on amino acid physicochemical properties. Following feature generation, we used statistical pruning and evolved neural networks (ENNs) to determine if we could successfully classify subtypes. Next, we used ENNs to identify the top five key Nef physicochemical features applied to specific immunoregulatory domains that differentiated subtypes. A signature pattern analysis was performed to the assess amino acid diversity in sub-domains that differentiated each subtype. RESULTS In validation studies, ENNs successfully differentiated each subtype at A1 (87.2%), subtype B (89.5%), subtype C (91.7%), and subtype D (85.1%). Our feature-based domain scoring, followed by t-tests, and a similar ENN identified subtype-specific domain-associated features. Subtype A1 was associated with alterations in Nef CD4 binding domain; subtype B was associated with alterations with the AP-2 Binding domain; subtype C was associated with alterations in a structural Alpha Helix domain; and, subtype D was associated with alterations in a Beta-Sheet domain. CONCLUSIONS Recent studies have focused on HIV Nef as a driver of immunoregulatory disease in those HIV infected and on ART. Nef acts through a complex mixture of interactions that are directly linked to the key features of the subtype-specific domains we identified with the ENN. The study supports the hypothesis that varied Nef subtypes contribute to subtype-specific disease progression.
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Affiliation(s)
| | | | - Enoch S Liu
- Natural Selection, San Diego, California, USA
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15
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Astorga-Gamaza A, Perea D, Sanchez-Gaona N, Calvet-Mirabent M, Gallego-Cortés A, Grau-Expósito J, Sanchez-Cerrillo I, Rey J, Castellví J, Curran A, Burgos J, Navarro J, Suanzes P, Falcó V, Genescà M, Martín-Gayo E, Buzon MJ. KLRG1 expression on natural killer cells is associated with HIV persistence, and its targeting promotes the reduction of the viral reservoir. Cell Rep Med 2023; 4:101202. [PMID: 37741278 PMCID: PMC10591043 DOI: 10.1016/j.xcrm.2023.101202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/25/2023] [Accepted: 08/29/2023] [Indexed: 09/25/2023]
Abstract
Human immunodeficiency virus (HIV) infection induces immunological dysfunction, which limits the elimination of HIV-infected cells during treated infection. Identifying and targeting dysfunctional immune cells might help accelerate the purging of the persistent viral reservoir. Here, we show that chronic HIV infection increases natural killer (NK) cell populations expressing the negative immune regulator KLRG1, both in peripheral blood and lymph nodes. Antiretroviral treatment (ART) does not reestablish these functionally impaired NK populations, and the expression of KLRG1 correlates with active HIV transcription. Targeting KLRG1 with specific antibodies significantly restores the capacity of NK cells to kill HIV-infected cells, reactivates latent HIV present in CD4+ T cells co-expressing KLRG1, and reduces the intact HIV genomes in samples from ART-treated individuals. Our data support the potential use of immunotherapy against the KLRG1 receptor to impact the viral reservoir during HIV persistence.
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Affiliation(s)
- Antonio Astorga-Gamaza
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - David Perea
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Nerea Sanchez-Gaona
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Marta Calvet-Mirabent
- Universidad Autónoma de Madrid, 28049 Madrid, Spain; Immunology Unit from Hospital Universitario de La Princesa and Instituto de Investigación Sanitaria Princesa, 28006 Madrid, Spain
| | - Ana Gallego-Cortés
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Judith Grau-Expósito
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Ildefonso Sanchez-Cerrillo
- Universidad Autónoma de Madrid, 28049 Madrid, Spain; Immunology Unit from Hospital Universitario de La Princesa and Instituto de Investigación Sanitaria Princesa, 28006 Madrid, Spain
| | - Joan Rey
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Josep Castellví
- Department of Pathology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Adrian Curran
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Joaquin Burgos
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Jordi Navarro
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Paula Suanzes
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Vicenç Falcó
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Meritxell Genescà
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Enrique Martín-Gayo
- Universidad Autónoma de Madrid, 28049 Madrid, Spain; Immunology Unit from Hospital Universitario de La Princesa and Instituto de Investigación Sanitaria Princesa, 28006 Madrid, Spain; Infectious Diseases CIBER (CIBERINFECC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Maria J Buzon
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
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16
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Yucha R, Litchford ML, Fish CS, Yaffe ZA, Richardson BA, Maleche-Obimbo E, John-Stewart G, Wamalwa D, Overbaugh J, Lehman DA. Higher HIV-1 Env gp120-Specific Antibody-Dependent Cellular Cytotoxicity (ADCC) Activity Is Associated with Lower Levels of Defective HIV-1 Provirus. Viruses 2023; 15:2055. [PMID: 37896832 PMCID: PMC10611199 DOI: 10.3390/v15102055] [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: 09/11/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
A cure for HIV-1 (HIV) remains unrealized due to a reservoir of latently infected cells that persist during antiretroviral therapy (ART), with reservoir size associated with adverse health outcomes and inversely with time to viral rebound upon ART cessation. Once established during ART, the HIV reservoir decays minimally over time; thus, understanding factors that impact the size of the HIV reservoir near its establishment is key to improving the health of people living with HIV and for the development of novel cure strategies. Yet, to date, few correlates of HIV reservoir size have been identified, particularly in pediatric populations. Here, we employed a cross-subtype intact proviral DNA assay (CS-IPDA) to quantify HIV provirus between one- and two-years post-ART initiation in a cohort of Kenyan children (n = 72), which had a median of 99 intact (range: 0-2469), 1340 defective (range: 172-3.84 × 104), and 1729 total (range: 178-5.11 × 104) HIV proviral copies per one million T cells. Additionally, pre-ART plasma was tested for HIV Env-specific antibody-dependent cellular cytotoxicity (ADCC) activity. We found that pre-ART gp120-specific ADCC activity inversely correlated with defective provirus levels (n = 68, r = -0.285, p = 0.0214) but not the intact reservoir (n = 68, r = -0.0321, p-value = 0.800). Pre-ART gp41-specific ADCC did not significantly correlate with either proviral population (n = 68; intact: r = -0.0512, p-value = 0.686; defective: r = -0.109, p-value = 0.389). This suggests specific host immune factors prior to ART initiation can impact proviruses that persist during ART.
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Affiliation(s)
- Ryan Yucha
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Morgan L. Litchford
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn S. Fish
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zak A. Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Dalton Wamalwa
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi P.O. Box 30197, Kenya
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Dara A. Lehman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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17
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Landovitz RJ, Scott H, Deeks SG. Prevention, treatment and cure of HIV infection. Nat Rev Microbiol 2023; 21:657-670. [PMID: 37344551 DOI: 10.1038/s41579-023-00914-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
The development of antiretroviral therapy for the prevention and treatment of HIV infection has been marked by a series of remarkable successes. However, the efforts to develop a vaccine have largely failed, and efforts to discover a cure are only now beginning to gain traction. In this Review, we describe recent progress on all fronts - pre-exposure prophylaxis, vaccines, treatment and cure - and we discuss the unmet needs, both current and in the coming years. We describe the emerging arsenal of drugs, biologics and strategies that will hopefully address these needs. Although HIV research has largely been siloed in the past, this is changing, as the emerging research agenda is marked by multiple cross-discipline synergies and collaborations. As the limitations of antiretroviral drugs as a means to truly end the epidemic are becoming more apparent, there is a great need for continued efforts to develop an effective preventative vaccine and a scalable cure, both of which remain formidable challenges.
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Affiliation(s)
- Raphael J Landovitz
- Center for Clinical AIDS Research and Education, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hyman Scott
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
- Division of HIV, Infectious Diseases & Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases & Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
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18
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Emert-Sedlak LA, Tice CM, Shi H, Alvarado JJ, Shu ST, Reitz AB, Smithgall TE. PROTAC-mediated Degradation of HIV-1 Nef Efficiently Restores Cell-surface CD4 and MHC-I Expression and Blocks HIV-1 Replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553289. [PMID: 37645900 PMCID: PMC10462000 DOI: 10.1101/2023.08.14.553289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The HIV-1 Nef accessory factor is critical to the viral life cycle in vivo where it promotes immune escape of HIV-infected cells and viral persistence. While these features identify Nef as an attractive antiretroviral drug target, Nef lacks enzymatic activity and an active site, complicating development of occupancy-based drugs. Here we describe the development of proteolysis targeting chimeras (PROTACs) for the targeted degradation of Nef. Nef-binding compounds, based on a previously reported hydroxypyrazole core, were coupled to ligands for ubiquitin E3 ligases via flexible linkers. The resulting bivalent PROTACs induced formation of a ternary complex between Nef and the Cereblon E3 ubiquitin ligase, resulting in ubiquitylation of Nef and proteolytic degradation. Nef-directed PROTACs efficiently rescued Nef-mediated MHC-I and CD4 downregulation in T cells and suppressed HIV-1 replication in donor PBMCs. Targeted degradation of Nef is anticipated to reverse all HIV-1 Nef functions and may help restore adaptive immune responses against HIV-1 reservoir cells in vivo .
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19
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Kuzmichev YV, Lackman-Smith C, Bakkour S, Wiegand A, Bale MJ, Musick A, Bernstein W, Aronson N, Ake J, Tovanabutra S, Stone M, Ptak RG, Kearney MF, Busch MP, Wonderlich ER, Kulpa DA. Application of ultrasensitive digital ELISA for p24 enables improved evaluation of HIV-1 reservoir diversity and growth kinetics in viral outgrowth assays. Sci Rep 2023; 13:10958. [PMID: 37414788 PMCID: PMC10326067 DOI: 10.1038/s41598-023-37223-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
The advent of combined antiretroviral therapy (cART) has been instrumental in controlling HIV-1 replication and transmission and decreasing associated morbidity and mortality. However, cART alone is not able to cure HIV-1 due to the presence of long-lived, latently infected immune cells, which re-seed plasma viremia when cART is interrupted. Assessment of HIV-cure strategies using ex vivo culture methods for further understanding of the diversity of reactivated HIV, viral outgrowth, and replication dynamics are enhanced using ultrasensitive digital ELISA based on single-molecule array (Simoa) technology to increase the sensitivity of endpoint detection. In viral outgrowth assays (VOA), exponential HIV-1 outgrowth has been shown to be dependent upon initial virus burst size surpassing a critical growth threshold of 5100 HIV-1 RNA copies. Here, we show an association between ultrasensitive HIV-1 Gag p24 concentrations and HIV-1 RNA copy number that characterize viral dynamics below the exponential replication threshold. Single-genome sequencing (SGS) revealed the presence of multiple identical HIV-1 sequences, indicative of low-level replication occurring below the threshold of exponential outgrowth early during a VOA. However, SGS further revealed diverse related HIV variants detectable by ultrasensitive methods that failed to establish exponential outgrowth. Overall, our data suggest that viral outgrowth occurring below the threshold necessary for establishing exponential growth in culture does not preclude replication competence of reactivated HIV, and ultrasensitive detection of HIV-1 p24 may provide a method to detect previously unquantifiable variants. These data strongly support the use of the Simoa platform in a multi-prong approach to measuring latent viral burden and efficacy of therapeutic interventions aimed at an HIV-1 cure.
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Affiliation(s)
- Yury V Kuzmichev
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA.
| | - Carol Lackman-Smith
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ann Wiegand
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew Musick
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Wendy Bernstein
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Naomi Aronson
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Julie Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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20
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Faua C, Fafi-Kremer S, Gantner P. Antigen specificities of HIV-infected cells: A role in infection and persistence? J Virus Erad 2023; 9:100329. [PMID: 37440870 PMCID: PMC10334354 DOI: 10.1016/j.jve.2023.100329] [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: 12/16/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Antigen-experienced memory CD4+ T cells are the major target of HIV infection and support both productive and latent infections, thus playing a key role in HIV dissemination and persistence, respectively. Here, we reviewed studies that have shown direct association between HIV infection and antigen specificity. During untreated infection, some HIV-specific cells host productive infection, while other pathogen-specific cells such as cytomegalovirus (CMV) and Mycobacterium tuberculosis also contribute to viral persistence on antiretroviral therapy (ART). These patterns could be explained by phenotypic features differing between these pathogen-specific cells. Mechanisms involved in these preferential infection and selection processes include HIV entry and restriction, cell exhaustion, survival, self-renewal and immune escape. For instance, MIP-1β expressing cells such as CMV-specific memory cells were shown to resist infection by HIV CCR5 coreceptor downregulation/inhibition. Conversely, HIV-infected CMV-specific cells undergo clonal expansion during ART. We have identified several research areas that need further focus such as the role of other pathogens, viral genome intactness, inducibility and phenotypic features. However, given the sheer diversity of both the CD4+ T cell repertoire and antigenic history of each individual, studying HIV-infected, antigen-experienced cells still imposes numerous challenges.
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Affiliation(s)
- Clayton Faua
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
| | - Samira Fafi-Kremer
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
- Medical Virology Laboratory, University Hospital of Strasbourg, Strasbourg, France
| | - Pierre Gantner
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
- Medical Virology Laboratory, University Hospital of Strasbourg, Strasbourg, France
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21
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Neary J, Fish CS, Cassidy NAJ, Wamalwa D, Langat A, Ngugi E, Benki-Nugent S, Moraa H, Richardson BA, Njuguna I, Slyker JA, Lehman DA, John-Stewart G. Predictors of intact HIV DNA levels among children in Kenya. AIDS 2023; 37:871-876. [PMID: 36723512 PMCID: PMC10079608 DOI: 10.1097/qad.0000000000003499] [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: 02/02/2023]
Abstract
OBJECTIVE We determined predictors of both intact (estimate of replication-competent) and total (intact and defective) HIV DNA in the reservoir among children with HIV. DESIGN HIV DNA in the reservoir was quantified longitudinally in children who initiated antiretroviral therapy (ART) at less than 1 year of age using a novel cross-subtype intact proviral DNA assay that measures both intact and total proviruses. Quantitative PCR was used to measure pre-ART cytomegalovirus (CMV) viral load. Linear mixed effects models were used to determine predictors of intact and total HIV DNA levels (log 10 copies/million). RESULTS Among 65 children, median age at ART initiation was 5 months and median follow-up was 5.2 years; 86% of children had CMV viremia pre-ART. Lower pre-ART CD4 + percentage [adjusted relative risk (aRR): 0.87, 95% confidence intervals (95% CI): 0.79-0.97; P = 0.009] and higher HIV RNA (aRR: 1.21, 95% CI: 1.06-1.39; P = 0.004) predicted higher levels of total HIV DNA during ART. Pre-ART CD4 + percentage (aRR: 0.76, 95% CI: 0.65-0.89; P < 0.001), CMV viral load (aRR: 1.16, 95% CI: 1.01-1.34; P = 0.041), and first-line protease inhibitor-based regimens compared with nonnucleoside reverse transcriptase-based regimens (aRR: 1.36, 95% CI: 1.04-1.77; P = 0.025) predicted higher levels of intact HIV DNA. CONCLUSION Pre-ART immunosuppression, first-line ART regimen, and CMV viral load may influence establishment and sustainment of intact HIV DNA in the reservoir.
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Affiliation(s)
- Jillian Neary
- Department of Epidemiology, University of Washington
| | | | | | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Agnes Langat
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Evelyn Ngugi
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | | | - Hellen Moraa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Barbra A Richardson
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Global Health
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Irene Njuguna
- Department of Global Health
- Kenyatta National Hospital, Nairobi, Kenya
| | - Jennifer A Slyker
- Department of Epidemiology, University of Washington
- Department of Global Health
| | - Dara A Lehman
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Global Health
| | - Grace John-Stewart
- Department of Epidemiology, University of Washington
- Department of Global Health
- Department of Medicine
- Department of Pediatrics, University of Washington, Seattle, WA, USA
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22
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536611. [PMID: 37090500 PMCID: PMC10120704 DOI: 10.1101/2023.04.12.536611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
| | | | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Experimental Medicine Program, University of British Columbia, Vancouver, BC
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby BC
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
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23
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Pasternak AO, Berkhout B. HIV persistence: silence or resistance? Curr Opin Virol 2023; 59:101301. [PMID: 36805974 DOI: 10.1016/j.coviro.2023.101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 02/19/2023]
Abstract
Despite decades of suppressive antiretroviral therapy, human immunodeficiency virus (HIV) reservoirs in infected individuals persist and fuel viral rebound once therapy is interrupted. The persistence of viral reservoirs is the main obstacle to achieving HIV eradication or a long-term remission. The last decade has seen a profound change in our understanding of the mechanisms behind HIV persistence, which appears to be much more complex than originally assumed. In addition to the persistence of transcriptionally silent proviruses in a stable latent reservoir that is invisible to the immune system, HIV is increasingly recognized to persist by resistance to the immune clearance, which appears to play a surprisingly prominent role in shaping the reservoir. In this review, we discuss some emerging insights into the mechanisms of HIV persistence, as well as their implications for the development of strategies towards an HIV cure.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
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24
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Duette G, Cronin S, Kelleher AD, Palmer S. Viral competition assay to assess the role of HIV-1 proteins in immune evasion. STAR Protoc 2023; 4:102025. [PMID: 36853860 PMCID: PMC9860156 DOI: 10.1016/j.xpro.2022.102025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/29/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
CD8+ T lymphocytes can recognize and eliminate cells infected by viruses. However, the human immunodeficiency virus (HIV-1) has developed mechanisms to evade CD8+ T-cell-mediated clearance. Here, we describe a protocol to assess the role of the HIV-1 protein Nef in immune evasion. The viral competition assay reveals the preferential killing of HIV-1-infected cells unable to express Nef. This methodology can be extended to study HIV-1 proteins involved in immune evasion and viral variants encoding cytotoxic T lymphocyte escape mutations. For complete details on the use and execution of this protocol, please refer to Duette et al. (2022).1.
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Affiliation(s)
- Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia.
| | - Samantha Cronin
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia.
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25
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White JA, Wu F, Yasin S, Moskovljevic M, Varriale J, Dragoni F, Camilo-Contreras A, Duan J, Zheng MY, Tadzong NF, Patel HB, Quiambao JMC, Rhodehouse K, Zhang H, Lai J, Beg SA, Delannoy M, Kilcrease C, Hoffmann CJ, Poulin S, Chano F, Tremblay C, Cherian J, Barditch-Crovo P, Chida N, Moore RD, Summers MF, Siliciano RF, Siliciano JD, Simonetti FR. Clonally expanded HIV-1 proviruses with 5'-leader defects can give rise to nonsuppressible residual viremia. J Clin Invest 2023; 133:165245. [PMID: 36602866 PMCID: PMC10014112 DOI: 10.1172/jci165245] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
BackgroundAntiretroviral therapy (ART) halts HIV-1 replication, decreasing viremia to below the detection limit of clinical assays. However, some individuals experience persistent nonsuppressible viremia (NSV) originating from CD4+ T cell clones carrying infectious proviruses. Defective proviruses represent over 90% of all proviruses persisting during ART and can express viral genes, but whether they can cause NSV and complicate ART management is unknown.MethodsWe undertook an in-depth characterization of proviruses causing NSV in 4 study participants with optimal adherence and no drug resistance. We investigated the impact of the observed defects on 5'-leader RNA properties, virus infectivity, and gene expression. Integration-site specific assays were used to track these proviruses over time and among cell subsets.ResultsClones carrying proviruses with 5'-leader defects can cause persistent NSV up to approximately 103 copies/mL. These proviruses had small, often identical deletions or point mutations involving the major splicing donor (MSD) site and showed partially reduced RNA dimerization and nucleocapsid binding. Nevertheless, they were inducible and produced noninfectious virions containing viral RNA, but lacking envelope.ConclusionThese findings show that proviruses with 5'-leader defects in CD4+ T cell clones can give rise to NSV, affecting clinical care. Sequencing of the 5'-leader can help in understanding failure to completely suppress viremia.FundingOffice of the NIH Director and National Institute of Dental and Craniofacial Research, NIH; Howard Hughes Medical Institute; Johns Hopkins University Center for AIDS Research; National Institute for Allergy and Infectious Diseases (NIAID), NIH, to the PAVE, BEAT-HIV, and DARE Martin Delaney collaboratories.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saif Yasin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Milica Moskovljevic
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Filippo Dragoni
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mei Y Zheng
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Ndeh F Tadzong
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Heer B Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Jeanelle Mae C Quiambao
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Delannoy
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christin Kilcrease
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher J Hoffmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Canada
| | - Jerald Cherian
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia Barditch-Crovo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natasha Chida
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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26
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Archin N, Bar K, Burdo T, Caskey M, Chahroudi A, Farzan M, Ho YC, Jones R, Kearney M, Kuritzkes D, Margolis D, Martinez-Picado J, Okoye A, Salgado M, Stevenson M. Highlights from the Tenth International Workshop on HIV Persistence during Therapy, December 13-16, 2022, Miami, Florida-USA. J Virus Erad 2023; 9:100315. [PMID: 36911658 PMCID: PMC9996320 DOI: 10.1016/j.jve.2023.100315] [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: 01/28/2023] Open
Abstract
The International Workshop on HIV Persistence during Therapy provides a forum in which HIV/AIDS researchers gather to share the latest research findings related to viral reservoirs and cure. The Tenth Workshop, which was attended by over 400 delegates, extended over 4 days and comprised eight sessions covering topics from the basic science of viral persistence to therapeutic approaches to HIV cure. Furthermore, satellite sessions on the first day of the Conference featuring cure research endeavours being pursued by the Bill and Melinda Gates Foundation as well as those being coordinated under the National Institutes of Health Martin Delaney Collaboratory program, provided important updates on research advances being made in these initiatives. As with previous conferences, the International Workshop on HIV Persistence during Therapy is primarily abstract-driven with only one invited talk for each of the sessions. This format, therefore, increases the number of presentations from early-stage investigators. Furthermore, presentations by Community representatives illustrated approaches to creating cure research literacy with effective messaging for the Community. The following article offers a synopsis of the meeting sessions. Due to space constraints, some presentations may have only been briefly discussed. Nevertheless, the Workshop abstracts can be found online (https://www/sciencedirect.com/journal/journal-of-virus-eradication/vol/8/suppl/S).
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Affiliation(s)
- N. Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, USA
| | - K.J. Bar
- Dept of Medicine, University of Pennsylvania, Philadelphia, USA
| | - T. Burdo
- Department of Microbiology, Immunology and Inflammation, Center for Neurovirology and Gene Editing, Temple University, Philadelphia, USA
| | - M. Caskey
- Rockefeller University, New York, USA
| | - A. Chahroudi
- Emory University, School of Medicine, Atlanta, USA
| | - M. Farzan
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, USA
| | - Y.-C. Ho
- HIV Reservoirs and Viral Eradication Transformative Science Group (Cure TSG), New Haven, USA
| | - R.B. Jones
- Dept of Medicine, Weill Cornell Medicine, New York, USA
| | - Mary Kearney
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, USA
| | - D. Kuritzkes
- Harvard Medical School Infectious Disease, Boston, USA
| | | | | | - A. Okoye
- Oregon Health and Science University, USA
| | - M. Salgado
- IrsiCaixa Institute for AIDS Research, Badalona, Spain
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27
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Dufour C, Richard C, Pardons M, Massanella M, Ackaoui A, Murrell B, Routy B, Thomas R, Routy JP, Fromentin R, Chomont N. Phenotypic characterization of single CD4+ T cells harboring genetically intact and inducible HIV genomes. Nat Commun 2023; 14:1115. [PMID: 36849523 PMCID: PMC9971253 DOI: 10.1038/s41467-023-36772-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
The phenotype of the rare HIV-infected cells persisting during antiretroviral therapies (ART) remains elusive. We developed a single-cell approach that combines the phenotypic analysis of HIV-infected cells with near full-length sequencing of their associated proviruses to characterize the viral reservoir in 6 male individuals on suppressive ART. We show that individual cells carrying clonally expanded identical proviruses display very diverse phenotypes, indicating that cellular proliferation contributes to the phenotypic diversification of the HIV reservoir. Unlike most viral genomes persisting on ART, inducible and translation-competent proviruses rarely present large deletions but are enriched in defects in the Ψ locus. Interestingly, the few cells harboring genetically intact and inducible viral genomes express higher levels of the integrin VLA-4 compared to uninfected cells or cells with defective proviruses. Viral outgrowth assay confirmed that memory CD4+ T cells expressing high levels of VLA-4 are highly enriched in replication-competent HIV (27-fold enrichment). We conclude that although clonal expansions diversify the phenotype of HIV reservoir cells, CD4+ T cells harboring replication-competent HIV retain VLA-4 expression.
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Affiliation(s)
- Caroline Dufour
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Corentin Richard
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Marion Pardons
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Marta Massanella
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Antoine Ackaoui
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Bertrand Routy
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Réjean Thomas
- Clinique médicale l'Actuel, Montreal, H2L 4P9, Quebec, Canada
| | - Jean-Pierre Routy
- Division of Hematology & Chronic Viral Illness Service, McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada.
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28
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Abdullah, Din M, Waris A, Khan M, Ali S, Muhammad R, Salman M. The contemporary immunoassays for HIV diagnosis: a concise overview. ASIAN BIOMED 2023; 17:3-12. [PMID: 37551202 PMCID: PMC10405330 DOI: 10.2478/abm-2023-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Recent advances in human immunodeficiency virus (HIV) diagnostics have improved the management of disease progression significantly, which have also boosted the efficacy of antiviral therapies. The detection of HIV at the earliest is very important. A highly recognized and effective virological biomarker for acute HIV infections is p24 antigen. This brief overview is based on advances of HIV diagnosis while focusing on the latest HIV testing technologies including HIV-specific antigens detecting assays of both anti-HIV antibodies and p24 antigen. In addition to other emerging molecular diagnostics for acute HIV infection, the utilization of p24 antigen has been summarized. Moreover, it has been explained how these immunoassays have reduced the window period for detection of HIV in the acute stage of infection.
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Affiliation(s)
- Abdullah
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar25000, Pakistan
| | - Misbahud Din
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad45320, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Shezhen518057, Hong Kong SAR
| | - Muddasir Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar25120, Pakistan
| | - Sajjad Ali
- Department of Zoology, University of Buner, Buner19281, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar25000, Pakistan
- Department of Zoology, Government Degree College Lakarai, Mohmand24651, Pakistan
| | - Muhammad Salman
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar25000, Pakistan
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok10330, Thailand
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29
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Wu VH, Nordin JML, Nguyen S, Joy J, Mampe F, Del Rio Estrada PM, Torres-Ruiz F, González-Navarro M, Luna-Villalobos YA, Ávila-Ríos S, Reyes-Terán G, Tebas P, Montaner LJ, Bar KJ, Vella LA, Betts MR. Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4 + T cell reservoir. Nat Immunol 2023; 24:359-370. [PMID: 36536105 PMCID: PMC9892009 DOI: 10.1038/s41590-022-01371-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a considerable impediment in research towards a cure for HIV. To address this, we developed a single-cell strategy to precisely define the unperturbed peripheral blood HIV-infected memory CD4+ T cell reservoir from ART-treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by new and known surface markers within total and individual memory CD4+ T cell subsets. We further uncovered new epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.
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Affiliation(s)
- Vincent H Wu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayme M L Nordin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jaimy Joy
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Felicity Mampe
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Perla M Del Rio Estrada
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio González-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yara Andrea Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Secretaría de Salud de México, Mexico City, Mexico
| | - Pablo Tebas
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luis J Montaner
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- The Wistar Institute, Philadelphia, PA, USA
| | - Katharine J Bar
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura A Vella
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA.
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30
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Fisher K, Schlub TE, Boyer Z, Rasmussen TA, Rhodes A, Hoh R, Hecht FM, Deeks SG, Lewin SR, Palmer S. Unequal distribution of genetically-intact HIV-1 proviruses in cells expressing the immune checkpoint markers PD-1 and/or CTLA-4. Front Immunol 2023; 14:1064346. [PMID: 36776833 PMCID: PMC9909745 DOI: 10.3389/fimmu.2023.1064346] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction HIV-1 persists in resting CD4+ T-cells despite antiretroviral therapy (ART). Determining the cell surface markers that enrich for genetically-intact HIV-1 genomes is vital in developing targeted curative strategies. Previous studies have found that HIV-1 proviral DNA is enriched in CD4+ T-cells expressing the immune checkpoint markers programmed cell death protein-1 (PD-1) or cytotoxic T-lymphocyte associated protein-4 (CTLA-4). There has also been some success in blocking these markers in an effort to reverse HIV-1 latency. However, it remains unclear whether cells expressing PD-1 and/or CTLA-4 are enriched for genetically-intact, and potentially replication-competent, HIV-1 genomes. Methods We obtained peripheral blood from 16 HIV-1-infected participants, and paired lymph node from four of these participants, during effective ART. Memory CD4+ T-cells from either site were sorted into four populations: PD-1-CTLA-4- (double negative, DN), PD-1+CTLA-4- (PD-1+), PD-1-CTLA-4+ (CTLA-4+) and PD-1+CTLA-4+ (double positive, DP). We performed an exploratory study using the full-length individual proviral sequencing (FLIPS) assay to identify genetically-intact and defective genomes from each subset, as well as HIV-1 genomes with specific intact open reading frames (ORFs). Results and Discussion In peripheral blood, we observed that proviruses found within PD-1+ cells are more likely to have intact ORFs for genes such as tat, rev and nef compared to DN, CTLA-4+ and DP cells, all of which may contribute to HIV-1 persistence. Conversely, we observed that CTLA-4 expression is a marker for cells harbouring HIV-1 provirus that is more likely to be defective, containing low levels of these intact ORFs. In the lymph node, we found evidence that CTLA-4+ cells contain lower levels of HIV-1 provirus compared to the other cell subsets. Importantly, however, we observed significant participant variation in the enrichment of HIV-1 proviruses with intact genomes or specific intact ORFs across these memory CD4+ T-cell subsets, and therefore consideration of additional cellular markers will likely be needed to consistently identify cells harbouring latent, and potentially replication-competent, HIV-1.
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Affiliation(s)
- Katie Fisher
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Timothy E Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Zoe Boyer
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Thomas A Rasmussen
- Department of Infectious Diseases, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Ajantha Rhodes
- Department of Infectious Diseases, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, CA, United States
| | - Frederick M Hecht
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, CA, United States
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, CA, United States
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, VIC, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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31
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Huang Y, Dhummakupt A, Khetan P, Nilles T, Zhou W, Mudvari P, Szewczyk J, Chen YH, Boritz E, Ji H, Agwu A, Persaud D. Immune activation and exhaustion marker expression on T-cell subsets in ART-treated adolescents and young adults with perinatal HIV-1 infection as correlates of viral persistence. Front Immunol 2023; 14:1007626. [PMID: 37033916 PMCID: PMC10076634 DOI: 10.3389/fimmu.2023.1007626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
HIV-1 infection in memory CD4+ T cells forms a latent reservoir that is a barrier to cure. Identification of immune biomarkers that correlate with HIV-1 reservoir size may aid with evaluating efficacy of HIV-1 eradication strategies, towards ART-free remission and cure. In adults living with non-perinatal HIV-1, the immune exhaustion marker PD-1 on central memory CD4+ T cells (Tcm) correlates with measures of HIV-1 reservoir size. Immune correlates of HIV-1 are less defined in adolescents and young adults with perinatal HIV-1. With multi-parameter flow cytometry, we examined immune activation (CD69, CD25, HLA-DR), and exhaustion (PD-1, TIGIT, TIM-3 and LAG-3) markers on CD4+ T cell subsets (naïve (Tn), central memory (Tcm), and the combination (Ttem) of transitional (Ttm) and effector memory (Tem) cells, in 10 adolescents and young adults living with perinatal HIV-1 (median age 15.9 years; median duration of virologic suppression 7.0 years), in whom HIV-1 reservoir size was measured with the Intact Proviral HIV-1 DNA Assay (IPDA) and an enhanced Tat/Rev limiting dilution assay (TILDA). RNA-seq was also performed on the unstimulated CD4+ T cells. The median total HIV-1 DNA concentration in memory CD4+ T cells was 211.90 copies per million CD4+ T cells. In the 7 participants with subtype B HIV-1 infection, the median intact proviral DNA load was 7.96 copies per million CD4+ T cells. Levels of HLA-DR and TIGIT on the Ttem were correlated with total HIV-1 DNA (r=0.76, p=0.015) and (r=0.72, p=0.023), respectively, but not with intact proviral load or induced reservoir size. HIV-1 DNA load was also positively correlated with transcriptional clusters associated with HLA-DR expression by RNA-seq. In contrast, PD-1 expression on Tcm was inversely correlated with total HIV-1 DNA (r=-0.67, p=0.039). Reservoir size by IPDA and TILDA were correlated (r=0.81, p=0.036). Thus, in this cohort of youths with long-standing treated perinatal infection, HLA-DR and TIGIT on Ttem were the key correlates of HIV-1 infected cell frequencies by total HIV-1 DNA, and not PD-1. Total HIV-1 DNA was negatively correlated with PD-1 expressing Tcm. These differences in longstanding perinatal HIV-1 infection compared with adult infection requires further study in larger cohorts.
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Affiliation(s)
- Yuyang Huang
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Adit Dhummakupt
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Priya Khetan
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Tricia Nilles
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Weiqiang Zhou
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, United States
| | - Joseph Szewczyk
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ya Hui Chen
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Eli Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, United States
| | - Hongkai Ji
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Allison Agwu
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Deborah Persaud
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Deborah Persaud,
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32
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Nolan DJ, Rose R, Zhang R, Leong A, Fogel GB, Scholte LLS, Bethony JM, Bracci P, Lamers SL, McGrath MS. The Persistence of HIV Diversity, Transcription, and Nef Protein in Kaposi's Sarcoma Tumors during Antiretroviral Therapy. Viruses 2022; 14:v14122774. [PMID: 36560778 PMCID: PMC9782636 DOI: 10.3390/v14122774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Epidemic Kaposi's sarcoma (KS), defined by co-infection with Human Herpes Virus 8 (HHV-8) and the Human Immunodeficiency Virus (HIV), is a major cause of mortality in sub-Saharan Africa. Antiretroviral therapy (ART) significantly reduces the risk of developing KS, and for those with KS, tumors frequently resolve with ART alone. However, for unknown reasons, a significant number of KS cases do not resolve and can progress to death. To explore how HIV responds to ART in the KS tumor microenvironment, we sequenced HIV env-nef found in DNA and RNA isolated from plasma, peripheral blood mononuclear cells, and tumor biopsies, before and after ART, in four Ugandan study participants who had unresponsive or progressive KS after 180-250 days of ART. We performed immunohistochemistry experiments to detect viral proteins in matched formalin-fixed tumor biopsies. Our sequencing results showed that HIV diversity and RNA expression in KS tumors are maintained after ART, despite undetectable plasma viral loads. The presence of spliced HIV transcripts in KS tumors after ART was consistent with a transcriptionally active viral reservoir. Immunohistochemistry staining found colocalization of HIV Nef protein and tissue-resident macrophages in the KS tumors. Overall, our results demonstrated that even after ART reduced plasma HIV viral load to undetectable levels and restored immune function, HIV in KS tumors continues to be transcriptionally and translationally active, which could influence tumor maintenance and progression.
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Affiliation(s)
- David J. Nolan
- Bioinfoexperts, LLC, Thibodaux, LA 70301, USA
- Correspondence:
| | | | - Rongzhen Zhang
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
| | - Alan Leong
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
| | | | - Larissa L. S. Scholte
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC 20037, USA
| | - Jeffrey M. Bethony
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC 20037, USA
| | - Paige Bracci
- The AIDS and Cancer Specimen Resource, San Francisco, CA 94110, USA
| | | | - Michael S. McGrath
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
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33
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Emert-Sedlak LA, Shi H, Tice CM, Chen L, Alvarado JJ, Shu ST, Du S, Thomas CE, Wrobel JE, Reitz AB, Smithgall TE. Antiretroviral Drug Discovery Targeting the HIV-1 Nef Virulence Factor. Viruses 2022; 14:v14092025. [PMID: 36146831 PMCID: PMC9503669 DOI: 10.3390/v14092025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
While antiretroviral drugs have transformed the lives of HIV-infected individuals, chronic treatment is required to prevent rebound from viral reservoir cells. People living with HIV also are at higher risk for cardiovascular and neurocognitive complications, as well as cancer. Finding a cure for HIV-1 infection is therefore an essential goal of current AIDS research. This review is focused on the discovery of pharmacological inhibitors of the HIV-1 Nef accessory protein. Nef is well known to enhance HIV-1 infectivity and replication, and to promote immune escape of HIV-infected cells by preventing cell surface MHC-I display of HIV-1 antigens. Recent progress shows that Nef inhibitors not only suppress HIV-1 replication, but also restore sufficient MHC-I to the surface of infected cells to trigger a cytotoxic T lymphocyte response. Combining Nef inhibitors with latency reversal agents and therapeutic vaccines may provide a path to clearance of viral reservoirs.
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Affiliation(s)
- Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Colin M. Tice
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Li Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J. Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Sherry T. Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Shoucheng Du
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Catherine E. Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jay E. Wrobel
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Allen B. Reitz
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
- Correspondence:
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34
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Weymar GHJ, Bar-On Y, Oliveira TY, Gaebler C, Ramos V, Hartweger H, Breton G, Caskey M, Cohn LB, Jankovic M, Nussenzweig MC. Distinct gene expression by expanded clones of quiescent memory CD4 + T cells harboring intact latent HIV-1 proviruses. Cell Rep 2022; 40:111311. [PMID: 36070690 PMCID: PMC9471989 DOI: 10.1016/j.celrep.2022.111311] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 01/26/2023] Open
Abstract
Antiretroviral therapy controls, but does not cure, HIV-1 infection due to a reservoir of rare CD4+ T cells harboring latent proviruses. Little is known about the transcriptional program of latent cells. Here, we report a strategy to enrich clones of latent cells carrying intact, replication-competent HIV-1 proviruses from blood based on their expression of unique T cell receptors. Latent cell enrichment enabled single-cell transcriptomic analysis of 1,050 CD4+ T cells belonging to expanded clones harboring intact HIV-1 proviruses from 6 different individuals. The analysis reveals that most of these cells are T effector memory cells that are enriched for expression of HLA-DR, HLA-DP, CD74, CCL5, granzymes A and K, cystatin F, LYAR, and DUSP2. We conclude that expanded clones of latent cells carrying intact HIV-1 proviruses persist preferentially in a distinct CD4+ T cell population, opening possibilities for eradication.
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Affiliation(s)
- Georg H J Weymar
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yotam Bar-On
- Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Lillian B Cohn
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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35
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Tanaka K, Kim Y, Roche M, Lewin SR. The role of latency reversal in HIV cure strategies. J Med Primatol 2022; 51:278-283. [PMID: 36029233 PMCID: PMC9514955 DOI: 10.1111/jmp.12613] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 12/03/2022]
Abstract
One strategy to eliminate latently infected cells that persist in people with HIV on antiretroviral therapy is to activate virus transcription and virus production to induce virus or immune‐mediated cell death. This is called latency reversal. Despite clear activity of multiple latency reversal agents in vitro, clinical trials of latency‐reversing agents have not shown significant reduction in latently infected cells. We review new insights into the biology of HIV latency and discuss novel approaches to enhance the efficacy of latency reversal agents.
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Affiliation(s)
- Kiho Tanaka
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Youry Kim
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael Roche
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
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36
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Stevenson EM, Terry S, Copertino D, Leyre L, Danesh A, Weiler J, Ward AR, Khadka P, McNeil E, Bernard K, Miller IG, Ellsworth GB, Johnston CD, Finkelsztein EJ, Zumbo P, Betel D, Dündar F, Duncan MC, Lapointe HR, Speckmaier S, Moran-Garcia N, Papa MP, Nicholes S, Stover CJ, Lynch RM, Caskey M, Gaebler C, Chun TW, Bosque A, Wilkin TJ, Lee GQ, Brumme ZL, Jones RB. SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8 + T-cells. Nat Commun 2022; 13:4888. [PMID: 35985993 PMCID: PMC9389512 DOI: 10.1038/s41467-022-32376-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/26/2022] [Indexed: 12/05/2022] Open
Abstract
Efforts to cure HIV have focused on reactivating latent proviruses to enable elimination by CD8+ cytotoxic T-cells. Clinical studies of latency reversing agents (LRA) in antiretroviral therapy (ART)-treated individuals have shown increases in HIV transcription, but without reductions in virologic measures, or evidence that HIV-specific CD8+ T-cells were productively engaged. Here, we show that the SARS-CoV-2 mRNA vaccine BNT162b2 activates the RIG-I/TLR - TNF - NFκb axis, resulting in transcription of HIV proviruses with minimal perturbations of T-cell activation and host transcription. T-cells specific for the early gene-product HIV-Nef uniquely increased in frequency and acquired effector function (granzyme-B) in ART-treated individuals following SARS-CoV-2 mRNA vaccination. These parameters of CD8+ T-cell induction correlated with significant decreases in cell-associated HIV mRNA, suggesting killing or suppression of cells transcribing HIV. Thus, we report the observation of an intervention-induced reduction in a measure of HIV persistence, accompanied by precise immune correlates, in ART-suppressed individuals. However, we did not observe significant depletions of intact proviruses, underscoring challenges to achieving (or measuring) HIV reservoir reductions. Overall, our results support prioritizing the measurement of granzyme-B-producing Nef-specific responses in latency reversal studies and add impetus to developing HIV-targeted mRNA therapeutic vaccines that leverage built-in LRA activity.
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Affiliation(s)
- Eva M Stevenson
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sandra Terry
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dennis Copertino
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Louise Leyre
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Ali Danesh
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jared Weiler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Adam R Ward
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Pragya Khadka
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Evan McNeil
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kevin Bernard
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Itzayana G Miller
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Grant B Ellsworth
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Carrie D Johnston
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Eli J Finkelsztein
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Paul Zumbo
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
| | - Doron Betel
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
| | - Friederike Dündar
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Nadia Moran-Garcia
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Michelle Premazzi Papa
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Samuel Nicholes
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Carissa J Stover
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Rebecca M Lynch
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID, NIH, Bethesda, MD, USA
| | - Alberto Bosque
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Timothy J Wilkin
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Guinevere Q Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - R Brad Jones
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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37
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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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38
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Hu W, Li YJ, Zhen C, Wang YY, Huang HH, Zou J, Zheng YQ, Huang GC, Meng SR, Jin JH, Li J, Zhou MJ, Fu YL, Zhang P, Li XY, Yang T, Wang XW, Yang XH, Song JW, Fan X, Jiao YM, Xu RN, Zhang JY, Zhou CB, Yuan JH, Huang L, Qin YQ, Wu FY, Shi M, Wang FS, Zhang C. CCL5-Secreting Virtual Memory CD8+ T Cells Inversely Associate With Viral Reservoir Size in HIV-1-Infected Individuals on Antiretroviral Therapy. Front Immunol 2022; 13:897569. [PMID: 35720272 PMCID: PMC9204588 DOI: 10.3389/fimmu.2022.897569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Recent studies highlighted that CD8+ T cells are necessary for restraining reservoir in HIV-1-infected individuals who undergo antiretroviral therapy (ART), whereas the underlying cellular and molecular mechanisms remain largely unknown. Here, we enrolled 60 virologically suppressed HIV-1-infected individuals, to assess the correlations of the effector molecules and phenotypic subsets of CD8+ T cells with HIV-1 DNA and cell-associated unspliced RNA (CA usRNA). We found that the levels of HIV-1 DNA and usRNA correlated positively with the percentage of CCL4+CCL5- CD8+ central memory cells (TCM) while negatively with CCL4-CCL5+ CD8+ terminally differentiated effector memory cells (TEMRA). Moreover, a virtual memory CD8+ T cell (TVM) subset was enriched in CCL4-CCL5+ TEMRA cells and phenotypically distinctive from CCL4+ TCM subset, supported by single-cell RNA-Seq data. Specifically, TVM cells showed superior cytotoxicity potentially driven by T-bet and RUNX3, while CCL4+ TCM subset displayed a suppressive phenotype dominated by JUNB and CREM. In viral inhibition assays, TVM cells inhibited HIV-1 reactivation more effectively than non-TVM CD8+ T cells, which was dependent on CCL5 secretion. Our study highlights CCL5-secreting TVM cells subset as a potential determinant of HIV-1 reservoir size. This might be helpful to design CD8+ T cell-based therapeutic strategies for cure of the disease.
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Affiliation(s)
- Wei Hu
- Medical School of Chinese People's Liberation Army (PLA), Beijing, China.,Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yan-Jun Li
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Cheng Zhen
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - You-Yuan Wang
- Medical School of Chinese People's Liberation Army (PLA), Beijing, China.,Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Hui-Huang Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jun Zou
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Yan-Qing Zheng
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Gui-Chan Huang
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Si-Run Meng
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Jie-Hua Jin
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jing Li
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ming-Ju Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yu-Long Fu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Peng Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xiao-Yu Li
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Tao Yang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xiu-Wen Wang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xiu-Han Yang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Wen Song
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xing Fan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yan-Mei Jiao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ruo-Nan Xu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ji-Yuan Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Chun-Bao Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Hong Yuan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Lei Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ya-Qin Qin
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Feng-Yao Wu
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Ming Shi
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Fu-Sheng Wang
- Medical School of Chinese People's Liberation Army (PLA), Beijing, China.,Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China.,Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Chao Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China.,Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
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39
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Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones. Immunity 2022; 55:1013-1031.e7. [PMID: 35320704 PMCID: PMC9203927 DOI: 10.1016/j.immuni.2022.03.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/19/2022] [Accepted: 03/08/2022] [Indexed: 02/02/2023]
Abstract
Understanding the drivers and markers of clonally expanding HIV-1-infected CD4+ T cells is essential for HIV-1 eradication. We used single-cell ECCITE-seq, which captures surface protein expression, cellular transcriptome, HIV-1 RNA, and TCR sequences within the same single cell to track clonal expansion dynamics in longitudinally archived samples from six HIV-1-infected individuals (during viremia and after suppressive antiretroviral therapy) and two uninfected individuals, in unstimulated conditions and after CMV and HIV-1 antigen stimulation. Despite antiretroviral therapy, persistent antigen and TNF responses shaped T cell clonal expansion. HIV-1 resided in Th1-polarized, antigen-responding T cells expressing BCL2 and SERPINB9 that may resist cell death. HIV-1 RNA+ T cell clones were larger in clone size, established during viremia, persistent after viral suppression, and enriched in GZMB+ cytotoxic effector memory Th1 cells. Targeting HIV-1-infected cytotoxic CD4+ T cells and drivers of clonal expansion provides another direction for HIV-1 eradication.
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40
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Kreider EF, Bar KJ. HIV-1 Reservoir Persistence and Decay: Implications for Cure Strategies. Curr HIV/AIDS Rep 2022; 19:194-206. [PMID: 35404007 PMCID: PMC10443186 DOI: 10.1007/s11904-022-00604-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), a viral reservoir persists in individuals living with HIV that can reignite systemic replication should treatment be interrupted. Understanding how HIV-1 persists through effective ART is essential to develop cure strategies to induce ART-free virus remission. RECENT FINDINGS The HIV-1 reservoir resides in a pool of CD4-expressing cells as a range of viral species, a subset of which is genetically intact. Recent studies suggest that the reservoir on ART is highly dynamic, with expansion and contraction of virus-infected cells over time. Overall, the intact proviral reservoir declines faster than defective viruses, suggesting enhanced immune clearance or cellular turnover. Upon treatment interruption, rebound viruses demonstrate escape from adaptive and innate immune responses, implicating these selective pressures in restriction of virus reactivation. Cure strategies employing immunotherapy are poised to test whether host immune pressure can be augmented to enhance reservoir suppression or clearance. Alternatively, genomic engineering approaches are being applied to directly eliminate intact viruses and shrink the replication-competent virus pool. New evidence suggests host immunity exerts selective pressure on reservoir viruses and clears HIV-1 infected cells over years on ART. Efforts to build on the detectable, but insufficient, reservoir clearance via empiric testing in clinical trials will inform our understanding of mechanisms of viral persistence and the direction of future cure strategies.
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Affiliation(s)
- Edward F Kreider
- Perelman School of Medicine, University of Pennsylvania, Stemmler Hall Room 130-150, 3450 Hamilton Walk, Philadelphia, PA, 19104-6073, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, 502D Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104‑0673, USA.
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41
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Astorga-Gamaza A, Grau-Expósito J, Burgos J, Navarro J, Curran A, Planas B, Suanzes P, Falcó V, Genescà M, Buzon M. Identification of HIV-reservoir cells with reduced susceptibility to antibody-dependent immune response. eLife 2022; 11:78294. [PMID: 35616530 PMCID: PMC9177146 DOI: 10.7554/elife.78294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
HIV establishes a persistent infection in heterogeneous cell reservoirs, which can be maintained by different mechanisms including cellular proliferation, and represent the main obstacle to curing the infection. The expression of the Fcγ receptor CD32 has been identified as a marker of the active cell reservoirs in people on antiretroviral therapy, but if its expression has any role in conferring advantage for viral persistence is unknown. Here, we report that HIV-infected cells expressing CD32 have reduced susceptibility to natural killer (NK) antibody-dependent cell cytotoxicity (ADCC) by a mechanism compatible with the suboptimal binding of HIV-specific antibodies. Infected CD32 cells have increased proliferative capacity in the presence of immune complexes, and are more resistant to strategies directed to potentiate NK function. Remarkably, reactivation of the latent reservoir from antiretroviral-treated people living with HIV increases the pool of infected CD32 cells, which are largely resistant to the ADCC immune mechanism. Thus, we report the existence of reservoir cells that evade part of the NK immune response through the expression of CD32.
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Affiliation(s)
| | | | - Joaquín Burgos
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Jordi Navarro
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Adrià Curran
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Bibiana Planas
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Paula Suanzes
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Vicenç Falcó
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Meritxell Genescà
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Maria Buzon
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
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42
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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: 0] [Impact Index Per Article: 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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43
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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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44
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Leyre L, Jones RB. Hide and seek: for HIV-infected CD4+ T cells, playing well comes with maturity. J Clin Invest 2022; 132:1-4. [PMID: 35362485 PMCID: PMC8976498 DOI: 10.1172/jci158872] [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] [Indexed: 11/17/2022] Open
Abstract
Antiretroviral therapy suppresses HIV replication but leaves a population of infected CD4+ T cells with integrated proviruses. While most of these proviruses contain defects, such as deletions, some intact proviruses persist and can reinitiate viral replication. In this issue of the JCI, Duette, Hiener, and colleagues performed a tour de force proviral landscape analysis on clinical samples collected over many years with in vitro functional assays. The researchers showed that effector memory CD4+ T cells provide partial sanctuary to intact proviruses from CD8+ T cells and this was associated with superior Nef-mediated MHC-I downregulation relative to less mature CD4+ T cell populations. This finding implicates differential immunoevasion as a cell-intrinsic property, influencing proviral persistence, and highlights Nef as a therapeutic target.
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