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Hetrick B, Siddiqui S, Spear M, Guo J, Liang H, Fu Y, Yang Z, Doyle-Meyers L, Pahar B, Veazey RS, Dufour J, Andalibi A, Ling B, Wu Y. Suppression of viral rebound by a Rev-dependent lentiviral particle in SIV-infected rhesus macaques. Gene Ther 2024:10.1038/s41434-024-00467-9. [PMID: 39025983 DOI: 10.1038/s41434-024-00467-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
Abstract
Persistence of human immunodeficiency virus (HIV) reservoirs prevents viral eradication, and consequently HIV-infected patients require lifetime treatment with antiretroviral therapy (ART) [1-5]. Currently, there are no effective therapeutics to prevent HIV rebound upon ART cessation. Here we describe an HIV/SIV Rev-dependent lentiviral particle that can be administered to inhibit viral rebound [6-9]. Using simian immunodeficiency virus (SIV)-infected rhesus macaques as a model, we demonstrate that the administration of pre-assembled SIV Rev-dependent lentiviral particles into SIVmac239-infected Indian rhesus macaques can lead to reduction of viral rebound upon ART termination. One of the injected animals, KC50, controlled plasma and CNS viremia to an undetectable level most of the time for over two years after ART termination. Surprisingly, detailed molecular and immunological characterization revealed that viremia control was concomitant with the induction of neutralizing antibodies (nAbs) following the administration of the Rev-dependent vectors. This study emphasizes the importance of neutralizing antibodies (nAbs) for viremia control [10-15], and also provides proof of concept that the Rev-dependent vector can be used to target viral reservoirs, including the CNS reservoirs, in vivo. However, future large-scale in vivo studies are needed to understand the potential mechanisms of viremia control induced by the Rev-dependent vector.
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Affiliation(s)
- Brian Hetrick
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA
| | - Summer Siddiqui
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, 70433, USA
| | - Mark Spear
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA
| | - Jia Guo
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA
| | - Huizhi Liang
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA
| | - Yajing Fu
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA
| | - Zhijun Yang
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA
| | - Lara Doyle-Meyers
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, 70433, USA
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, 70433, USA
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, 70433, USA
| | - Jason Dufour
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, 70433, USA
| | - Ali Andalibi
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA
| | - Binhua Ling
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, 70433, USA
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, 8715 W Military Dr., San Antonio, TX, 78227, USA
| | - Yuntao Wu
- Center for Infectious Disease Research, George Mason University, Manassas, VA, 20110, USA.
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2
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Immonen TT, Fennessey CM, Lipkey L, Newman L, Macairan A, Bosche M, Waltz N, Del Prete GQ, Lifson JD, Keele BF. No evidence for ongoing replication on ART in SIV-infected macaques. Nat Commun 2024; 15:5093. [PMID: 38877003 PMCID: PMC11178840 DOI: 10.1038/s41467-024-49369-9] [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: 02/27/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
The capacity of HIV-1 to replicate during optimal antiretroviral therapy (ART) is challenging to assess directly. To gain greater sensitivity to detect evolution on ART, we used a nonhuman primate (NHP) model providing precise control over the level of pre-ART evolution and more comprehensive analyses than are possible with clinical samples. We infected 21 rhesus macaques (RMs) with the barcoded virus SIVmac239M and initiated ART early to minimize baseline genetic diversity. RMs were treated for 285-1200 days. We used several tests of molecular evolution to compare 1352 near-full-length (nFL) SIV DNA single genome sequences from PBMCs, lymph nodes, and spleen obtained near the time of ART initiation and those present after long-term ART, none of which showed significant changes to the SIV DNA population during ART in any animal. To investigate the possibility of ongoing replication in unsampled putative tissue sanctuaries during ART, we discontinued treatment in four animals and confirmed that none of the 336 nFL SIV RNA sequences obtained from rebound plasma viremia showed evidence of evolution. The rigorous nature of our analyses reinforced the emerging consensus of a lack of appreciable ongoing replication on effective ART and validates the relevance of this NHP model for cure studies.
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Affiliation(s)
- Taina T Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Laura Newman
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Agatha Macairan
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Marjorie Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Nora Waltz
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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3
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Lee SK, Sondgeroth A, Xu Y, Warren J, Zhou S, Gilleece M, Hauser BM, Gay CL, Kuruc JD, Archin NM, Eron JJ, Margolis DM, Goonetilleke N, Swanstrom R. Sequence Analysis of Inducible, Replication-Competent Virus Reveals No Evidence of HIV-1 Evolution During Suppressive Antiviral Therapy, Indicating a Lack of Ongoing Viral Replication. Open Forum Infect Dis 2024; 11:ofae212. [PMID: 38756763 PMCID: PMC11097118 DOI: 10.1093/ofid/ofae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/14/2024] [Indexed: 05/18/2024] Open
Abstract
Background Persistence of HIV-1 in reservoirs necessitates life-long antiretroviral therapy (ART). There are conflicting data using genetic analysis on whether persistence includes an actively replicating reservoir with strong evidence arguing against replication. Methods We investigated the possibility of ongoing viral evolution during suppressive therapy by comparing near full-length viral genomic sequences using phylogenetic analysis of viral RNA in plasma before therapy initiation early after infection and from virus induced to grow from the latent reservoir after a period of suppressive ART. We also focused our analysis on evidence of selective pressure by drugs in the treatment regimen and at sites of selective pressure by the adaptive immune response. Results Viral genomes induced to grow from the latent reservoir from 10 participants with up to 9 years on suppressive ART were highly similar to the nearly homogeneous sequences in plasma taken early after infection at ART initiation. This finding was consistent across the entire genome and when the analysis focused on sites targeted by the drug regimen and by host selective pressure of antibody and cytotoxic T cells. The lack of viral evolution away from pretherapy sequences in spite of demonstrated selective pressure is most consistent with a lack of viral replication during reservoir persistence. Conclusions These results do not support ongoing viral replication as a mechanism of HIV-1 persistence during suppressive ART.
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Affiliation(s)
- Sook-Kyung Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amy Sondgeroth
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yinyan Xu
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joanna Warren
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maria Gilleece
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Blake M Hauser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Cynthia L Gay
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - JoAnn D Kuruc
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancie M Archin
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M Margolis
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nilu Goonetilleke
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
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4
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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5
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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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6
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Guo Q, Zhang J, Parikh K, Brinkley A, Lin S, Zakarian C, Pernet O, Shimizu S, Khamaikawin W, Hacke K, Kasahara N, An DS. In vivo selection of anti-HIV-1 gene-modified human hematopoietic stem/progenitor cells to enhance engraftment and HIV-1 inhibition. Mol Ther 2024; 32:384-394. [PMID: 38087779 PMCID: PMC10862071 DOI: 10.1016/j.ymthe.2023.12.007] [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: 08/28/2023] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/26/2023] Open
Abstract
Hematopoietic stem/progenitor cell (HSPC)-based anti-HIV-1 gene therapy holds great promise to eradicate HIV-1 or to provide long-term remission through a continuous supply of anti-HIV-1 gene-modified cells without ongoing antiretroviral therapy. However, achieving sufficient engraftment levels of anti-HIV gene-modified HSPC to provide therapeutic efficacy has been a major limitation. Here, we report an in vivo selection strategy for anti-HIV-1 gene-modified HSPC by introducing 6-thioguanine (6TG) chemoresistance through knocking down hypoxanthine-guanine phosphoribosyl transferase (HPRT) expression using RNA interference (RNAi). We developed a lentiviral vector capable of co-expressing short hairpin RNA (shRNA) against HPRT alongside two anti-HIV-1 genes: shRNA targeting HIV-1 co-receptor CCR5 and a membrane-anchored HIV-1 fusion inhibitor, C46, for efficient in vivo selection of anti-HIV-1 gene-modified human HSPC. 6TG-mediated preconditioning and in vivo selection significantly enhanced engraftment of HPRT-knockdown anti-HIV-1 gene-modified cells (>2-fold, p < 0.0001) in humanized bone marrow/liver/thymus (huBLT) mice. Viral load was significantly reduced (>1 log fold, p < 0.001) in 6TG-treated HIV-1-infected huBLT mice compared to 6TG-untreated mice. We demonstrated that 6TG-mediated preconditioning and in vivo selection considerably improved engraftment of HPRT-knockdown anti-HIV-1 gene-modified HSPC and repopulation of anti-HIV-1 gene-modified hematopoietic cells in huBLT mice, allowing for efficient HIV-1 inhibition.
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Affiliation(s)
- Qi Guo
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA
| | - Jian Zhang
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA
| | - Keval Parikh
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA
| | - Alexander Brinkley
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA
| | - Samantha Lin
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA
| | - Christina Zakarian
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA
| | - Olivier Pernet
- Maternal, Child, and Adolescent Center for Infectious Diseases, University of Southern California, Los Angeles, CA 90089, USA
| | - Saki Shimizu
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA
| | - Wannisa Khamaikawin
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA; Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Katrin Hacke
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Phoenix, AZ 85054, USA
| | - Noriyuki Kasahara
- UCSF, Neurological Surgery, Radiation Oncology, San Francisco, CA 94158, USA
| | - Dong Sung An
- UCLA AIDS Institute, UCLA, Los Angeles, CA 90024, USA; UCLA School of Nursing, UCLA, Los Angeles, CA 90095, USA.
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7
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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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8
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Paryad-Zanjani S, Jagarapu A, Piovoso MJ, Zurakowski R. Ongoing HIV replication in lymph node sanctuary sites in treated individuals contributes to the total latent HIV at a very slow rate. J Theor Biol 2023; 575:111651. [PMID: 37898364 PMCID: PMC10680438 DOI: 10.1016/j.jtbi.2023.111651] [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: 03/29/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
Lymph nodes (LNs) serve as a sanctuary site for HIV viruses due to the heterogeneous distribution of the antiretrovirals (ARVs) inside the LNs. There is an ongoing debate whether this represents ongoing cycles of viral replication in the LNs or merely residual virus production by latently infected cells. Previous work has claimed that the measured levels of genetic variation in proviruses sampled from the blood were inconsistent with ongoing replication. However, it is not clear what rate of variation is consistent with ongoing replication in small sanctuary sites. In this study, we used a spherically symmetric compartmental ODE model to track the HIV viral dynamics in the LN and predict the contribution of ongoing replication within the LN to the whole-body proviral pool in an ARV-suppressed person living with HIV. This model tracks the reaction-diffusion dynamics of uninfected, actively infected, and latently infected T-cells as well as free virus within the LN parenchyma and the blood, and distinguishes between latently infected cells created before ARV therapy and during ARV therapy. We simulated suppressive therapy beginning in year 5 post-infection. Each LN sanctuary site had a volume of 1 ml, and we considered cases of 1 ml, 30 ml, and 250 ml total volume, which represent a single active sanctuary site, moderate systemic involvement, and involvement of the total lymphoid tissue. Viral load in the blood rapidly dropped and remained below the limit of detection in all cases but remained high in the LN sanctuary sites. Novel latent cells increased systemically over time but very slowly, taking between 25 and 50 years to reach 5 % of the total latent pool, depending on the volume of lymphoid tissue involvement. Putative sanctuary sites in LNs are limited in volume and produce novel latent cells slowly. Assays to detect genetic drift due to such sites would require very deep sequencing if sampling only from the blood. Previous studies showing a lack of genetic drift are consistent with the expected contribution of ongoing replication in lymph node sanctuary sites.
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Affiliation(s)
| | - Aditya Jagarapu
- Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Michael J Piovoso
- Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Ryan Zurakowski
- Biomedical Engineering, University of Delaware, Newark, DE, USA.
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9
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Sambaturu N, Fray EJ, Wu F, Zitzmann C, Simonetti FR, Barouch DH, Siliciano JD, Siliciano RF, Ribeiro RM, Perelson AS, Molina-París C, Leitner T. Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565539. [PMID: 37961482 PMCID: PMC10635124 DOI: 10.1101/2023.11.03.565539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
HIV can persist in a latent form as integrated DNA (provirus) in resting CD4+ T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when virus is deposited in the latent reservoir have come to contradictory conclusions. To reexamine the genetic variation of HIV in CD4+ T cells during ART, we determined the divergence in envelope sequences collected from 10 SIV infected rhesus macaques. We found that the macaques displayed a biphasic decline of the viral divergence over time, where the first phase lasted for an average of 11.6 weeks (range 4-28 weeks). Motivated by recent observations that the HIV-infected CD4+ T cell population is composed of short- and long-lived subsets, we developed a model to study the divergence dynamics. We found that SIV in short-lived cells was on average more diverged, while long-lived cells harbored less diverged virus. This suggests that the long-lived cells harbor virus deposited starting earlier in infection and continuing throughout infection, while short-lived cells predominantly harbor more recent virus. As these cell populations decayed, the overall proviral divergence decline matched that observed in the empirical data. This model explains previous seemingly contradictory results on the timing of virus deposition into the latent reservoir, and should provide guidance for future eradication efforts.
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Affiliation(s)
- Narmada Sambaturu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Carolin Zitzmann
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Carmen Molina-París
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
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10
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Ikeogu N, Ajibola O, Zayats R, Murooka TT. Identifying physiological tissue niches that support the HIV reservoir in T cells. mBio 2023; 14:e0205323. [PMID: 37747190 PMCID: PMC10653859 DOI: 10.1128/mbio.02053-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Abstract
Successful antiretroviral therapy (ART) can efficiently suppress Human Immunodeficiency Virus-1 (HIV-1) replication to undetectable levels, but rare populations of infected memory CD4+ T cells continue to persist, complicating viral eradication efforts. Memory T cells utilize distinct homing and adhesion molecules to enter, exit, or establish residence at diverse tissue sites, integrating cellular and environmental cues that maintain homeostasis and life-long protection against pathogens. Critical roles for T cell receptor and cytokine signals driving clonal expansion and memory generation during immunity generation are well established, but whether HIV-infected T cells can utilize similar mechanisms for their own long-term survival is unclear. How infected, but transcriptionally silent T cells maintain their recirculation potential through blood and peripheral tissues, or whether they acquire new capabilities to establish unique peripheral tissue niches, is also not well understood. In this review, we will discuss the cellular and molecular cues that are important for memory T cell homeostasis and highlight opportunities for HIV to hijack normal immunological processes to establish long-term viral persistence.
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Affiliation(s)
- Nnamdi Ikeogu
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Oluwaseun Ajibola
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Romaniya Zayats
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Thomas T. Murooka
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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11
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Banga R, Procopio FA, Lana E, Gladkov GT, Roseto I, Parsons EM, Lian X, Armani-Tourret M, Bellefroid M, Gao C, Kauzlaric A, Foglierini M, Alfageme-Abello O, Sluka SHM, Munoz O, Mastrangelo A, Fenwick C, Muller Y, Mkindi CG, Daubenberger C, Cavassini M, Trunfio R, Déglise S, Corpataux JM, Delorenzi M, Lichterfeld M, Pantaleo G, Perreau M. Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART. Cell Host Microbe 2023; 31:1714-1731.e9. [PMID: 37751747 PMCID: PMC11068440 DOI: 10.1016/j.chom.2023.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/02/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Although gut and lymph node (LN) memory CD4 T cells represent major HIV and simian immunodeficiency virus (SIV) tissue reservoirs, the study of the role of dendritic cells (DCs) in HIV persistence has long been limited to the blood due to difficulties to access lymphoid tissue samples. In this study, we show that LN migratory and resident DC subpopulations harbor distinct phenotypic and transcriptomic profiles. Interestingly, both LN DC subpopulations contain HIV intact provirus and inducible replication-competent HIV despite the expression of the antiviral restriction factor SAMHD1. Notably, LN DC subpopulations isolated from HIV-infected individuals treated for up to 14 years are transcriptionally silent but harbor replication-competent virus that can be induced upon TLR7/8 stimulation. Taken together, these results uncover a potential important contribution of LN DCs to HIV infection in the presence of ART.
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Affiliation(s)
- Riddhima Banga
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Francesco Andrea Procopio
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Erica Lana
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | | | | | - Elizabeth M Parsons
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Annamaria Kauzlaric
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathilde Foglierini
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Oscar Alfageme-Abello
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Susanna H M Sluka
- Newborn Screening Switzerland, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Olivia Munoz
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Andrea Mastrangelo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Craig Fenwick
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Yannick Muller
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Catherine Gerald Mkindi
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania; Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Matthias Cavassini
- Services of Infectious Diseases, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rafael Trunfio
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sébastien Déglise
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Pantaleo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Matthieu Perreau
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
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12
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Jörimann L, Tschumi J, Zeeb M, Leemann C, Schenkel CD, Neumann K, Chaudron SE, Zaheri M, Frischknecht P, Neuner-Jehle N, Kuster H, Braun DL, Grube C, Kouyos R, Metzner KJ, Günthard HF. Absence of Proviral Human Immunodeficiency Virus (HIV) Type 1 Evolution in Early-Treated Individuals With HIV Switching to Dolutegravir Monotherapy During 48 Weeks. J Infect Dis 2023; 228:907-918. [PMID: 37498738 PMCID: PMC10547464 DOI: 10.1093/infdis/jiad292] [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: 05/05/2023] [Revised: 07/07/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is treated with antiretroviral therapy (ART), usually consisting of 2-3 different drugs, referred to as combination ART (cART). Our recent randomized clinical trial comparing a switch to dolutegravir monotherapy with continuation of cART in early-treated individuals demonstrated sustained virological suppression over 48 weeks. Here, we characterize the longitudinal landscape of the HIV-1 reservoir in these participants, with particular attention to potential differences between treatment groups regarding evidence of evolution as a proxy for low-level replication. Near full-length HIV-1 proviral polymerase chain reaction and next-generation sequencing was applied to longitudinal peripheral blood mononuclear cell samples to assess proviral evolution and the potential emergence of drug resistance mutations (DRMs). Neither an increase in genetic distance nor diversity over time was detected in participants of both treatment groups. Single proviral analysis showed high proportions of defective proviruses and low DRM numbers. No evidence for evolution during dolutegravir monotherapy was found in these early-treated individuals.
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Affiliation(s)
- Lisa Jörimann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Jasmin Tschumi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Marius Zeeb
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Christine Leemann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Corinne D Schenkel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Sandra E Chaudron
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Nadia Neuner-Jehle
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Herbert Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Christina Grube
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Roger Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
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13
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Dufour C, Ruiz MJ, Pagliuzza A, Richard C, Shahid A, Fromentin R, Ponte R, Cattin A, Wiche Salinas TR, Salahuddin S, Sandstrom T, Schinkel SB, Costiniuk CT, Jenabian MA, Ancuta P, Routy JP, Cohen ÉA, Brumme ZL, Power C, Angel JB, Chomont N. Near full-length HIV sequencing in multiple tissues collected postmortem reveals shared clonal expansions across distinct reservoirs during ART. Cell Rep 2023; 42:113053. [PMID: 37676762 DOI: 10.1016/j.celrep.2023.113053] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/05/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
HIV persists in tissues during antiretroviral therapy (ART), but the relative contribution of different anatomical compartments to the viral reservoir in humans remains unknown. We performed an extensive characterization of HIV reservoirs in two men who donated their bodies to HIV cure research and who had been on suppressive ART for years. HIV DNA is detected in all tissues, with large variations across anatomical compartments and between participants. Intact HIV genomes represent 2% and 25% of all proviruses in the two participants and are mainly detected in secondary lymphoid organs, with the spleen and mediastinal lymph nodes harboring intact viral genomes in both individuals. Multiple copies of identical HIV genomes are found in all tissues, indicating that clonal expansions are common in anatomical sites. The majority (>85%) of these expanded clones are shared across multiple tissues. These findings suggest that infected cells expand, migrate, and possibly circulate between anatomical sites.
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Affiliation(s)
- Caroline Dufour
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Maria Julia Ruiz
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | | | | | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Rémi Fromentin
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Rosalie Ponte
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada; Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Amélie Cattin
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Tomas Raul Wiche Salinas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Syim Salahuddin
- Département de Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada
| | - Teslin Sandstrom
- Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | | | - Cecilia T Costiniuk
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada; Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Mohammad-Ali Jenabian
- Département de Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada
| | - Petronela Ancuta
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Jean-Pierre Routy
- Research Institute of McGill University Health Centre, Montreal, QC, Canada; Division of Hematology, McGill University Health Centre, Montreal, QC, Canada
| | - Éric A Cohen
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Christopher Power
- Department of Medicine (Neurology), University of Alberta, 6-11 Heritage Medical Research Center, Edmonton, AB, Canada; Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Jonathan B Angel
- Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada; Division of Infectious Diseases, Ottawa Hospital-General Campus, Ottawa, ON, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada.
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14
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de Azevedo SSD, Côrtes FH, Villela LM, Hoagland B, Grinsztejn B, Veloso VG, Morgado MG, Bello G. Ongoing HIV-1 evolution and reservoir reseeding in two elite controllers with genetically diverse peripheral proviral quasispecies. Mem Inst Oswaldo Cruz 2023; 118:e230066. [PMID: 37283423 DOI: 10.1590/0074-02760230066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Elite controllers (EC) are human immunodeficiency virus (HIV)-positive individuals who can maintain low viral loads for extended periods without antiretroviral therapy due to multifactorial and individual characteristics. Most have a small HIV-1 reservoir composed of identical proviral sequences maintained by clonal expansion of infected CD4+ T cells. However, some have a more diverse peripheral blood mononuclear cell (PBMC)-associated HIV-1 reservoir with unique sequences. OBJECTIVES To understand the turnover dynamics of the PBMC-associated viral quasispecies in ECs with relatively diverse circulating proviral reservoirs. METHODS We performed single genome amplification of the env gene at three time points during six years in two EC with high intra-host HIV DNA diversity. FINDINGS Both EC displayed quite diverse PBMCs-associated viral quasispecies (mean env diversity = 1.9-4.1%) across all time-points comprising both identical proviruses that are probably clonally expanded and unique proviruses with evidence of ongoing evolution. HIV-1 env glycosylation pattern suggests that ancestral and evolving proviruses may display different phenotypes of resistance to broadly neutralising antibodies consistent with persistent immune pressure. Evolving viruses may progressively replace the ancestral ones or may remain as minor variants in the circulating proviral population. MAIN CONCLUSIONS These findings support that the high intra-host HIV-1 diversity of some EC resulted from long-term persistence of archival proviruses combined with the continuous reservoir's reseeding and low, but measurable, viral evolution despite undetectable viremia.
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Affiliation(s)
| | - Fernanda Heloise Côrtes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Larissa M Villela
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Brenda Hoagland
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Beatriz Grinsztejn
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Valdilea Gonçalvez Veloso
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Mariza G Morgado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
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15
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Lisco A, Lange C, Manion M, Kuriakose S, Dewar R, Gorelick RJ, Huik K, Yu Q, Hammoud DA, Smith BR, Muranski P, Rehm C, Sherman BT, Sykes C, Lindo N, Ye P, Bricker KM, Keele BF, Fennessey CM, Maldarelli F, Sereti I. Immune reconstitution inflammatory syndrome drives emergence of HIV drug resistance from multiple anatomic compartments in a person living with HIV. Nat Med 2023; 29:1364-1369. [PMID: 37322122 PMCID: PMC10494392 DOI: 10.1038/s41591-023-02387-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Reservoirs of HIV maintained in anatomic compartments during antiretroviral therapy prevent HIV eradication. However, mechanisms driving their persistence and interventions to control them remain elusive. Here we report the presence of an inducible HIV reservoir within antigen-specific CD4+T cells in the central nervous system of a 59-year-old male with progressive multifocal leukoencephalopathy immune reconstitution inflammatory syndrome (PML-IRIS). HIV production during PML-IRIS was suppressed by modulating inflammation with corticosteroids; selection of HIV drug resistance caused subsequent breakthrough viremia. Therefore, inflammation can influence the composition, distribution and induction of HIV reservoirs, warranting it as a key consideration for developing effective HIV remission strategies.
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Affiliation(s)
- Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Camille Lange
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
- Military HIV Research Program, Walter Reed Army Institute of Research, Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD, USA.
| | - Maura Manion
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Safia Kuriakose
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Robin Dewar
- Virus Isolation and Serology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristi Huik
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Quan Yu
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dima A Hammoud
- Center for Infectious Disease Imaging, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Bryan R Smith
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Pawel Muranski
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine Rehm
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brad T Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Craig Sykes
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Lindo
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Peiying Ye
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Katherine M Bricker
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank Maldarelli
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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16
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Abstract
Acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), has become a heavy burden of disease and an important public health problem in the world. Although current antiretroviral therapy (ART) is effective at suppressing the virus in the blood, HIV still remains in two different types of reservoirs-the latently infected cells (represented by CD4+ T cells) and the tissues containing those cells, which may block access to ART, HIV-neutralizing antibodies and latency-reversing agents. The latter is the focus of our review, as blood viral load drops below detectable levels after ART, a deeper and more systematic understanding of the HIV tissue reservoirs is imperative. In this review, we take the lymphoid system (including lymph nodes, gut-associated lymphoid tissue, spleen and bone marrow), nervous system, respiratory system, reproductive system (divided into male and female), urinary system as the order, focusing on the particularity and importance of each tissue in HIV infection, the infection target cell types of each tissue, the specific infection situation of each tissue quantified by HIV DNA or HIV RNA and the evidence of compartmentalization and pharmacokinetics. In summary, we found that the present state of HIV in different tissues has both similarities and differences. In the future, the therapeutic principle we need to follow is to respect the discrepancy on the basis of grasping the commonality. The measures taken to completely eliminate the virus in the whole body cannot be generalized. It is necessary to formulate personalized treatment strategies according to the different characteristics of the HIV in the various tissues, so as to realize the prospect of curing AIDS as soon as possible.
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Affiliation(s)
- Kangpeng Li
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Bo Liu
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Rui Ma
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qiang Zhang
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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17
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Rong SY, Guo T, Smith JT, Wang X. The role of cell-to-cell transmission in HIV infection: insights from a mathematical modeling approach. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:12093-12117. [PMID: 37501434 DOI: 10.3934/mbe.2023538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
HIV infection remains a serious global public health problem. Although current drug treatment is effective and can reduce plasma viral loads below the level of detection, it cannot eradicate the virus. The reasons for the low virus persistence despite long-term therapy have not been fully elucidated. In addition, multiple HIV infection, i.e., infection of a cell by multiple viruses, is common and can facilitate viral recombination and mutations, evading the immune system and conferring resistance to drug treatment. The mechanisms for multiple HIV infection formation and their respective contributions remain unclear. To answer these questions, we developed a mathematical modeling framework that encompasses cell-free viral infection and cell-to-cell spread. We fit sub-models that only have one transmission route and the full model containing both to the multi-infection data from HIV-infected patients, and show that the multi-infection data can only be reproduced if these two transmission routes are both considered. Computer simulations with the best-fitting parameter values indicate that cell-to-cell spread leads to the majority of multiple infection and also accounts for the majority of overall infection. Sensitivity analysis shows that cell-to-cell spread has reduced susceptibility to treatment and may explain low HIV persistence. Taken together, this work indicates that cell-to-cell spread plays a crucial role in the development of HIV multi-infection and low HIV persistence despite long-term therapy, and therefore has important implications for understanding HIV pathogenesis and developing more effective treatment strategies to control or even eliminate the disease.
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Affiliation(s)
| | - Ting Guo
- Aliyun School of Big Data, Changzhou University, Changzhou 213164, China
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
| | - J Tyler Smith
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
| | - Xia Wang
- School of Mathematics and Statistics, Xinyang Normal University, Xinyang 464000, China
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
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18
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Jeewanraj N, Mandizvo T, Mulaudzi T, Gumede N, Ndhlovu Z, Ndung'u T, Gounder K, Mann J. Partial compartmentalisation of HIV-1 subtype C between lymph nodes, peripheral blood mononuclear cells and plasma. Virology 2023; 582:62-70. [PMID: 37030154 PMCID: PMC10132742 DOI: 10.1016/j.virol.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
HIV-1 compartmentalisation is likely to have important implications for a preventative vaccine as well as eradication strategies. We genetically characterised HIV-1 subtype C variants in lymph nodes, peripheral blood mononuclear cells and plasma of six antiretroviral (ART) naïve individuals and four individuals on ART. Full-length env (n = 171) and gag (n = 250) sequences were generated from participants using single genome amplification. Phylogenetic relatedness of sequences was assessed, and compartmentalisation was determined using both distance and tree-based methods implemented in HyPhy. Additionally, potential associations between compartmentalisation and immune escape mutations were assessed. Partial viral compartmentalisation was present in nine of the ten participants. Broadly neutralising antibody (bnAb) escape was found to be associated with partial env compartmentalisation in some individuals, while cytotoxic T lymphocyte escape mutations in Gag were limited and did not differ between compartments. Viral compartmentalisation may be an important consideration for bnAb use in viral eradication.
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Affiliation(s)
- Neschika Jeewanraj
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tawanda Mandizvo
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa
| | - Takalani Mulaudzi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombali Gumede
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Zaza Ndhlovu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kamini Gounder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa
| | - Jaclyn Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
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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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20
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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: 39] [Impact Index Per Article: 39.0] [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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21
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Yu T, Zhang M, Zhang H, Zheng J, Shen C, Jiang N, Zou L, Wang J, Yu Y, Zhang Q, Yu S, Huang Y, Huang Y, Zhang J, Qiu C, Zhang W, Meng Z. Evidence of Residual Ongoing Viral Replication in Chronic Hepatitis B Patients Successfully Treated With Nucleos(t)ide Analogues. J Infect Dis 2023; 227:675-685. [PMID: 36546708 DOI: 10.1093/infdis/jiac493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/17/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Chronic hepatitis B is usually treated with nucleos(t)ide analogues (NAs). However, a cure is rarely achieved, even with years of treatment. Here, we investigated whether viral replication is completely halted and how long covalently closed circular DNA (cccDNA) persists in patients successfully treated with NAs. METHODS A series of longitudinal serum samples and a collection of cross-sectional liver biopsies were obtained from patients successfully treated with NAs. Viral variants in serum HBV RNA were enumerated by deep sequencing. Viral replication intermediates in hepatocytes were directly visualized by in situ hybridization. The apparent half-life of each cccDNA was estimated. RESULTS Three of 6 successfully treated patients demonstrated clear evidence of a small proportion of virus evolution, although the overwhelming proportion of variants were identical or possessed a similar degree of divergence through time. The apparent half-life of variants was estimated to be from approximately 7.42 weeks to infinite. Hepatocytes remained positive for cytoplasmic nucleocapsids-associated relaxed circular DNA in 4 of 7 liver needle biopsies. CONCLUSIONS We conclude that even after prolonged treatment, a small proportion of the cccDNA reservoir is constantly replenished by continued low-level HBV replication, whereas a large proportion of the cccDNA reservoir persists over time.
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Affiliation(s)
- Tong Yu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Miaoqu Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Hanyue Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Jianming Zheng
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Chuan Shen
- Department of Infectious Disease, The Third Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
- Clinical Research Center for Infectious Disease of Hebei Province, Shijiazhuang, China
| | - Ning Jiang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Lei Zou
- Department of Infectious Disease, Yancheng Second People's Hospital, Yancheng, China
| | - Jing Wang
- Department of Infectious Disease, Jingan District Central Hospital of Shanghai, Shanghai, China
| | - Yiqi Yu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Qiran Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Shuili Yu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Yanfang Huang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Yuxian Huang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Jiming Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Chao Qiu
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Zhefeng Meng
- Minhang Hospital and Institutes of Biomedical Sciences and Huashan Hospital, Fudan University, Shanghai, China
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22
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Paryad-Zanjani S, Jagarapu A, Piovoso MJ, Zurakowski R. Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.18.529086. [PMID: 36909554 PMCID: PMC10002652 DOI: 10.1101/2023.02.18.529086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Lymph nodes (LNs) serve as a sanctuary site for HIV viruses due to the heterogeneous distribution of the antiretrovirals (ARVs) inside the LNs. There is an ongoing debate whether this represents ongoing cycles of viral replication in the LNs or merely residual virus production by latently infected cells. Previous work has claimed that the measured levels of genetic variation in proviruses sampled from the blood were inconsistent with ongoing replication. However, it is not clear what rate of variation is consistent with ongoing replication in small sanctuary sites. In this study, we used a spherically symmetric compartmental ODE model to track the HIV viral dynamics in the LN and predict the contribution of ongoing replication within the LN to the wholebody proviral pool in an ARV-suppressed patient. This model tracks the reaction-diffusion dynamics of uninfected, actively infected, and latently infected T-cells as well as free virus within the LN parenchyma and the blood, and distinguishes between latently infected cells created before ARV therapy and during ARV therapy. We simulated suppressive therapy beginning in year 5 post-infection. Each LN sanctuary site had a volume of 1 ml, and we considered cases of 1ml, 30ml, and 250ml total volume, which represent a single active sanctuary site, moderate systemic involvement, and involvement of the total lymphoid tissue. Viral load in the blood rapidly dropped and remained below the limit of detection in all cases but remained high in the LN sanctuary sites. Novel latent cells increased systemically over time but very slowly, taking between 25 and 50 years to reach 5% of the total latent pool, depending on the volume of lymphoid tissue involvement. Putative sanctuary sites in LNs are limited in volume and produce novel latent cells slowly. Assays to detect genetic drift due to such sites would require very deep sequencing if sampling only from the blood. Previous studies showing a lack of genetic drift are consistent with the expected contribution of ongoing replication in lymph node sanctuary sites.
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23
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HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy. PLoS Pathog 2022; 18:e1010613. [PMID: 36331974 PMCID: PMC9668181 DOI: 10.1371/journal.ppat.1010613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/16/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The lung is an understudied site of HIV persistence. We isolated 898 subgenomic proviral sequences (nef) by single-genome approaches from blood and lung from nine individuals on long-term suppressive antiretroviral therapy (ART), and characterized genetic diversity and compartmentalization using formal tests. Consistent with clonal expansion as a driver of HIV persistence, identical sequences comprised between 8% to 86% of within-host datasets, though their location (blood vs. lung) followed no consistent pattern. The majority (77%) of participants harboured at least one sequence shared across blood and lung, supporting the migration of clonally-expanded cells between sites. The extent of blood proviral diversity on ART was also a strong indicator of diversity in lung (Spearman's ρ = 0.98, p<0.0001). For three participants, insufficient lung sequences were recovered to reliably investigate genetic compartmentalization. Of the remainder, only two participants showed statistically significant support for compartmentalization when analysis was restricted to distinct proviruses per site, and the extent of compartmentalization was modest in both cases. When all within-host sequences (including duplicates) were considered, the number of compartmentalized datasets increased to four. Thus, while a subset of individuals harbour somewhat distinctive proviral populations in blood and lung, this can simply be due to unequal distributions of clonally-expanded sequences. For two participants, on-ART proviruses were also phylogenetically analyzed in context of plasma HIV RNA populations sampled up to 18 years prior, including pre-ART and during previous treatment interruptions. In both participants, on-ART proviruses represented the most ancestral sequences sampled within-host, confirming that HIV sequences can persist in the body for decades. This analysis also revealed evidence of re-seeding of the reservoir during treatment interruptions. Results highlight the genetic complexity of proviruses persisting in lung and blood during ART, and the uniqueness of each individual's proviral composition. Personalized HIV remission and cure strategies may be needed to overcome these challenges.
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24
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Wang C, Schlub TE, Yu WH, Tan CS, Stefic K, Gianella S, Smith DM, Lauffenburger DA, Chaillon A, Julg B. Landscape of Human Immunodeficiency Virus Neutralization Susceptibilities Across Tissue Reservoirs. Clin Infect Dis 2022; 75:1342-1350. [PMID: 35234862 PMCID: PMC9555844 DOI: 10.1093/cid/ciac164] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) sequence diversity and the presence of archived epitope muta-tions in antibody binding sites are a major obstacle for the clinical application of broadly neutralizing antibodies (bNAbs) against HIV-1. Specifically, it is unclear to what degree the viral reservoir is compartmentalized and if virus susceptibility to antibody neutralization differs across tissues. METHODS The Last Gift cohort enrolled 7 people with HIV diagnosed with a terminal illness and collected antemortem blood and postmortem tissues across 33 anatomical compartments for near full-length env HIV genome sequencing. Using these data, we applied a Bayesian machine-learning model (Markov chain Monte Carlo-support vector machine) that uses HIV-1 envelope sequences and approximated glycan-occupancy information to quantitatively predict the half-maximal inhib-itory concentrations (IC50) of bNAbs, allowing us to map neutralization resistance pattern across tissue reservoirs. RESULTS Predicted mean susceptibilities across tissues within participants were relatively homogenous, and the susceptibility pattern observed in blood often matched what was predicted for tissues. However, selected tissues, such as the brain, showed ev-idence of compartmentalized viral populations with distinct neutralization susceptibilities in some participants. Additionally, we found substantial heterogeneity in the range of neutralization susceptibilities across tissues within and between indi-viduals, and between bNAbs within individuals (standard deviation of log2(IC50) >3.4). CONCLUSIONS Blood-based screening methods to determine viral susceptibility to bNAbs might underestimate the presence of resistant viral variants in tissues. The extent to which these resistant viruses are clinically relevant, that is, lead to bNAb therapeutic failure, needs to be further explored.
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Affiliation(s)
- Chuangqi Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Timothy E Schlub
- University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney, New South Wales, Australia
| | - Wen Han Yu
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, USA
| | - C Sabrina Tan
- Division of Infectious Diseases, Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Karl Stefic
- Department of Virology, Tours University Hospital, Tours, France
| | - Sara Gianella
- Division of Infectious Diseases and Global Public Health, University of California–San Diego, San Diego, California, USA
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California–San Diego, San Diego, California, USA
- VA San Diego Healthcare System, San Diego, California, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California–San Diego, San Diego, California, USA
| | - Boris Julg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
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25
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Adams P, Berkhout B, Pasternak AO. Towards a molecular profile of antiretroviral therapy-free HIV remission. Curr Opin HIV AIDS 2022; 17:301-307. [PMID: 35938464 DOI: 10.1097/coh.0000000000000749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW To summarize the current status and highlight recent findings on predictive biomarkers for posttreatment HIV control (PTC) and virological remission. While historically, many studies focused on virological markers, there is an increasing tendency to enter immune and metabolic factors into the equation. RECENT FINDINGS On the virological side, several groups reported that cell-associated HIV RNA could predict time to viral rebound. Recent data hints at the possible importance of the genic location and chromatin context of the integrated provirus, although these factors still need to be assessed in relation to PTC and virological remission. Evidence from immunological studies highlighted innate and humoral immunity as important factors for prolonged HIV remission. Interestingly, novel metabolic markers have emerged, which offer additional angles to our understanding of latency and viral rebound. SUMMARY Facilitating PTC and virological remission remain top priorities for the HIV cure research. We advocate for clear and precise definitions for both phenomena in order to avoid misconceptions and to strengthen the conclusions that can be drawn. As no one-size-fits-all marker has emerged yet, more biomarkers are on the horizon, and viral rebound is a complex and heterogeneous process, it is likely that a combination of various biomarkers in cohesion will be necessary for a more accurate prediction of antiretroviral therapy-free HIV remission.
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Affiliation(s)
- Philipp Adams
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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26
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Devanathan AS, White NR, Desyaterik Y, De la Cruz G, Nekorchuk M, Terry M, Busman-Sahay K, Adamson L, Luciw P, Fedoriw Y, Estes JD, Rosen EP, Kashuba ADM. Quantitative Imaging Analysis of the Spatial Relationship between Antiretrovirals, Reverse Transcriptase Simian-Human Immunodeficiency Virus RNA, and Fibrosis in the Spleens of Nonhuman Primates. Antimicrob Agents Chemother 2022; 66:e0060922. [PMID: 35856680 PMCID: PMC9380553 DOI: 10.1128/aac.00609-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/07/2022] [Indexed: 01/22/2023] Open
Abstract
Although current antiretroviral therapy (ART) has increased life expectancy, a cure for human immunodeficiency virus (HIV) remains elusive due to the persistence of the virus in tissue reservoirs. In the present study, we sought to elucidate the relationship between antiretrovirals (ARVs) and viral expression in the spleen. We performed mass spectrometry imaging (MSI) of 6 different ARVs, RNAscope in situ hybridization of viral RNA, and immunohistochemistry of three different fibrosis markers in the spleens of 8 uninfected and 10 reverse transcriptase simian-human immunodeficiency virus (RT-SHIV)-infected rhesus macaques (infected for 6 weeks) that had been dosed for 10 days with combination ART. Using MATLAB, computational quantitative imaging analysis was performed to evaluate the spatial and pharmacological relationships between the 6 ARVs, viral RNA, and fibrotic deposition. In these spleens, >50% of the spleen tissue area was not covered by any detectable ARV response (any concentration above the limits of detection for individual ARVs). The median spatial ARV coverage across all tissues was driven by maraviroc followed by efavirenz. Yet >50% of RNA-positive cells were not exposed to any detectable ARV. Quantifiable maraviroc and efavirenz colocalization with RNA-positive cells was usually greater than the in vitro concentration inhibiting 50% replication (IC50). Fibrosis markers covered more than 50% of the spleen tissue area and had negative relationships with cumulative ARV coverages. Our findings suggest that a heterogeneous ARV spatial distribution must be considered when evaluating viral persistence in lymphoid tissue reservoirs.
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Affiliation(s)
| | - Nicole R. White
- UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Yury Desyaterik
- UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Gabriela De la Cruz
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Margaret Terry
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | | | - Paul Luciw
- University of California at Davis, Davis, California, USA
| | - Yuri Fedoriw
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Elias P. Rosen
- UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Angela D. M. Kashuba
- UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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HIV drug resistance in various body compartments. Curr Opin HIV AIDS 2022; 17:205-212. [PMID: 35762375 DOI: 10.1097/coh.0000000000000741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW HIV drug resistance testing using blood plasma or dried blood spots forms part of international guidelines. However, as the clinical utility of assessing drug resistance in other body compartments is less well established, we review this for blood cells and samples from other body compartments. RECENT EVIDENCE Although clinical benefit is not clear, drug resistance testing in blood cells is often performed when patients with suppressed plasma viral loads require a treatment substitution. In patients with HIV neurocognitive disease, cerebral spinal fluid (CSF) drug resistance is rarely discordant with plasma but has nevertheless been used to guide antiretroviral drug substitutions. Cases with HIV drug resistance in genital fluids have been documented but this does not appear to indicate transmission risk when blood plasma viral loads are suppressed. SUMMARY Drug-resistant variants, which may be selected in tissues under conditions of variable adherence and drug penetration, appear to disseminate quickly, and become detectable in blood. This may explain why drug resistance discordance between plasma and these compartments is rarely found. Partial compartmentalization of HIV populations is well established for the CSF and the genital tract but other than blood plasma, evidence is lacking to support drug resistance testing in body compartments.
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Genotypic and Phenotypic Diversity of the Replication-Competent HIV Reservoir in Treated Patients. Microbiol Spectr 2022; 10:e0078422. [PMID: 35770985 PMCID: PMC9431663 DOI: 10.1128/spectrum.00784-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In HIV infection, viral rebound after treatment discontinuation is considered to originate predominantly from viral genomes integrated in resting CD4+ T lymphocytes. Replication-competent proviral genomes represent a minority of the total HIV DNA. While the quantification of the HIV reservoir has been extensively studied, the diversity of genomes that compose the reservoir was less explored. Here, we measured the genotypic and phenotypic diversity in eight patients with different treatment histories. Between 4 and 14 (mean, 8) individual viral isolates per patient were obtained using a virus outgrowth assay, and their near-full-length genomes were sequenced. The mean pairwise distance (MPD) observed in different patients correlated with the time before undetectable viremia was achieved (r = 0.864, P = 0.0194), suggesting that the complexity of the replication-competent reservoir mirrors that present at treatment initiation. No correlation was instead observed between MPD and the duration of successful treatment (mean, 8 years; range, 2 to 21 years). For 5 of the 8 patients, genotypically identical viral isolates were observed in independent wells, suggesting clonal expansion of infected cells. Identical viruses represented between 25 and 60% of the isolates (mean, 48%). The proportion of identical viral isolates correlated with the duration of treatment (r = 0.822, P = 0.0190), suggesting progressive clonal expansion of infected cells during ART. A broader range of infectivity was also observed among isolates from patients with delayed viremia control (r = 0.79, P = 0.025). This work unveiled differences in the genotypic and phenotypic features of the replication-competent reservoir from treated patients and suggests that delaying treatment results in increased diversity of the reservoir. IMPORTANCE In HIV-infected and effectively treated individuals, integrated proviral genomes may persist for decades. The vast majority of the genomes, however, are defective, and only the replication-competent fraction represents a threat of viral reemergence. The quantification of the reservoir has been thoroughly explored, while the diversity of the genomes has been insufficiently studied. Its characterization, however, is relevant for the design of strategies aiming the reduction of the reservoir. Here, we explored the replication-competent near-full-length HIV genomes of eight patients who experienced differences in the delay before viremia control and in treatment duration. We found that delayed effective treatment was associated with increased genetic diversity of the reservoir. The duration of treatment did not impact the diversity but was associated with higher frequency of clonally expanded sequences. Thus, early treatment initiation has the double advantage of reducing both the size and the diversity of the reservoir.
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Fletcher CV, Kroon E, Schacker T, Pinyakorn S, Chomont N, Chottanapund S, Prueksakaew P, Benjapornpong K, Buranapraditkun S, Phanuphak N, Ananworanich J, Vasan S, Hsu D. Persistent HIV transcription and variable antiretroviral drug penetration in lymph nodes during plasma viral suppression. AIDS 2022; 36:985-990. [PMID: 35184069 PMCID: PMC9167254 DOI: 10.1097/qad.0000000000003201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The ability of antiretroviral drugs to penetrate and suppress viral replication in tissue reservoir sites is critical for HIV remission. We evaluated antiretroviral concentrations in lymph nodes and their impact on HIV transcription. METHODS Participants of the RV254/SEARCH010 Acute HIV Infection Cohort in Thailand were enrolled. Group 1 (n = 6) initiated and continued antiretrovirals with two nucleoside reverse transcriptase inhibitors (NRTIs), dolutegravir (DTG) and mar- aviroc (MVC). Group 2 (n = 12) initiated antiretrovirals with two NRTIs as well as efavirenz and were switched to two NRTIs as well as DTG. Antiretroviral concentrations were measured by mass spectroscopy. HIV RNA+ and DNA+ cells were measured by in-situ hybridization. RESULTS All participants were MSM. At lymph node biopsy, all had plasma HIV RNA less than 20 copies/ml. Group 2 had longer durations of antiretroviral and DTG use (medians of 135 and 63 weeks, respectively) compared with Group 1 (median 44 weeks for both). TFV-DP, 3TC-TP, DTG and MVC were quantifiable in all lymph node samples from participants receiving those drugs versus carbovir-triphosphate (CBV-TP) in four out of 14. Median ratios of lymph node to peripheral blood concentrations were DTG, 0.014; MVC, 6.9; CBV-TP, 0.38; 3TC-TP, 0.32; and TFV-DP, 3.78. Median inhibitory quotients [ratios of lymph node concentrations to in-vitro inhibitory levels (IC50-or-90)] were DTG, 0.8; MVC, 38.8; CBV-TP, 0.5; 3TC- TP, 4.1; and TFV-DP, 1.8. Ongoing viral transcription was detected in lymph node of all participants. Median lymph node RNA+ cells were 71 350 versus 99 750 cells/g for Groups 1 and 2, respectively (P = 0.111). CONCLUSION MVC has enhanced lymph node penetration and thereby may contribute to more complete viral suppression in the lymph node.
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Affiliation(s)
- Courtney V Fletcher
- Antiviral Pharmacology Laboratory, UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Eugène Kroon
- SEARCH, Institute of HIV Research and Innovation (IHRI), Bangkok, Thailand
| | - Timothy Schacker
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Universite de Montréal, Montréal, Quebec, Canada
| | | | | | | | | | - Nittaya Phanuphak
- SEARCH, Institute of HIV Research and Innovation (IHRI), Bangkok, Thailand
| | - Jintanat Ananworanich
- Department of Global Health, Amsterdam Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Denise Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
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Rosen EP, Deleage C, White N, Sykes C, Brands C, Adamson L, Luciw P, Estes JD, Kashuba ADM. Antiretroviral drug exposure in lymph nodes is heterogeneous and drug dependent. J Int AIDS Soc 2022; 25:e25895. [PMID: 35441468 PMCID: PMC9018350 DOI: 10.1002/jia2.25895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction HIV reservoirs and infected cells may persist in tissues with low concentrations of antiretrovirals (ARVs). Traditional pharmacology methods cannot assess variability in ARV concentrations within morphologically complex tissues, such as lymph nodes (LNs). We evaluated the distribution of six ARVs into LNs and the proximity of these ARVs to CD4+ T cells and cell‐associated RT‐SHIV viral RNA. Methods Between December 2014 and April 2017, RT‐SHIV infected (SHIV+; N = 6) and healthy (SHIV–; N = 6) male rhesus macaques received two selected four‐drug combinations of six ARVs over 10 days to attain steady‐state conditions. Serial cryosections of axillary LN were analysed by a multimodal imaging approach that combined mass spectrometry imaging (MSI) for ARV disposition, RNAscope in situ hybridization for viral RNA (vRNA) and immunohistochemistry for CD4+ T cell and collagen expression. Spatial relationships across these four imaging domains were investigated by nearest neighbour search on co‐registered images using MATLAB. Results Through MSI, ARV‐dependent, heterogeneous concentrations were observed in different morphological LN regions, such as the follicles and medullary sinuses. After 5–6 weeks of infection, more limited ARV penetration into LN tissue relative to the blood marker heme was found in SHIV+ animals (SHIV+: 0.7 [0.2–1.4] mm; SHIV–: 1.3 [0.5–1.7] mm), suggesting alterations in the microcirculation. However, we found no detectable increase in collagen deposition. Regimen‐wide maps of composite ARV distribution indicated that up to 27% of SHIV+ LN tissue area was not exposed to detectable ARVs. Regions associated with B cell follicles had median 1.15 [0.94–2.69] ‐fold reduction in areas with measurable drug, though differences were only statistically significant for tenofovir (p = 0.03). Median co‐localization of drug with CD4+ target cells and vRNA varied widely by ARV (5.1–100%), but nearest neighbour analysis indicated that up to 10% of target cells and cell‐associated vRNA were not directly contiguous to at least one drug at concentrations greater than the IC50 value. Conclusions Our investigation of the spatial distributions of drug, virus and target cells underscores the influence of location and microenvironment within LN, where a small population of T cells may remain vulnerable to infection and low‐level viral replication during suppressive ART.
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Affiliation(s)
- Elias P Rosen
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Nicole White
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Craig Sykes
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catherine Brands
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Lourdes Adamson
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Paul Luciw
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Angela D M Kashuba
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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31
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Huang H, Song B, Gao L, Cheng J, Mao Y, Zhao H, Tu B, Huang S, Zhang J, Chen D, Zhao P, Jiao YM, Jiang T. Incidence of and risk factors for liver damage in patients with HIV-1 mono-infection receiving antiretroviral therapy. HIV Med 2022; 23 Suppl 1:14-22. [PMID: 35293106 DOI: 10.1111/hiv.13245] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVES The study aimed to investigate the incidence of and risk factors for liver damage in patients with human immunodeficiency virus type-1 (HIV-1) mono-infection receiving antiretroviral therapy (ART). METHODS We retrospectively analyzed the clinical data of patients who were diagnosed with HIV-1 infection and initiated ART from January to December 2017. Among them, 382 patients with HIV-1 mono-infection and normal baseline liver function were included in the analysis. The incidence of liver damage at each follow-up point, and possible risk factors for liver damage were evaluated via COX regression survival analyses. RESULTS The overall incidence of liver damage (grade I-IV) was 27.23% (interquartile range [IQR]: 26.38%-28.72%). Grade I liver damage was most common and accounted for 22.13% of cases (IQR: 21.06%-24.04%), while grade II liver damage accounted for 3.40% of cases (IQR: 3.19%-4.26%). COX regression and survival analyses revealed that baseline body mass index (BMI), alanine aminotransferase (ALT) level, CD4+ T cell count, HIV-1 viral load, and the antiretroviral regimen were significantly correlated with the occurrence of liver damage. Moreover, baseline ALT levels and HIV-1 viral load were identified as independent risk factors for liver damage in patients with HIV-1 mono-infection. CONCLUSION Liver damage is common in patients with HIV-1 mono-infection undergoing ART. Patients with risk factors for liver damage should be well-informed before the initiation of ART, and liver function should be closely monitored during ART even in patients with normal liver function before ART.
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Affiliation(s)
- Huihuang Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Bing Song
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lin Gao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.,Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
| | - Juan Cheng
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yufeng Mao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.,Bengbu Medical College, Bengbu, China
| | - Hua Zhao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Bo Tu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Shun Huang
- Critical Care Unit, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jieli Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Dianjie Chen
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Peng Zhao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yan-Mei Jiao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Tianjun Jiang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
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32
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Lau CY, Adan MA, Maldarelli F. Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. Viruses 2021; 13:2512. [PMID: 34960781 PMCID: PMC8708047 DOI: 10.3390/v13122512] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antiretroviral therapy (ART) effectively reduces cycles of viral replication but does not target proviral populations in cells that persist for prolonged periods and that can undergo clonal expansion. Consequently, chronic human immunodeficiency virus (HIV) infection is sustained during ART by a reservoir of long-lived latently infected cells and their progeny. This proviral landscape undergoes change over time on ART. One of the forces driving change in the landscape is the clonal expansion of infected CD4 T cells, which presents a key obstacle to HIV eradication. Potential mechanisms of clonal expansion include general immune activation, antigenic stimulation, homeostatic proliferation, and provirus-driven clonal expansion, each of which likely contributes in varying, and largely unmeasured, amounts to maintaining the reservoir. The role of clinical events, such as infections or neoplasms, in driving these mechanisms remains uncertain, but characterizing these forces may shed light on approaches to effectively eradicate HIV. A limited number of individuals have been cured of HIV infection in the setting of bone marrow transplant; information from these and other studies may identify the means to eradicate or control the virus without ART. In this review, we describe the mechanisms of HIV-1 persistence and clonal expansion, along with the attempts to modify these factors as part of reservoir reduction and cure strategies.
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Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
- Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
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33
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Siliciano JD, Siliciano RF. In Vivo Dynamics of the Latent Reservoir for HIV-1: New Insights and Implications for Cure. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:271-294. [PMID: 34736342 DOI: 10.1146/annurev-pathol-050520-112001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although antiretroviral therapy (ART) can reduce viremia to below the limit of detection and allow persons living with HIV-1 (PLWH) to lead relatively normal lives, viremia rebounds when treatment is interrupted. Rebound reflects viral persistence in a stable latent reservoir in resting CD4+ T cells. This reservoir is now recognized as the major barrier to cure and is the focus of intense international research efforts. Strategies to cure HIV-1 infection include interventions to eliminate this reservoir, to prevent viral rebound from the reservoir, or to enhance immune responses such that viral replication is effectively controlled. Here we consider recent developments in understanding the composition of the reservoir and how it can be measured in clinical studies. We also discuss exciting new insights into the in vivo dynamics of the reservoir and the reasons for its remarkable stability. Finally we discuss recent discoveries on the complex processes that govern viral rebound. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; .,Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA
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34
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Guo AL, Zhao JF, Gao L, Huang HH, Zhang JY, Zhang C, Song JW, Xu RN, Fan X, Shi M, Jiao YM, Wang FS. HIV-1-Specific CD11c + CD8 + T Cells Display Low PD-1 Expression and Strong Anti-HIV-1 Activity. Front Immunol 2021; 12:757457. [PMID: 34721433 PMCID: PMC8554207 DOI: 10.3389/fimmu.2021.757457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
Exhaustion of HIV-1-specific CD8+ T cells prevents optimal control of HIV-1 infection. Identifying unconventional CD8+ T cell subsets to effectively control HIV-1 replication is vital. In this study, the role of CD11c+ CD8+ T cells during HIV-1 infection was evaluated. The frequencies of CD11c+ CD8+ T cells significantly increased and were negatively correlated with viral load in HIV-1-infected treatment-naïve patients. HIV-1-specific cells were enriched more in CD11c+ CD8+ T cells than in CD11c- CD8+ T cells, which could be induced by HIV-1-derived overlapping peptides, marking an HIV-1-specific CD8+ T cell population. This subset expressed higher levels of activating markers (CD38 and HLA-DR), cytotoxic markers (granzyme B, perforin, and CD107a), and cytokines (IL-2 and TNF-α), with lower levels of PD-1 compared to the CD11c- CD8+ T cell subset. In vitro analysis verified that CD11c+ CD8+ T cells displayed a stronger HIV-1-specific killing capacity than the CD11c- counterparts. These findings indicate that CD11c+ CD8+ T cells have potent immunotherapeutic efficacy in controlling HIV-1 infection.
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Affiliation(s)
- An-Liang Guo
- Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Fang Zhao
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Lin Gao
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China.,Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
| | - Hui-Huang Huang
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ji-Yuan Zhang
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Chao Zhang
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Wen Song
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ruo-Nan Xu
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xing Fan
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ming Shi
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yan-Mei Jiao
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
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35
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Abstract
Future HIV-1 curative therapies require a thorough understanding of the distribution of genetically-intact HIV-1 within T-cell subsets during antiretroviral therapy (ART) and the cellular mechanisms that maintain this reservoir. Therefore, we sequenced near-full-length HIV-1 genomes and identified genetically-intact and genetically-defective genomes from resting naive, stem-cell memory, central memory, transitional memory, effector memory, and terminally-differentiated CD4+ T-cells with known cellular half-lives from 11 participants on ART. We find that a higher infection frequency with any HIV-1 genome was significantly associated with a shorter cellular half-life, such as transitional and effector memory cells. A similar enrichment of genetically-intact provirus was observed in these cells with relatively shorter half-lives. We found that effector memory and terminally-differentiated cells also had significantly higher levels of expansions of genetically-identical sequences, while only transitional and effector memory cells contained genetically-intact proviruses that were part of a cluster of identical sequences. Expansions of identical sequences were used to infer cellular proliferation from clonal expansion. Altogether, this indicates that specific cellular mechanisms such as short half-life and proliferative potential contribute to the persistence of genetically-intact HIV-1. IMPORTANCE The design of future HIV-1 curative therapies requires a more thorough understanding of the distribution of genetically-intact HIV-1 within T-cell subsets as well as the cellular mechanisms that maintain this reservoir. These genetically-intact and presumably replication-competent proviruses make up the latent HIV-1 reservoir. Our investigations into the possible cellular mechanisms maintaining the HIV-1 reservoir in different T-cell subsets have revealed a link between the half-lives of T-cells and the level of proviruses they contain. Taken together, we believe our study shows that more differentiated and proliferative cells, such as transitional and effector memory T-cells, contain the highest levels of genetically-intact proviruses, and the rapid turnover rate of these cells contributes to the expansion of genetically-intact proviruses within them. Therefore, our study delivers an in-depth assessment of the cellular mechanisms, such as cellular proliferation and half-life, that contribute to and maintain the latent HIV-1 reservoir.
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36
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Coffin JM, Hughes SH. Clonal Expansion of Infected CD4+ T Cells in People Living with HIV. Viruses 2021; 13:v13102078. [PMID: 34696507 PMCID: PMC8537114 DOI: 10.3390/v13102078] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 01/16/2023] Open
Abstract
HIV infection is not curable with current antiretroviral therapy (ART) because a small fraction of CD4+ T cells infected prior to ART initiation persists. Understanding the nature of this latent reservoir and how it is created is essential to development of potentially curative strategies. The discovery that a large fraction of the persistently infected cells in individuals on suppressive ART are members of large clones greatly changed our view of the reservoir and how it arises. Rather than being the products of infection of resting cells, as was once thought, HIV persistence is largely or entirely a consequence of infection of cells that are either expanding or are destined to expand, primarily due to antigen-driven activation. Although most of the clones carry defective proviruses, some carry intact infectious proviruses; these clones comprise the majority of the reservoir. A large majority of both the defective and the intact infectious proviruses in clones of infected cells are transcriptionally silent; however, a small fraction expresses a few copies of unspliced HIV RNA. A much smaller fraction is responsible for production of low levels of infectious virus, which can rekindle infection when ART is stopped. Further understanding of the reservoir will be needed to clarify the mechanism(s) by which provirus expression is controlled in the clones of cells that constitute the reservoir.
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Affiliation(s)
- John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA;
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute in Frederick, Frederick, MD 21702, USA
- Correspondence:
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37
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Devanathan AS, Kashuba AD. Human Immunodeficiency Virus Persistence in the Spleen: Opportunities for Pharmacologic Intervention. AIDS Res Hum Retroviruses 2021; 37:725-735. [PMID: 33499746 DOI: 10.1089/aid.2020.0266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The persistence of HIV in the spleen, despite combination antiretroviral therapy, is not well understood. Sustained immune dysregulation and delayed immune recovery, in addition to immune cell exhaustion, may contribute to persistence of infection in the spleen. Eliminating HIV from this secondary lymphoid organ will require a thorough understanding of antiretroviral (ARV) pharmacology in the spleen, which has been minimally investigated. Low ARV exposure within the spleen may hinder the achievement of a functional or sterilizing cure if cells are not protected from HIV infection. In this study, we provide an overview of the anatomy and physiology of the spleen, review the evidence of the spleen as a site for persistence of HIV, discuss the consequences of persistence of HIV in the spleen, address challenges to eradicating HIV in the spleen, and examine opportunities for future curative efforts.
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Affiliation(s)
| | - Angela D.M. Kashuba
- UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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38
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Siliciano JD, Siliciano RF. Low Inducibility of Latent Human Immunodeficiency Virus Type 1 Proviruses as a Major Barrier to Cure. J Infect Dis 2021; 223:13-21. [PMID: 33586775 DOI: 10.1093/infdis/jiaa649] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The latent reservoir for human immunodeficiency virus type 1 (HIV-1) in resting CD4+ T cells is a major barrier to cure. The dimensions of the reservoir problem can be defined with 2 assays. A definitive minimal estimate of the frequency of latently infected cells is provided by the quantitative viral outgrowth assay (QVOA), which detects cells that can be induced by T-cell activation to release infectious virus. In contrast, the intact proviral DNA assay (IPDA) detects all genetically intact proviruses and provides a more accurate upper limit on reservoir size than standard single-amplicon polymerase chain reaction assays which mainly detect defective proviruses. The frequency of cells capable of initiating viral rebound on interruption of antiretroviral therapy lies between the values produced by the QVOA and the IPDA. We argue here that the 1-2-log difference between QVOA and IPDA values in part reflects that the fact that many replication-competent proviruses are not readily induced by T-cell activation. Findings of earlier studies suggest that latently infected cells can be activated to proliferate in vivo without expressing viral genes. The proliferating cells nevertheless retain the ability to produce virus on subsequent stimulation. The low inducibility of latent proviruses is a major problem for the shock-and-kill strategy for curing HIV-1 infection, which uses latency-reversing agents to induce viral gene expression and render infected cells susceptible to immune clearance. The latency-reversing agents developed to date are much less effective at reversing latency than T-cell activation. Taken together, these results indicate that HIV-1 eradication will require the discovery of much more effective ways to induce viral gene expression.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, 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
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39
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Li Y, Mohammadi A, Li JZ. Challenges and Promise of Human Immunodeficiency Virus Remission. J Infect Dis 2021; 223:4-12. [PMID: 33586773 DOI: 10.1093/infdis/jiaa568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Antiretroviral therapy effectively controls human immunodeficiency virus (HIV) replication but it is unable to fully eradicate the HIV reservoir and treatment must be life-long. Progress toward a strategy for HIV remission will require overcoming key hurdles to fill gaps in our understanding of HIV persistence, but the identification of individuals who have attained sterilizing or functional HIV cure show that such a goal is achievable. In this review, we first outline challenges in targeting the HIV reservoir, including difficulties identifying HIV-infected cells, ongoing work elucidating the complex intracellular environment that contribute to HIV latency, and barriers to reactivating and clearing the HIV reservoir. We then review reported cases of HIV sterilizing cure and explore natural models of HIV remission and the promise that such HIV spontaneous and posttreatment controllers may hold in our search for a broadly-applicable strategy for the millions of patients living with HIV.
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Affiliation(s)
- Yijia Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Abbas Mohammadi
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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40
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Abstract
PURPOSE OF REVIEW HIV persists in distinct cellular and anatomical compartments in the body including blood, Central nervous system, and lymphoid tissues (spleen, lymph nodes [LNs], gut-associated lymphoid tissue) by diverse mechanisms despite antiretroviral therapy. Within LNs, human and animal studies have highlighted that a specific CD4 T cell subset - called T follicular helper cells locating in B cell follicles is enriched in cells containing replication-competent HIV as compared to extra-follicular CD4 T cells. Therefore, the objective of the present review is to focus on the potential mechanisms allowing HIV to persist within LN microenvironment. RECENT FINDINGS The combination of factors that might be involved in the regulation of HIV persistence within LNs remain to be fully identified but may include - the level of activation, antiretroviral drug concentrations, presence of cytolytic mechanisms and/or regulatory cells, in addition to cell survival and proliferation propensity which would ultimately determine the fate of HIV-infected cells within LN tissue areas. SUMMARY HIV persistence in blood and distinct body compartments despite long-standing and potent therapy is one of the major barriers to a cure. Given that the HIV reservoir is established early and is highly complex based on composition, viral diversity, distribution, replication competence, migration dynamics across the human body and possible compartmentalization in specific tissues, combinatorial therapeutic approaches are needed that may synergize to target multiple viral reservoirs to achieve a cure for HIV infection.
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Affiliation(s)
- Riddhima Banga
- Divisions of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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Pasternak AO, Vroom J, Kootstra NA, Wit FW, de Bruin M, De Francesco D, Bakker M, Sabin CA, Winston A, Prins JM, Reiss P, Berkhout B. Non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy is associated with lower cell-associated HIV RNA and DNA levels as compared with therapy based on protease inhibitors. eLife 2021; 10:68174. [PMID: 34387543 PMCID: PMC8460250 DOI: 10.7554/elife.68174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/07/2021] [Indexed: 11/28/2022] Open
Abstract
Background: It remains unclear whether combination antiretroviral therapy (ART) regimens differ in their ability to fully suppress human immunodeficiency virus (HIV) replication. Here, we report the results of two cross-sectional studies that compared levels of cell-associated (CA) HIV markers between individuals receiving suppressive ART containing either a non-nucleoside reverse transcriptase inhibitor (NNRTI) or a protease inhibitor (PI). Methods: CA HIV unspliced RNA and total HIV DNA were quantified in two cohorts (n = 100, n = 124) of individuals treated with triple ART regimens consisting of two nucleoside reverse transcriptase inhibitors (NRTIs) plus either an NNRTI or a PI. To compare CA HIV RNA and DNA levels between the regimens, we built multivariable models adjusting for age, gender, current and nadir CD4+ count, plasma viral load zenith, duration of virological suppression, NRTI backbone composition, low-level plasma HIV RNA detectability, and electronically measured adherence to ART. Results: In both cohorts, levels of CA HIV RNA and DNA strongly correlated (rho = 0.70 and rho = 0.54) and both markers were lower in NNRTI-treated than in PI-treated individuals. In the multivariable analysis, CA RNA in both cohorts remained significantly reduced in NNRTI-treated individuals (padj = 0.02 in both cohorts), with a similar but weaker association between the ART regimen and total HIV DNA (padj = 0.048 and padj = 0.10). No differences in CA HIV RNA or DNA levels were observed between individual NNRTIs or individual PIs, but CA HIV RNA was lower in individuals treated with either nevirapine or efavirenz, compared to PI-treated individuals. Conclusions: All current classes of antiretroviral drugs only prevent infection of new cells but do not inhibit HIV RNA transcription in long-lived reservoir cells. Therefore, these differences in CA HIV RNA and DNA levels by treatment regimen suggest that NNRTIs are more potent in suppressing HIV residual replication than PIs, which may result in a smaller viral reservoir size. Funding: This work was supported by ZonMw (09120011910035) and FP7 Health (305522).
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Affiliation(s)
- Alexander O Pasternak
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jelmer Vroom
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ferdinand Wnm Wit
- Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marijn de Bruin
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Davide De Francesco
- Institute for Global Health, University College London, London, United Kingdom
| | - Margreet Bakker
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, United Kingdom
| | - Alan Winston
- Medicine, Imperial College London, London, United Kingdom
| | - Jan M Prins
- Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, New Caledonia
| | - Peter Reiss
- Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Berkhout
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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42
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Martin AR, Bender AM, Hackman J, Kwon KJ, Lynch BA, Bruno D, Martens C, Beg S, Florman SS, Desai N, Segev D, Laird GM, Siliciano JD, Quinn TC, Tobian AAR, Durand CM, Siliciano RF, Redd AD. Similar Frequency and Inducibility of Intact Human Immunodeficiency Virus-1 Proviruses in Blood and Lymph Nodes. J Infect Dis 2021; 224:258-268. [PMID: 33269401 PMCID: PMC8280486 DOI: 10.1093/infdis/jiaa736] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/25/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The human immunodeficiency virus (HIV)-1 latent reservoir (LR) in resting CD4+ T cells is a barrier to cure. LR measurements are commonly performed on blood samples and therefore may miss latently infected cells residing in tissues, including lymph nodes. METHODS We determined the frequency of intact HIV-1 proviruses and proviral inducibility in matched peripheral blood (PB) and lymph node (LN) samples from 10 HIV-1-infected patients on antiretroviral therapy (ART) using the intact proviral DNA assay and a novel quantitative viral induction assay. Prominent viral sequences from induced viral RNA were characterized using a next-generation sequencing assay. RESULTS The frequencies of CD4+ T cells with intact proviruses were not significantly different in PB versus LN (61/106 vs 104/106 CD4+ cells), and they were substantially lower than frequencies of CD4+ T cells with defective proviruses. The frequencies of CD4+ T cells induced to produce high levels of viral RNA were not significantly different in PB versus LN (4.3/106 vs 7.9/106), but they were 14-fold lower than the frequencies of cells with intact proviruses. Sequencing of HIV-1 RNA from induced proviruses revealed comparable sequences in paired PB and LN samples. CONCLUSIONS These results further support the use of PB as an appropriate proxy for the HIV-1 LR in secondary lymphoid organs.
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Affiliation(s)
- Alyssa R Martin
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexandra M Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Jada Hackman
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Briana A Lynch
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Niraj Desai
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dorry Segev
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christine M Durand
- Department of Medicine, Johns Hopkins University School of Medicine, 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
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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43
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Fletcher CV, Dyavar SR, Acharya A, Byrareddy SN. The Contributions of Clinical Pharmacology to HIV Cure Research. Clin Pharmacol Ther 2021; 110:334-345. [PMID: 33763860 DOI: 10.1002/cpt.2237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/10/2021] [Indexed: 01/26/2023]
Abstract
Combination antiretroviral therapy (ART) can suppress plasma HIV-RNA to < 50 copies/mL, decrease HIV transmission, reduce mortality, and improve quality of life for people living with HIV. ART cannot, however, eliminate HIV from an infected individual. The primary barrier to cure HIV infection is the multiple reservoir sites, including adipose tissue, bone marrow, central nervous system, liver, lungs, male and female reproductive system, secondary lymph nodes, and gut-associated lymphoid tissue, established 1 to 2 weeks after acquisition of HIV. Additional challenges include understanding the mechanism(s) by which HIV is maintained at low or undetectable levels and developing treatments that will eradicate or produce a sustained suppression of virus without ART. To date, the most extensive clinical investigations of cure strategies have been the shock-and-kill approach using histone deacetylase inhibitors (HDACis) to induce reactivation of latent HIV. Despite evidence for HIV latency reversal, HDACis alone have not decreased the size of the latent reservoir. Clinical pharmacologic explanations for these results include a low inhibitory quotient (i.e., low potency) within the reservoir sites and intrinsic (e.g., sex differences and reservoir size) and extrinsic (physiochemical and pharmacokinetic drug characteristics) factors. We offer an outline of desired clinical pharmacologic attributes for therapeutics intended for clinical HIV cure research and call for research teams to have early and ongoing involvement of clinical pharmacologists. We believe such a collective effort will provide a solid scientific basis and hope for reaching the goal of a cure for HIV infection.
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Affiliation(s)
- Courtney V Fletcher
- Antiviral Pharmacology Laboratory, Center for Drug Discovery, University of Nebraska Medical Center (UNMC), Omaha, Nebraska, USA
| | - Shetty Ravi Dyavar
- Antiviral Pharmacology Laboratory, Center for Drug Discovery, University of Nebraska Medical Center (UNMC), Omaha, Nebraska, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, UNMC, Omaha, Nebraska, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, UNMC, Omaha, Nebraska, USA
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44
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Abstract
HIV-1 integrates its genome into the DNA of host cells. Consequently, HIV-1 genomes are copied with the host cell DNA during cellular division. Little is known about the emergence and persistence of human immunodeficiency virus (HIV)-infected T-cell clones in perinatally infected children. We analyzed peripheral blood mononuclear cells (PBMCs) for clonal expansion in 11 children who initiated antiretroviral therapy (ART) between 1.8 and 17.4 months of age and with viremia suppressed for 6 to 9 years. We obtained 8,662 HIV type 1 (HIV-1) integration sites from pre-ART samples and 1,861 sites from on-ART samples. Expanded clones of infected cells were detected pre-ART in 10/11 children. In 8 children, infected cell clones detected pre-ART persisted for 6 to 9 years on ART. A comparison of integration sites in the samples obtained on ART with healthy donor PBMCs infected ex vivo showed selection for cells with proviruses integrated in BACH2 and STAT5B. Our analyses indicate that, despite marked differences in T-cell composition and dynamics between children and adults, HIV-infected cell clones are established early in children, persist for up to 9 years on ART, and can be driven by proviral integration in proto-oncogenes.
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45
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Ferreira RC, Prodger JL, Redd AD, Poon AFY. Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir. Virus Evol 2021; 7:veaa104. [PMID: 33505711 PMCID: PMC7816690 DOI: 10.1093/ve/veaa104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Among people living with human immunodeficiency virus type 1 (HIV-1), the long-term persistence of a population of cells carrying transcriptionally silent integrated viral DNA (provirus) remains the primary barrier to developing an effective cure. Ongoing cell division via proliferation is generally considered to be the driving force behind the persistence of this latent HIV-1 reservoir. The contribution of this mechanism (clonal expansion) is supported by the observation that proviral sequences sampled from the reservoir are often identical. This outcome is quantified as the ‘clonality’ of the sample population, e.g. the fraction of provirus sequences observed more than once. However, clonality as a quantitative measure is inconsistently defined and its statistical properties are not well understood. In this Reflections article, we use mathematical and phylogenetic frameworks to formally examine the inherent problems of using clonality to characterize the dynamics and proviral composition of the reservoir. We describe how clonality is not adequate for this task due to the inherent complexity of how infected cells are ‘labeled’ by proviral sequences—the outcome of a sampling process from the evolutionary history of active viral replication before treatment—as well as variation in cell birth and death rates among lineages and over time. Lastly, we outline potential directions in statistical and phylogenetic research to address these issues.
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Affiliation(s)
- Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, 1151 Richmond Street London, ON, Canada
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, 1151 Richmond Street London, ON, Canada
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5640 Fishers Lane Rockville, MD 20852, USA.,Department of Medicine, Johns Hopkins School of Medicine, 600 N. Wolfe Street Baltimore, MD 21205-2196, USA
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, 1151 Richmond Street London, ON, Canada
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46
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Abstract
Currently, the incidence of HIV infection exceeds the death rate from HIV, and as a result, the prevalence of individuals living with the infection continues to increase. A critical limitation preventing the development of curative strategies is the lack of knowledge regarding mechanisms that allow HIV-infected cells to persist in individuals during combination antiviral therapy (ART). In this issue of the JCI, Chaillon and coworkers assessed HIV-infected cells from various anatomic compartments obtained through a rapid autopsy program of individuals undergoing long-term ART. This study, made possible with strong community collaboration, provides new insights on the potential locations of reservoirs of HIV-infected cells that persist during therapy.
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47
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Hu X, Ni Y, Wang F, Ni Z, Jin T, Li Y, Ni M. Identification of molecular mechanisms for achieving HIV-1 control in the absence of antiretroviral therapy. Life Sci 2020; 265:118857. [PMID: 33301809 DOI: 10.1016/j.lfs.2020.118857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 11/26/2022]
Abstract
AIMS Antiretroviral therapy (ART) controls viral replication but cannot eradicate an infected virus and restore the immune response of patients. MATERIALS AND METHODS The gene expression profiles of whole blood, PBMCs, CD4+ and CD8+ T cells were obtained from GSE108297. Coexpression analysis was carried out to evaluate differentially expressed genes (DEGs) between strong and weak responder HIV controllers (HICs). Enrichment analysis was used to explore the biological functions of DEGs. The key genes with common DEGs were screened using the Lasso Cox model. Then, the immune scores of HICs and HAART were calculated by ssGSEA. The content of CD4+ and CD8+ T cells, key genes were verified by flow cytometry, RT-PCR and Western blot analysis. KEY FINDINGS DEGs were clustered into 24 coexpression modules. DEGs related to general immune responses had the highest correlation with strong responding HICs, while DEGs mainly related to the apoptotic process had the highest correlation with weak responder HICs. The hub genes CD8A and CCT2, as well as the key genes TMEM132C and S100A9, were DEGs in HICs and HARRT. The immune score and flow cytometry showed that CD4+ and CD8+ T cells of HICs were lower than those of HARRT in whole blood. Experiments confirmed the expression of key genes in HICs and HARRT. SIGNIFICANCE The key genes identified in this study highlight the strong responder HICs features that to help the immune system control HIV-1 infection. These results will be useful for developing therapeutic targets.
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Affiliation(s)
- Xiaoyuan Hu
- Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, No. 380 Jianquan 1 road, Tianshan District, Urumqi, Xinjiang 830001, China
| | - Yongkang Ni
- School of Public Health, Xinjiang Medical University, No.4 Liyushan Road, Xinshi District, Urumqi, Xinjiang 830000, China
| | - Fengying Wang
- Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, No. 380 Jianquan 1 road, Tianshan District, Urumqi, Xinjiang 830001, China
| | - Zhen Ni
- Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, No. 380 Jianquan 1 road, Tianshan District, Urumqi, Xinjiang 830001, China
| | - Tao Jin
- Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, No. 380 Jianquan 1 road, Tianshan District, Urumqi, Xinjiang 830001, China
| | - Yuefei Li
- School of Public Health, Xinjiang Medical University, No.4 Liyushan Road, Xinshi District, Urumqi, Xinjiang 830000, China
| | - Mingjian Ni
- Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, No. 380 Jianquan 1 road, Tianshan District, Urumqi, Xinjiang 830001, China.
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48
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Wilson A, Lynch RM. Embracing diversity: how can broadly neutralizing antibodies effectively target a diverse HIV-1 reservoir? Curr Opin Pharmacol 2020; 54:173-178. [PMID: 33189993 DOI: 10.1016/j.coph.2020.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022]
Abstract
Genetic diversity in the latent proviral reservoir of HIV-1 infected individuals poses a challenge to cure strategies. It has become increasingly evident that diversity increases proportionally with length of active infection, and that functional and/or sterilizing cure strategies will need to overcome this obstacle in individuals who initiated antiretroviral therapy (ART) during chronic infection. Analyzing the results of analytic treatment interruption (ATI) has allowed for the evaluation of such therapeutic strategies in HIV+ individuals. Strategies to overcome the genetic diversity of the HIV-1 reservoir include antibody combinations, pre-screening individuals for bNAb sensitivity, focusing on low-diversity individuals as well as targeting host proteins.
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Affiliation(s)
- Andrew Wilson
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine & Health Sciences, Washington DC, USA
| | - Rebecca M Lynch
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine & Health Sciences, Washington DC, USA.
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49
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Gantner P, Pagliuzza A, Pardons M, Ramgopal M, Routy JP, Fromentin R, Chomont N. Single-cell TCR sequencing reveals phenotypically diverse clonally expanded cells harboring inducible HIV proviruses during ART. Nat Commun 2020; 11:4089. [PMID: 32796830 PMCID: PMC7427996 DOI: 10.1038/s41467-020-17898-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
Clonal expansions occur in the persistent HIV reservoir as shown by the duplication of proviral integration sites. However, the source of the proliferation of HIV-infected cells remains unclear. Here, we analyze the TCR repertoire of single HIV-infected cells harboring translation-competent proviruses in longitudinal samples from eight individuals on antiretroviral therapy (ART). When compared to uninfected cells, the TCR repertoire of reservoir cells is heavily biased: expanded clonotypes are present in all individuals, account for the majority of reservoir cells and are often maintained over time on ART. Infected T cell clones are detected at low frequencies in the long-lived central memory compartment and overrepresented in the most differentiated memory subsets. Our results indicate that clonal expansions highly contribute to the persistence of the HIV reservoir and suggest that reservoir cells displaying a differentiated phenotype are the progeny of infected central memory cells undergoing antigen-driven clonal expansion during ART. The cause of clonal expansions in the HIV reservoir remains unclear. Here, Gantner et al. perform single-cell TCR sequencing on longitudinal samples from eight individuals on antiretroviral therapy and find that antigens inducing clonal expansions of memory cells are major contributors to the HIV reservoir.
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Affiliation(s)
- Pierre Gantner
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Marion Pardons
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Moti Ramgopal
- Midway Immunology & Research Center, Fort Pierce, FL, USA
| | - Jean-Pierre Routy
- Division of Hematology & Chronic Viral Illness Service, McGill University Heath Centre, Montreal, QC, Canada
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada. .,Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada.
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50
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Kuo HH, Banga R, Lee GQ, Gao C, Cavassini M, Corpataux JM, Blackmer JE, zur Wiesch S, Yu XG, Pantaleo G, Perreau M, Lichterfeld M. Blood and Lymph Node Dissemination of Clonal Genome-Intact Human Immunodeficiency Virus 1 DNA Sequences During Suppressive Antiretroviral Therapy. J Infect Dis 2020; 222:655-660. [PMID: 32236405 PMCID: PMC8493664 DOI: 10.1093/infdis/jiaa137] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/31/2020] [Indexed: 09/09/2023] Open
Abstract
The majority of cells with latent human immunodeficiency virus 1 infection are located in lymphoid tissues that are difficult to access. In the current study, we used single-genome near-full-length proviral sequencing to evaluate intact and defective proviruses in blood and lymph node CD4 T cells enriched for specific functional polarizations. We observed minor variations between the frequencies of proviral sequences within individual CD4 T-cell subsets and across tissue compartments. However, we noted multiple clonal clusters of identical intact or defective proviral sequences from distinct compartments and CD4 T-cell subpopulations, suggesting frequent interchanges between viral reservoir cells in blood and tissues.
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Affiliation(s)
- Hsiao-Hsuan Kuo
- Infectious Disease Division, Brigham and Women’s Hospital,
Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge,
Massachusetts, USA
| | - Riddhima Banga
- University of Lausanne, Lausanne, Switzerland
- Service of Immunology and Allergy, Lausanne University Hospital,
Lausanne, Switzerland
| | - Guinevere Q Lee
- Infectious Disease Division, Brigham and Women’s Hospital,
Boston, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge,
Massachusetts, USA
| | - Matthias Cavassini
- University of Lausanne, Lausanne, Switzerland
- Service of Immunology and Allergy, Lausanne University Hospital,
Lausanne, Switzerland
| | - Jean-Marc Corpataux
- University of Lausanne, Lausanne, Switzerland
- Service of Immunology and Allergy, Lausanne University Hospital,
Lausanne, Switzerland
| | - Jane E Blackmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge,
Massachusetts, USA
| | | | - Xu G Yu
- Infectious Disease Division, Brigham and Women’s Hospital,
Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge,
Massachusetts, USA
| | - Giuseppe Pantaleo
- University of Lausanne, Lausanne, Switzerland
- Service of Immunology and Allergy, Lausanne University Hospital,
Lausanne, Switzerland
| | - Matthieu Perreau
- University of Lausanne, Lausanne, Switzerland
- Service of Immunology and Allergy, Lausanne University Hospital,
Lausanne, Switzerland
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women’s Hospital,
Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge,
Massachusetts, USA
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