1
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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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2
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Klenchin VA, Clark NM, Keles NK, Capuano S, Mason R, Gao G, Broman A, Kose E, Immonen TT, Fennessey CM, Keele BF, Lifson JD, Roederer M, Gardner MR, Evans DT. Adeno-associated viral delivery of Env-specific antibodies prevents SIV rebound after discontinuing antiretroviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.593694. [PMID: 38895320 PMCID: PMC11185534 DOI: 10.1101/2024.05.30.593694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
An alternative to lifelong antiretroviral therapy (ART) is needed to achieve durable control of HIV-1. Here we show that adeno-associated virus (AAV)-delivery of two rhesus macaque antibodies to the SIV envelope glycoprotein (Env) with potent neutralization and antibody-dependent cellular cytotoxicity can prevent viral rebound in macaques infected with barcoded SIVmac239M after discontinuing suppressive ART. Following AAV administration, sustained antibody expression with minimal anti-drug antibody responses was achieved in all but one animal. After ART withdrawal, SIV replication rebounded within two weeks in all of the control animals but remained below the threshold of detection in plasma (<15 copies/mL) for more than a year in four of the eight animals that received AAV vectors encoding Env-specific antibodies. Viral sequences from animals with delayed rebound exhibited restricted barcode diversity and antibody escape. Thus, sustained expression of antibodies with potent antiviral activity can afford durable, ART-free containment of pathogenic SIV infection.
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Affiliation(s)
- Vadim A. Klenchin
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Natasha M. Clark
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Nida K. Keles
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, WI, 53715, USA
| | - Rosemarie Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD, 20892, USA
| | - Guangping Gao
- Deparment of Microbiology and Physiological Systems, University of Massachusetts Medical School; Worcester, MA, 01605, USA
| | - Aimee Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Emek Kose
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research; Frederick, MD, 21702, USA
| | - 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
| | - Brandon F. Keele
- 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
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD, 20892, USA
| | - Matthew R. Gardner
- Division of Infectious Diseases, Department of Medicine, Emory University; Atlanta, GA, 30329, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, WI, 53715, USA
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3
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Keele BF, Okoye AA, Fennessey CM, Varco-Merth B, Immonen TT, Kose E, Conchas A, Pinkevych M, Lipkey L, Newman L, Macairan A, Bosche M, Bosche WJ, Berkemeier B, Fast R, Hull M, Oswald K, Shoemaker R, Silipino L, Gorelick RJ, Duell D, Marenco A, Brantley W, Smedley J, Axthelm M, Davenport MP, Lifson JD, Picker LJ. Early antiretroviral therapy in SIV-infected rhesus macaques reveals a multiphasic, saturable dynamic accumulation of the rebound competent viral reservoir. PLoS Pathog 2024; 20:e1012135. [PMID: 38593120 PMCID: PMC11003637 DOI: 10.1371/journal.ppat.1012135] [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: 12/31/2023] [Accepted: 03/19/2024] [Indexed: 04/11/2024] Open
Abstract
The rebound competent viral reservoir (RCVR)-virus that persists during antiretroviral treatment (ART) and can reignite systemic infection when treatment is stopped-is the primary barrier to eradicating HIV. We used time to initiation of ART during primary infection of rhesus macaques (RMs) after intravenous challenge with barcoded SIVmac239 as a means to elucidate the dynamics of RCVR establishment in groups of RMs by creating a multi-log range of pre-ART viral loads and then assessed viral time-to-rebound and reactivation rates resulting from the discontinuation of ART after one year. RMs started on ART on days 3, 4, 5, 6, 7, 9 or 12 post-infection showed a nearly 10-fold difference in pre-ART viral measurements for successive ART-initiation timepoints. Only 1 of 8 RMs initiating ART on days 3 and 4 rebounded after ART interruption despite measurable pre-ART plasma viremia. Rebounding plasma from the 1 rebounding RM contained only a single barcode lineage detected at day 50 post-ART. All RMs starting ART on days 5 and 6 rebounded between 14- and 50-days post-ART with 1-2 rebounding variants each. RMs starting ART on days 7, 9, and 12 had similar time-to-measurable plasma rebound kinetics despite multiple log differences in pre-ART plasma viral load (pVL), with all RMs rebounding between 7- and 16-days post-ART with 3-28 rebounding lineages. Calculated reactivation rates per pre-ART pVL were highest for RMs starting ART on days 5, 6, and 7 after which the rate of accumulation of the RCVR markedly decreased for RMs treated on days 9 and 12, consistent with multiphasic establishment and near saturation of the RCVR within 2 weeks post infection. Taken together, these data highlight the heterogeneity of the RCVR between RMs, the stochastic establishment of the very early RCVR, and the saturability of the RCVR prior to peak viral infection.
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Affiliation(s)
- Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Afam A. Okoye
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Benjamin Varco-Merth
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Taina T. Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Emek Kose
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Andrew Conchas
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Laura Newman
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Agatha Macairan
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Marjorie Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - William J. Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Randy Fast
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mike Hull
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Lorna Silipino
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Derick Duell
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Alejandra Marenco
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - William Brantley
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Michael Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Louis J. Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
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4
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Ferreira EA, Clements JE, Veenhuis RT. HIV-1 Myeloid Reservoirs - Contributors to Viral Persistence and Pathogenesis. Curr HIV/AIDS Rep 2024; 21:62-74. [PMID: 38411842 DOI: 10.1007/s11904-024-00692-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
PURPOSE OF REVIEW HIV reservoirs are the main barrier to cure. CD4+ T cells have been extensively studied as the primary HIV-1 reservoir. However, there is substantial evidence that HIV-1-infected myeloid cells (monocytes/macrophages) also contribute to viral persistence and pathogenesis. RECENT FINDINGS Recent studies in animal models and people with HIV-1 demonstrate that myeloid cells are cellular reservoirs of HIV-1. HIV-1 genomes and viral RNA have been reported in circulating monocytes and tissue-resident macrophages from the brain, urethra, gut, liver, and spleen. Importantly, viral outgrowth assays have quantified persistent infectious virus from monocyte-derived macrophages and tissue-resident macrophages. The myeloid cell compartment represents an important target of HIV-1 infection. While myeloid reservoirs may be more difficult to measure than CD4+ T cell reservoirs, they are long-lived, contribute to viral persistence, and, unless specifically targeted, will prevent an HIV-1 cure.
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Affiliation(s)
- Edna A Ferreira
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Janice E Clements
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Rebecca T Veenhuis
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA.
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5
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Mudd JC. Quantitative and Qualitative Distinctions between HIV-1 and SIV Reservoirs: Implications for HIV-1 Cure-Related Studies. Viruses 2024; 16:514. [PMID: 38675857 PMCID: PMC11054464 DOI: 10.3390/v16040514] [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: 02/02/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 04/28/2024] Open
Abstract
The persistence of the latent viral reservoir is the main hurdle to curing HIV-1 infection. SIV infection of non-human primates (NHPs), namely Indian-origin rhesus macaques, is the most relevant and widely used animal model to evaluate therapies that seek to eradicate HIV-1. The utility of a model ultimately rests on how accurately it can recapitulate human disease, and while reservoirs in the NHP model behave quantitatively very similar to those of long-term suppressed persons with HIV-1 (PWH) in the most salient aspects, recent studies have uncovered key nuances at the clonotypic level that differentiate the two in qualitative terms. In this review, we will highlight differences relating to proviral intactness, clonotypic structure, and decay rate during ART between HIV-1 and SIV reservoirs and discuss the relevance of these distinctions in the interpretation of HIV-1 cure strategies. While these, to some degree, may reflect a unique biology of the virus or host, distinctions among the proviral landscape in SIV are likely to be shaped significantly by the condensed timeframe of NHP studies. ART is generally initiated earlier in the disease course, and animals are virologically suppressed for shorter periods before receiving interventions. Because these are experimental variables dictated by the investigator, we offer guidance on study design for cure-related studies performed in the NHP model. Finally, we highlight the case of GS-9620 (Vesatolimod), an antiviral TLR7 agonist tested in multiple independent pre-clinical studies in which virological outcomes may have been influenced by study-related variables.
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Affiliation(s)
- Joseph C. Mudd
- Tulane National Primate Research Center, Covington, LA 70433, USA;
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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6
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Lim SY, Lee J, Osuna CE, Vikhe P, Schalk DR, Chen E, Fray E, Kumar M, Schultz-Darken N, Rakasz E, Capuano S, Ladd RA, Gil HM, Evans DT, Jeng EK, Seaman M, Martin M, Van Dorp C, Perelson AS, Wong HC, Siliciano JD, Siliciano R, Safrit JT, Nixon DF, Soon-Shiong P, Nussenzweig M, Whitney JB. Induction of durable remission by dual immunotherapy in SHIV-infected ART-suppressed macaques. Science 2024; 383:1104-1111. [PMID: 38422185 PMCID: PMC11022498 DOI: 10.1126/science.adf7966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The eradication of the viral reservoir represents the major obstacle to the development of a clinical cure for established HIV-1 infection. Here, we demonstrate that the administration of N-803 (brand name Anktiva) and broadly neutralizing antibodies (bNAbs) results in sustained viral control after discontinuation of antiretroviral therapy (ART) in simian-human AD8 (SHIV-AD8)-infected, ART-suppressed rhesus macaques. N-803+bNAbs treatment induced immune activation and transient viremia but only limited reductions in the SHIV reservoir. Upon ART discontinuation, viral rebound occurred in all animals, which was followed by durable control in approximately 70% of all N-803+bNAb-treated macaques. Viral control was correlated with the reprogramming of CD8+ T cells by N-803+bNAb synergy. Thus, complete eradication of the replication-competent viral reservoir is likely not a prerequisite for the induction of sustained remission after discontinuation of ART.
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Affiliation(s)
- So-Yon Lim
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jina Lee
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christa E. Osuna
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Pratik Vikhe
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Dane R. Schalk
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Elsa Chen
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Emily Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mithra Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nancy Schultz-Darken
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Eva Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Ruby A Ladd
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Hwi Min Gil
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - David T. Evans
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | | | - Michael Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Malcolm Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Alan S. Perelson
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | | | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - James B. Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
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7
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Koofhethile CK, Gao C, Chang C, Lian X, Shapiro R, Yu XG, Lichterfeld M, Kanki PJ. The HIV-2 proviral landscape is dominated by defective proviruses. AIDS 2024; 38:309-316. [PMID: 37916471 PMCID: PMC10842655 DOI: 10.1097/qad.0000000000003776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Compared with HIV-1 infection, HIV-2 infection is associated with a slower progression to AIDS. Understanding the persistence of HIV-2 infection might inform the mechanisms responsible for differences in the pathogenicity of HIV-2 versus HIV-1. METHODS In this study, we analyzed the genetic composition of the proviral reservoir in archived blood samples collected from 13 untreated HIV-2-infected adults from Senegal. We used single-genome, near-full-length individual proviral sequencing (FLIP-Seq) to assess the relative frequency of intact and defective proviruses. RESULTS Ten out of 13 (77%) study participants demonstrated virologic suppression (<90 HIV RNA copies/ml) while the remaining 3 (23%) had detectable HIV RNA. We obtained 363 proviral sequences from peripheral blood mononuclear cells (PBMCs) from the 13 study participants. Within these sequences, 342 (94%) defective proviruses were detected. Twenty-one (6%) intact proviruses were detected from three study participants, with one study participant displaying a large clone consisting of 16 genome-intact sequences. CONCLUSION This data suggests that similar to HIV-1 infection, the proviral landscape of HIV-2 is dominated by defective proviruses.
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Affiliation(s)
- Catherine K. Koofhethile
- Harvard T.H. Chan School of Public Health, Boston
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | | | | | | | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
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8
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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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9
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Mu W, Patankar V, Kitchen S, Zhen A. Examining Chronic Inflammation, Immune Metabolism, and T Cell Dysfunction in HIV Infection. Viruses 2024; 16:219. [PMID: 38399994 PMCID: PMC10893210 DOI: 10.3390/v16020219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Chronic Human Immunodeficiency Virus (HIV) infection remains a significant challenge to global public health. Despite advances in antiretroviral therapy (ART), which has transformed HIV infection from a fatal disease into a manageable chronic condition, a definitive cure remains elusive. One of the key features of HIV infection is chronic immune activation and inflammation, which are strongly associated with, and predictive of, HIV disease progression, even in patients successfully treated with suppressive ART. Chronic inflammation is characterized by persistent inflammation, immune cell metabolic dysregulation, and cellular exhaustion and dysfunction. This review aims to summarize current knowledge of the interplay between chronic inflammation, immune metabolism, and T cell dysfunction in HIV infection, and also discusses the use of humanized mice models to study HIV immune pathogenesis and develop novel therapeutic strategies.
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Affiliation(s)
- Wenli Mu
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- UCLA AIDS Institute and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Vaibhavi Patankar
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- UCLA AIDS Institute and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Scott Kitchen
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- UCLA AIDS Institute and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Anjie Zhen
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- UCLA AIDS Institute and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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10
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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to plasma viral clonotypes early after antiretroviral therapy interruption in SIV-infected rhesus macaques. Sci Transl Med 2023; 15:eadi9867. [PMID: 38091409 DOI: 10.1126/scitranslmed.adi9867] [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: 06/01/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023]
Abstract
The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood and tissues from secondary lymphoid organs (spleen, mesenteric lymph nodes, and inguinal lymph nodes) and from the colon, ileum, lung, liver, and brain were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX and RNAscope in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy, although plasma viral RNA remained below 22 copies per milliliter. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. CD4+ T cells were the main cell type harboring viral RNA after ATI. Furthermore, T cell zones in lymphoid tissues showed higher viral RNA abundance than B cell zones for most animals. These findings are consistent with lymphoid tissues contributing to the virus present in plasma early after ATI.
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Affiliation(s)
- Antonio Solis-Leal
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Nongthombam Boby
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Suvadip Mallick
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yilun Cheng
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Fei Wu
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Grey De La Torre
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Jason Dufour
- Tulane National Primate Research Center, 18703 Three Rivers Rd, Covington, LA 70433, USA
| | - Xavier Alvarez
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Vinay Shivanna
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yaozhong Liu
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, New Orleans, LA 70112, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Qingsheng Li
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Binhua Ling
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
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11
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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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12
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Kumar MR, Fray EJ, Bender AM, Zitzmann C, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir. Proc Natl Acad Sci U S A 2023; 120:e2313209120. [PMID: 37844236 PMCID: PMC10614214 DOI: 10.1073/pnas.2313209120] [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: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4+ T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t1/2 = 30.1 d) and a slower second phase (t1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.
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Affiliation(s)
- Mithra R. Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Emily J. Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Alexandra M. Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA02215
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Baltimore, MD21205
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13
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Reeves DB, Bacchus-Souffan C, Fitch M, Abdel-Mohsen M, Hoh R, Ahn H, Stone M, Hecht F, Martin J, Deeks SG, Hellerstein MK, McCune JM, Schiffer JT, Hunt PW. Estimating the contribution of CD4 T cell subset proliferation and differentiation to HIV persistence. Nat Commun 2023; 14:6145. [PMID: 37783718 PMCID: PMC10545742 DOI: 10.1038/s41467-023-41521-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
Persistence of HIV in people living with HIV (PWH) on suppressive antiretroviral therapy (ART) has been linked to physiological mechanisms of CD4+ T cells. Here, in the same 37 male PWH on ART we measure longitudinal kinetics of HIV DNA and cell turnover rates in five CD4 cell subsets: naïve (TN), stem-cell- (TSCM), central- (TCM), transitional- (TTM), and effector-memory (TEM). HIV decreases in TTM and TEM but not in less-differentiated subsets. Cell turnover is ~10 times faster than HIV clearance in memory subsets, implying that cellular proliferation consistently creates HIV DNA. The optimal mathematical model for these integrated data sets posits HIV DNA also passages between CD4 cell subsets via cellular differentiation. Estimates are heterogeneous, but in an average participant's year ~10 (in TN and TSCM) and ~104 (in TCM, TTM, TEM) proviruses are generated by proliferation while ~103 proviruses passage via cell differentiation (per million CD4). In simulations, therapies blocking proliferation and/or enhancing differentiation could reduce HIV DNA by 1-2 logs over 3 years. In summary, HIV exploits cellular proliferation and differentiation to persist during ART but clears faster in more proliferative/differentiated CD4 cell subsets and the same physiological mechanisms sustaining HIV might be temporarily modified to reduce it.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
- Department of Global Health, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA.
| | | | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | | | - Rebecca Hoh
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Mars Stone
- Vitalant Research Institute, 360 Spear St Suite 200, San Francisco, CA, 94105, USA
| | - Frederick Hecht
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Jeffrey Martin
- Epidemiology & Biostatistics, University of California San Francisco School of Medicine, 550 16th Street, San Francisco, CA, 94158, USA
| | - Steven G Deeks
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Marc K Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | - Joseph M McCune
- HIV Frontiers, Global Health Accelerator, Bill & Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98109, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
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14
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Harwood OE, Matschke LM, Moriarty RV, Balgeman AJ, Weaver AJ, Ellis-Connell AL, Weiler AM, Winchester LC, Fletcher CV, Friedrich TC, Keele BF, O’Connor DH, Lang JD, Reynolds MR, O’Connor SL. CD8+ cells and small viral reservoirs facilitate post-ART control of SIV replication in M3+ Mauritian cynomolgus macaques initiated on ART two weeks post-infection. PLoS Pathog 2023; 19:e1011676. [PMID: 37747933 PMCID: PMC10553806 DOI: 10.1371/journal.ppat.1011676] [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: 04/27/2023] [Revised: 10/05/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). None of the MCMs possessed MHC haplotypes previously associated with SIV control. For six months after ART withdrawal, we observed undetectable or transient viremia in seven of the eight MCMs, despite detecting replication competent SIV using quantitative viral outgrowth assays. In vivo depletion of CD8α+ cells induced rebound in all animals, indicating the observed PTC was mediated, at least in part, by CD8α+ cells. With intact proviral DNA assays, we found that MCMs had significantly smaller viral reservoirs two wpi than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. We found a similarly small viral reservoir among six additional SIV+ MCMs in which ART was initiated at eight wpi, some of whom exhibited viral rebound. These results suggest that an unusually small viral reservoir is a hallmark among SIV+ MCMs. By evaluating immunological differences between MCMs that did and did not rebound, we identified that PTC was associated with a reduced frequency of CD4+ and CD8+ lymphocyte subsets expressing exhaustion markers. Together, these results suggest a combination of small reservoirs and immune-mediated virus suppression contribute to PTC in MCMs. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.
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Affiliation(s)
- Olivia E. Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lea M. Matschke
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexis J. Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Abigail J. Weaver
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amy L. Ellis-Connell
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Lee C. Winchester
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Courtney V. Fletcher
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Jessica D. Lang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew R. Reynolds
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
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15
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Wu HL, Busman-Sahay K, Weber WC, Waytashek CM, Boyle CD, Bateman KB, Reed JS, Hwang JM, Shriver-Munsch C, Swanson T, Northrup M, Armantrout K, Price H, Robertson-LeVay M, Uttke S, Kumar MR, Fray EJ, Taylor-Brill S, Bondoc S, Agnor R, Junell SL, Legasse AW, Moats C, Bochart RM, Sciurba J, Bimber BN, Sullivan MN, Dozier B, MacAllister RP, Hobbs TR, Martin LD, Panoskaltsis-Mortari A, Colgin LMA, Siliciano RF, Siliciano JD, Estes JD, Smedley JV, Axthelm MK, Meyers G, Maziarz RT, Burwitz BJ, Stanton JJ, Sacha JB. Allogeneic immunity clears latent virus following allogeneic stem cell transplantation in SIV-infected ART-suppressed macaques. Immunity 2023; 56:1649-1663.e5. [PMID: 37236188 PMCID: PMC10524637 DOI: 10.1016/j.immuni.2023.04.019] [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: 08/15/2022] [Revised: 01/30/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023]
Abstract
Allogeneic hematopoietic stem cell transplantation (alloHSCT) from donors lacking C-C chemokine receptor 5 (CCR5Δ32/Δ32) can cure HIV, yet mechanisms remain speculative. To define how alloHSCT mediates HIV cure, we performed MHC-matched alloHSCT in SIV+, anti-retroviral therapy (ART)-suppressed Mauritian cynomolgus macaques (MCMs) and demonstrated that allogeneic immunity was the major driver of reservoir clearance, occurring first in peripheral blood, then peripheral lymph nodes, and finally in mesenteric lymph nodes draining the gastrointestinal tract. While allogeneic immunity could extirpate the latent viral reservoir and did so in two alloHSCT-recipient MCMs that remained aviremic >2.5 years after stopping ART, in other cases, it was insufficient without protection of engrafting cells afforded by CCR5-deficiency, as CCR5-tropic virus spread to donor CD4+ T cells despite full ART suppression. These data demonstrate the individual contributions of allogeneic immunity and CCR5 deficiency to HIV cure and support defining targets of alloimmunity for curative strategies independent of HSCT.
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Affiliation(s)
- Helen L Wu
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Kathleen Busman-Sahay
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Whitney C Weber
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Courtney M Waytashek
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Carla D Boyle
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Katherine B Bateman
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jason S Reed
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Joseph M Hwang
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Christine Shriver-Munsch
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Tonya Swanson
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Mina Northrup
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Kimberly Armantrout
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Heidi Price
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Mitch Robertson-LeVay
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Samantha Uttke
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Mithra R Kumar
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Emily J Fray
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Sol Taylor-Brill
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Stephen Bondoc
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Rebecca Agnor
- Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stephanie L Junell
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alfred W Legasse
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Cassandra Moats
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Rachele M Bochart
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Joseph Sciurba
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Michelle N Sullivan
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Brandy Dozier
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Rhonda P MacAllister
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Theodore R Hobbs
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Lauren D Martin
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Angela Panoskaltsis-Mortari
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Lois M A Colgin
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Robert F Siliciano
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Janet D Siliciano
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Jacob D Estes
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jeremy V Smedley
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Michael K Axthelm
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Gabrielle Meyers
- Division of Blood and Marrow Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Richard T Maziarz
- Division of Blood and Marrow Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin J Burwitz
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jeffrey J Stanton
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jonah B Sacha
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA.
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16
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Bauer A, Lindemuth E, Marino FE, Krause R, Joy J, Docken SS, Mallick S, McCormick K, Holt C, Georgiev I, Felber B, Keele BF, Veazey R, Davenport MP, Li H, Shaw GM, Bar KJ. Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques. PLoS Pathog 2023; 19:e1011059. [PMID: 37399208 PMCID: PMC10348547 DOI: 10.1371/journal.ppat.1011059] [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: 12/10/2022] [Revised: 07/14/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Transmitted/founder (TF) simian-human immunodeficiency viruses (SHIVs) express HIV-1 envelopes modified at position 375 to efficiently infect rhesus macaques while preserving authentic HIV-1 Env biology. SHIV.C.CH505 is an extensively characterized virus encoding the TF HIV-1 Env CH505 mutated at position 375 shown to recapitulate key features of HIV-1 immunobiology, including CCR5-tropism, a tier 2 neutralization profile, reproducible early viral kinetics, and authentic immune responses. SHIV.C.CH505 is used frequently in nonhuman primate studies of HIV, but viral loads after months of infection are variable and typically lower than those in people living with HIV. We hypothesized that additional mutations besides Δ375 might further enhance virus fitness without compromising essential components of CH505 Env biology. From sequence analysis of SHIV.C.CH505-infected macaques across multiple experiments, we identified a signature of envelope mutations associated with higher viremia. We then used short-term in vivo mutational selection and competition to identify a minimally adapted SHIV.C.CH505 with just five amino acid changes that substantially improve virus replication fitness in macaques. Next, we validated the performance of the adapted SHIV in vitro and in vivo and identified the mechanistic contributions of selected mutations. In vitro, the adapted SHIV shows improved virus entry, enhanced replication on primary rhesus cells, and preserved neutralization profiles. In vivo, the minimally adapted virus rapidly outcompetes the parental SHIV with an estimated growth advantage of 0.14 days-1 and persists through suppressive antiretroviral therapy to rebound at treatment interruption. Here, we report the successful generation of a well-characterized, minimally adapted virus, termed SHIV.C.CH505.v2, with enhanced replication fitness and preserved native Env properties that can serve as a new reagent for NHP studies of HIV-1 transmission, pathogenesis, and cure.
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Affiliation(s)
- Anya Bauer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emily Lindemuth
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Francesco Elia Marino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ryan Krause
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jaimy Joy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Suvadip Mallick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kevin McCormick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Clinton Holt
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ivelin Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Barbara Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ronald Veazey
- Department of Pathology and Laboratory Medicine, Tulane School of Medicine, New Orleans, Louisiana, United States of America
| | | | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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17
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Zhang C, Zaman LA, Poluektova LY, Gorantla S, Gendelman HE, Dash PK. Humanized Mice for Studies of HIV-1 Persistence and Elimination. Pathogens 2023; 12:879. [PMID: 37513726 PMCID: PMC10383313 DOI: 10.3390/pathogens12070879] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
A major roadblock to achieving a cure for human immunodeficiency virus type one (HIV-1) is the persistence of latent viral infections in the cells and tissue compartments of an infected human host. Latent HIV-1 proviral DNA persists in resting memory CD4+ T cells and mononuclear phagocytes (MPs; macrophages, microglia, and dendritic cells). Tissue viral reservoirs of both cell types reside in the gut, lymph nodes, bone marrow, spleen, liver, kidney, skin, adipose tissue, reproductive organs, and brain. However, despite the identification of virus-susceptible cells, several limitations persist in identifying broad latent reservoirs in infected persons. The major limitations include their relatively low abundance, the precise identification of latently infected cells, and the lack of biomarkers for identifying latent cells. While primary MP and CD4+ T cells and transformed cell lines are used to interrogate mechanisms of HIV-1 persistence, they often fail to accurately reflect the host cells and tissue environments that carry latent infections. Given the host specificity of HIV-1, there are few animal models that replicate the natural course of viral infection with any precision. These needs underlie the importance of humanized mouse models as both valuable and cost-effective tools for studying viral latency and subsequently identifying means of eliminating it. In this review, we discuss the advantages and limitations of humanized mice for studies of viral persistence and latency with an eye toward using these models to test antiretroviral and excision therapeutics. The goals of this research are to use the models to address how and under which circumstances HIV-1 latency can be detected and eliminated. Targeting latent reservoirs for an ultimate HIV-1 cure is the task at hand.
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Affiliation(s)
| | | | | | | | | | - Prasanta K. Dash
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA (S.G.)
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18
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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to viral clonotypes present in plasma at early post-ATI in SIV-infected rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542512. [PMID: 37398418 PMCID: PMC10312542 DOI: 10.1101/2023.05.30.542512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The rebound-competent viral reservoir (RCVR), comprised of virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after antiretroviral therapy interruption (ATI), remains the biggest obstacle to the eradication of HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop targeted therapeutic strategies for reducing the RCVR. In this study, barcoded SIVmac239M was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood, lymphoid tissues (LTs, spleen, mesenteric and inguinal lymph nodes), and non-lymphoid tissues (NLTs, colon, ileum, lung, liver, and brain) were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX/RNAscope/ in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy although plasma viral RNA remained < 22 copies/mL. Among the tissues studied, mesenteric and inguinal lymph nodes, and spleen contained viral barcodes detected in plasma, and trended to have higher cell-associated viral loads, higher intact provirus levels, and greater diversity of viral barcodes. CD4+ T cells were the main cell type harboring viral RNA (vRNA) after ATI. Further, T cell zones in LTs showed higher vRNA levels than B cell zones for most animals. These findings are consistent with LTs contributing to virus present in plasma early after ATI. One Sentence Summary The reemerging of SIV clonotypes at early post-ATI are likely from the secondary lymphoid tissues.
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19
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Fray EJ, Wu F, Simonetti FR, Zitzmann C, Sambaturu N, Molina-Paris C, Bender AM, Liu PT, Ventura JD, Wiseman RW, O'Connor DH, Geleziunas R, Leitner T, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants. Cell Host Microbe 2023; 31:356-372.e5. [PMID: 36809762 PMCID: PMC10583177 DOI: 10.1016/j.chom.2023.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 01/24/2023] [Indexed: 02/22/2023]
Abstract
The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in macaques starting ART ∼1 year after infection. Intact SIV genomes in circulating CD4+T cells showed triphasic decay with an initial phase slower than the decay of the plasma virus, a second phase faster than the second phase decay of intact HIV-1, and a stable third phase reached after 1.6-2.9 years. Hypermutated proviruses showed bi- or mono-phasic decay, reflecting different selective pressures. Viruses replicating at ART initiation had mutations conferring antibody escape. With time on ART, viruses with fewer mutations became more prominent, reflecting decay of variants replicating at ART initiation. Collectively, these findings confirm ART efficacy and indicate that cells enter the reservoir throughout untreated infection.
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Affiliation(s)
- Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | - Alexandra M Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Po-Ting Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | | | - Thomas Leitner
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - 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, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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20
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Harwood OE, Matschke LM, Moriarty RV, Balgeman AJ, Weaver AJ, Ellis-Connell AL, Weiler AM, Winchester LC, Fletcher CV, Friedrich TC, Keele BF, O'Connor DH, Lang JD, Reynolds MR, O'Connor SL. CD8+ cells and small viral reservoirs facilitate post-ART control of SIV in Mauritian cynomolgus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530655. [PMID: 36909458 PMCID: PMC10002716 DOI: 10.1101/2023.03.01.530655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). For six months after ART withdrawal, we observed undetectable or transient viremia in seven of eight MCMs. In vivo depletion of CD8α+ cells induced rebound in all animals, indicating the PTC was mediated, at least in part, by CD8α+ cells. We found that MCMs had smaller acute viral reservoirs than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. The mechanisms by which unusually small viral reservoirs and CD8α+ cell-mediated virus suppression enable PTC can be investigated using this MHC-haplomatched MCM model. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.
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Affiliation(s)
- Olivia E Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Lea M Matschke
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
| | - Ryan V Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Alexis J Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Abigail J Weaver
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Amy L Ellis-Connell
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Lee C Winchester
- College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198
| | | | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Jessica D Lang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Matthew R Reynolds
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
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21
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Statzu M, Jin W, Fray EJ, Wong AKH, Kumar MR, Ferrer E, Docken SS, Pinkevych M, McBrien JB, Fennessey CM, Keele BF, Liang S, Harper JL, Mutascio S, Franchitti L, Wang H, Cicetti D, Bosinger SE, Carnathan DG, Vanderford TH, Margolis DM, Garcia-Martinez JV, Chahroudi A, Paiardini M, Siliciano J, Davenport MP, Kulpa DA, Siliciano RS, Silvestri G. CD8 + lymphocytes do not impact SIV reservoir establishment under ART. Nat Microbiol 2023; 8:299-308. [PMID: 36690860 PMCID: PMC9894752 DOI: 10.1038/s41564-022-01311-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/15/2022] [Indexed: 01/24/2023]
Abstract
Persistence of the human immunodeficiency virus type-1 (HIV-1) latent reservoir in infected individuals remains a problem despite fully suppressive antiretroviral therapy (ART). While reservoir formation begins during acute infection, the mechanisms responsible for its establishment remain unclear. CD8+ T cells are important during the initial control of viral replication. Here we examined the effect of CD8+ T cells on formation of the latent reservoir in simian immunodeficiency virus (SIV)-infected macaques by performing experimental CD8+ depletion either before infection or before early (that is, day 14 post-infection) ART initiation. We found that CD8+ depletion resulted in slower decline of viremia, indicating that CD8+ lymphocytes reduce the average lifespan of productively infected cells during acute infection and early ART, presumably through SIV-specific cytotoxic T lymphocyte (CTL) activity. However, CD8+ depletion did not change the frequency of infected CD4+ T cells in the blood or lymph node as measured by the total cell-associated viral DNA or intact provirus DNA assay. In addition, the size of the persistent reservoir remained the same when measuring the kinetics of virus rebound after ART interruption. These data indicate that during early SIV infection, the viral reservoir that persists under ART is established largely independent of CTL control.
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Grants
- P30 AI050409 NIAID NIH HHS
- 75N91019D00024 NCI NIH HHS
- P51 OD011132 NIH HHS
- R01 AI143414 NIAID NIH HHS
- UM1 AI164562 NIAID NIH HHS
- UM1 AI164567 NIAID NIH HHS
- R01 AI125064 NIAID NIH HHS
- CU | National Cancer Institute, Cairo University (NCI)
- National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024/HHSN261201500003I.
- This work was supported by UM1AI164562, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases (to G.S., D.A.K., M.P.1), and NIH NIAID R01-AI143414 (to G.S. and D.A.K), and R01-AI125064 (to G.S., A.C., D.A.K.).
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Affiliation(s)
- Maura Statzu
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Wang Jin
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Kam Ho Wong
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Ferrer
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steffen S Docken
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Mykola Pinkevych
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Julia B McBrien
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shan Liang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Justin L Harper
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Simona Mutascio
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Hong Wang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Davide Cicetti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Diane G Carnathan
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David M Margolis
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - J Victor Garcia-Martinez
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - Ann Chahroudi
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Janet Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Deanna A Kulpa
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Robert S Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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22
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Dai W, Wu F, McMyn N, Song B, Walker-Sperling VE, Varriale J, Zhang H, Barouch DH, Siliciano JD, Li W, Siliciano RF. Genome-wide CRISPR screens identify combinations of candidate latency reversing agents for targeting the latent HIV-1 reservoir. Sci Transl Med 2022; 14:eabh3351. [PMID: 36260688 PMCID: PMC9705157 DOI: 10.1126/scitranslmed.abh3351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Reversing HIV-1 latency promotes killing of infected cells and is essential for cure strategies; however, no single latency reversing agent (LRA) or LRA combination have been shown to reduce HIV-1 latent reservoir size in persons living with HIV-1 (PLWH). Here, we describe an approach to systematically identify LRA combinations to reactivate latent HIV-1 using genome-wide CRISPR screens. Screens on cells treated with suboptimal concentrations of an LRA can identify host genes whose knockout enhances viral gene expression. Therefore, inhibitors of these genes should synergize with the LRA. We tested this approach using AZD5582, an activator of the noncanonical nuclear factor κB (ncNF-κB) pathway, as an LRA and identified histone deacetylase 2 (HDAC2) and bromodomain-containing protein 2 (BRD2), part of the bromodomain and extra-terminal motif (BET) protein family targeted by BET inhibitors, as potential targets. Using CD4+ T cells from PLWH, we confirmed synergy between AZD5582 and several HDAC inhibitors and between AZD5582 and the BET inhibitor, JQ1. A reciprocal screen using suboptimal concentrations of an HDAC inhibitor as an LRA identified BRD2 and ncNF-κB regulators, especially BIRC2, as synergistic candidates for use in combination with HDAC inhibition. Moreover, we identified and validated additional synergistic drug candidates in latency cell line cells and primary lymphocytes isolated from PLWH. Specifically, the knockout of genes encoding CYLD or YPEL5 displayed synergy with existing LRAs in inducing HIV mRNAs. Our study provides insights into the roles of host factors in HIV-1 reactivation and validates a system for identifying drug combinations for HIV-1 latency reversal.
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Affiliation(s)
- Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bicna Song
- Center for Genetic Medicine Research, Children’s National Hospital. 111 Michigan Ave NW, Washington, DC 20010,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010
| | - Victoria E. Walker-Sperling
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hao Zhang
- 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, Massachusetts 02215, USA,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Wei Li
- Center for Genetic Medicine Research, Children’s National Hospital. 111 Michigan Ave NW, Washington, DC 20010,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010,To whom correspondence should be addressed; ;
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205,To whom correspondence should be addressed; ;
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23
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Measuring the latent reservoir for HIV-1: Quantification bias in near full-length genome sequencing methods. PLoS Pathog 2022; 18:e1010845. [PMID: 36074794 PMCID: PMC9488763 DOI: 10.1371/journal.ppat.1010845] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/20/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Antiretroviral therapy (ART) effectively inhibits HIV-1 replication but is not curative due to the persistence of a latent viral reservoir in resting CD4+ T cells. This reservoir is a major barrier to cure. Sequencing studies have revealed that the population of proviruses persisting in ART-treated individuals is dominated by defective proviruses that cannot give rise to viral rebound due to fatal defects including large deletions and APOBEC3-mediated hypermutation. Near full genome sequencing (nFGS) of individual proviruses is used in reservoir assays to provide an estimate of the fraction of proviruses that are intact. nFGS methods rely on a long-distance outer PCR capturing most (~9 kb) of the genome, followed by nested inner PCRs. The outer PCR is carried out at limit dilution, and interpretation of the results is based on the assumption that all proviruses are quantitatively captured. Here, we evaluate nFGS methods using the intact proviral DNA assay (IPDA), a multiplex digital droplet PCR assay that quantitates intact and defective proviruses with single molecule sensitivity using only short, highly efficient amplicons. We analyzed proviral templates of known sequence to avoid the additional complication of sequence polymorphism. With the IPDA, we quantitated molecular yields at each step of nFGS methods. We demonstrate that nFGS methods are inefficient and miss ~70% of full-length proviruses due to amplification failure at the initial outer PCR step. In contrast, proviruses with large internal deletions encompassing 70% of the genome can be quantitatively amplified under the same conditions. Accurate measurement of the latent reservoir of HIV-1 is essential for evaluating the efficacy of cure strategies, and the bias against full length proviruses in nFGS methods must be considered. Despite antiretroviral therapy, HIV-1 persists in a small population of resting memory CD4+ T cells carrying a latent viral genome. This latent reservoir is the major barrier to cure. Accurate reservoir assays are critical for evaluating therapies aimed at reducing the reservoir. Sequencing studies have shown that defective proviruses greatly outnumber the intact, replication-competent proviruses responsible for viral rebound, and reservoir assays that rely on near full-genome sequencing (nFGS) have provided important qualitative information about intact and defective proviruses. However, it is assumed that all proviruses are amplified with equal efficiency in nFGS methods, regardless of sequence length. Here, we rigorously measure the efficiency with which nFGS methods detect intact and defective proviruses using a highly efficient multiplex digital droplet PCR assay, the intact proviral DNA assay. This assay allows direct counting of input proviral template molecules as well as PCR amplified products generated with different nFGS methods. We determined that nFGS methods do not provide an accurate quantitative measure of intact proviruses. Only ~30% of intact proviruses were detected, while proviruses with large internal deletions were amplified at expected frequencies. Our study demonstrates that nFGS methods do not provide accurate quantitative information about the size and composition of the latent reservoir.
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Limited impact of fingolimod treatment during the initial weeks of ART in SIV-infected rhesus macaques. Nat Commun 2022; 13:5055. [PMID: 36030289 PMCID: PMC9420154 DOI: 10.1038/s41467-022-32698-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Antiretroviral therapy (ART) is not curative due to the persistence of a reservoir of HIV-infected cells, particularly in tissues such as lymph nodes, with the potential to cause viral rebound after treatment cessation. In this study, fingolimod (FTY720), a lysophospholipid sphingosine-1-phosphate receptor modulator is administered to SIV-infected rhesus macaques at initiation of ART to block the egress from lymphoid tissues of natural killer and T-cells, thereby promoting proximity between cytolytic cells and infected CD4+ T-cells. When compared with the ART-only controls, FTY720 treatment during the initial weeks of ART induces a profound lymphopenia and increases frequencies of CD8+ T-cells expressing perforin in lymph nodes, but not their killing capacity; FTY720 also increases frequencies of cytolytic NK cells in lymph nodes. This increase of cytolytic cells, however, does not limit measures of viral persistence during ART, including intact proviral genomes. After ART interruption, a subset of animals that initially receives FTY720 displays a modest delay in viral rebound, with reduced plasma viremia and frequencies of infected T follicular helper cells. Further research is needed to optimize the potential utility of FTY720 when coupled with strategies that boost the antiviral function of T-cells in lymphoid tissues.
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25
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Wang X, Vincent E, Siddiqui S, Turnbull K, Lu H, Blair R, Wu X, Watkins M, Ziani W, Shao J, Doyle-Meyers LA, Russell-Lodrigue KE, Bohm RP, Veazey RS, Xu H. Early treatment regimens achieve sustained virologic remission in infant macaques infected with SIV at birth. Nat Commun 2022; 13:4823. [PMID: 35973985 PMCID: PMC9381774 DOI: 10.1038/s41467-022-32554-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 08/04/2022] [Indexed: 01/28/2023] Open
Abstract
Early antiretroviral therapy (ART) in HIV-infected infants generally fails to achieve a sustained state of ART-free virologic remission, even after years of treatment. Our studies show that viral reservoir seeding is different in neonatal macaques intravenously exposed to SIV at birth, in contrast to adults. Furthermore, one month of ART including an integrase inhibitor, initiated at day 3, but not day 4 or 5 post infection, efficiently and rapidly suppresses viremia to undetectable levels. Intervention initiated at day 3 post infection and continued for 9 months achieves a sustained virologic remission in 4 of 5 infants. Collectively, an early intervention strategy within a key timeframe and regimen may result in viral remission or successful post-exposure prophylaxis for neonatal SIV infection, which may be clinically relevant for optimizing treatment strategies for HIV-infected or exposed infants.
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Affiliation(s)
- Xiaolei Wang
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Eunice Vincent
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Summer Siddiqui
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Katherine Turnbull
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Robert Blair
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Meagan Watkins
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Widade Ziani
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Jiasheng Shao
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Lara A Doyle-Meyers
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Kasi E Russell-Lodrigue
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Rudolf P Bohm
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Huanbin Xu
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA.
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26
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Nelson AN, Dennis M, Mangold JF, Li K, Saha PT, Cronin K, Cross KA, Kumar A, Mangan RJ, Shaw GM, Bar KJ, Haynes B, Moody AM, Munir Alam S, Pollara J, Hudgens MG, Van Rompay KKA, De Paris K, Permar SR. Leveraging antigenic seniority for maternal vaccination to prevent mother-to-child transmission of HIV-1. NPJ Vaccines 2022; 7:87. [PMID: 35907918 PMCID: PMC9338948 DOI: 10.1038/s41541-022-00505-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/01/2022] [Indexed: 01/21/2023] Open
Abstract
The development of a maternal HIV vaccine to synergize with current antiretroviral drug prophylaxis can overcome implementation challenges and further reduce mother-to-child transmission (MTCT) of HIV. Both the epitope-specificity and autologous neutralization capacity of maternal HIV envelope (Env)-specific antibodies have been implicated in decreased risk of MTCT of HIV. Our goal was to determine if heterologous HIV Env immunization of SHIV.C.CH505-infected, ART-suppressed female rhesus macaques (RMs) could boost autologous Env-specific antibodies. SHIV.C.CH505-infected female RMs (n = 12), began a daily ART regimen at 12 weeks post-infection (wpi), which was continued for 12 weeks. Starting 2 weeks after ART initiation, RMs received 3 monthly immunizations with HIV b.63521/1086.C gp120 or placebo (n = 6/group) vaccine with adjuvant STR8S-C. Compared to the placebo-immunized animals, Env-vaccinated, SHIV-infected RMs exhibited enhanced IgG binding, avidity, and ADCC responses against the vaccine immunogens and the autologous SHIV.C.CH505 Env. Notably, the Env-specific memory B cells elicited by heterologous vaccination were dominated by cells that recognized the SHIV.C.CH505 Env, the antigen of primary exposure. Thus, vaccination of SHIV-infected, ART-suppressed RMs with heterologous HIV Envs can augment multiple components of the antibody response against the Env antigen of primary exposure, suggesting antigenic seniority. Our results suggest that a universal maternal HIV vaccination regimen can be developed to leverage antigenic seniority in targeting the maternal autologous virus pool.
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Affiliation(s)
- Ashley N Nelson
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Maria Dennis
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Jesse F Mangold
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Katherine Li
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Pooja T Saha
- Gillings School of Public Health and Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Cronin
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Kaitlyn A Cross
- Gillings School of Public Health and Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amit Kumar
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Riley J Mangan
- Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharine J Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Barton Haynes
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Anthony M Moody
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - S Munir Alam
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Justin Pollara
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Michael G Hudgens
- Gillings School of Public Health and Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Kristina De Paris
- Department of Microbiology and Immunology and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sallie R Permar
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA.
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27
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Tokarev A, Machmach K, Creegan M, Kim D, Eller MA, Bolton DL. Single-Cell Profiling of Latently SIV-Infected CD4 + T Cells Directly Ex Vivo to Reveal Host Factors Supporting Reservoir Persistence. Microbiol Spectr 2022; 10:e0060422. [PMID: 35510859 PMCID: PMC9241701 DOI: 10.1128/spectrum.00604-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/02/2022] [Indexed: 11/20/2022] Open
Abstract
HIV-1 cure strategies aiming to eliminate persistent infected cell reservoirs are hampered by a poor understanding of cells harboring viral DNA in vivo. We describe a novel method to identify, enumerate, and characterize in detail individual cells infected in vivo using a combination of single-cell multiplexed assays for integrated proviral DNA, quantitative viral and host gene expression, and quantitative surface protein expression without any in vitro manipulation. Latently infected CD4+ T cells, defined as harboring integrated provirus in the absence of spliced viral mRNA, were identified from macaque lymph nodes during acute, chronic, and combination antiretroviral therapy (cART)-suppressed simian immunodeficiency virus (SIV) infection. Latently infected CD4+ T cells were most abundant during acute SIV (~8% of memory CD4+ T cells) and persisted in chronic and cART-suppressed infection. Productively infected cells actively transcribing viral mRNA, by contrast, were much more labile and declined substantially between acute and chronic or cART-suppressed infection. Expression of most surface proteins and host genes was similar between latently infected cells and uninfected cells. Elevated FLIP mRNA and surface CD3 expression among latently infected cells suggest increased survival potential and capacity to respond to T cell receptor stimulation. These findings point to a large pool of latently infected CD4+ T cells established very early in acute infection and upregulated host factors that may facilitate their persistence in vivo, both of which pose potential challenges to eliminating HIV-1 reservoirs. IMPORTANCE Effective combination antiretroviral therapy controls HIV-1 infection but fails to eliminate latent viral reservoirs that give rise to viremia upon treatment interruption. Strategies to eradicate latently infected cells require a better understanding of their biology and distinguishing features to promote their elimination. Tools for studying these cells from patients are currently limited. Here, we developed a single-cell method to identify cells latently infected in vivo and to characterize these cells for expression of surface proteins and host genes without in vitro manipulation, capturing their in vivo state from SIV-infected macaques. Host factors involved in cell survival and proliferation were upregulated in latently infected cells, which were abundant in the earliest stages of acute infection. These studies provide insight into the basic biology of latently infected cells as well as potential mechanisms underlying the persistence of HIV-1/SIV reservoirs to inform development of novel HIV-1 cure strategies.
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Affiliation(s)
- Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Matthew Creegan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Dohoon Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Michael A. Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
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28
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Walker-Sperling VEK, Mercado NB, Chandrashekar A, Borducchi EN, Liu J, Nkolola JP, Lewis M, Murry JP, Yang Y, Geleziunas R, Robb ML, Michael NL, Pau MG, Wegmann F, Schuitemaker H, Fray EJ, Kumar MR, Siliciano JD, Siliciano RF, Barouch DH. Therapeutic efficacy of combined active and passive immunization in ART-suppressed, SHIV-infected rhesus macaques. Nat Commun 2022; 13:3463. [PMID: 35710819 PMCID: PMC9203527 DOI: 10.1038/s41467-022-31196-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/08/2022] [Indexed: 12/19/2022] Open
Abstract
The latent viral reservoir is the critical barrier for developing an HIV-1 cure. Previous studies have shown that therapeutic vaccination or broadly neutralizing antibody (bNAb) administration, together with a Toll-like receptor 7 (TLR7) agonist, enhanced virologic control or delayed viral rebound, respectively, following discontinuation of antiretroviral therapy (ART) in SIV- or SHIV-infected rhesus macaques. Here we show that the combination of active and passive immunization with vesatolimod may lead to higher rates of post-ART virologic control compared to either approach alone. Therapeutic Ad26/MVA vaccination and PGT121 administration together with TLR7 stimulation with vesatolimod resulted in 70% post-ART virologic control in SHIV-SF162P3-infected rhesus macaques. These data suggest the potential of combining active and passive immunization targeting different immunologic mechanisms as an HIV-1 cure strategy.
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Affiliation(s)
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Erica N Borducchi
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | | | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Maria G Pau
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | - Frank Wegmann
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | | | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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29
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Kreider EF, Bar KJ. HIV-1 Reservoir Persistence and Decay: Implications for Cure Strategies. Curr HIV/AIDS Rep 2022; 19:194-206. [PMID: 35404007 PMCID: PMC10443186 DOI: 10.1007/s11904-022-00604-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), a viral reservoir persists in individuals living with HIV that can reignite systemic replication should treatment be interrupted. Understanding how HIV-1 persists through effective ART is essential to develop cure strategies to induce ART-free virus remission. RECENT FINDINGS The HIV-1 reservoir resides in a pool of CD4-expressing cells as a range of viral species, a subset of which is genetically intact. Recent studies suggest that the reservoir on ART is highly dynamic, with expansion and contraction of virus-infected cells over time. Overall, the intact proviral reservoir declines faster than defective viruses, suggesting enhanced immune clearance or cellular turnover. Upon treatment interruption, rebound viruses demonstrate escape from adaptive and innate immune responses, implicating these selective pressures in restriction of virus reactivation. Cure strategies employing immunotherapy are poised to test whether host immune pressure can be augmented to enhance reservoir suppression or clearance. Alternatively, genomic engineering approaches are being applied to directly eliminate intact viruses and shrink the replication-competent virus pool. New evidence suggests host immunity exerts selective pressure on reservoir viruses and clears HIV-1 infected cells over years on ART. Efforts to build on the detectable, but insufficient, reservoir clearance via empiric testing in clinical trials will inform our understanding of mechanisms of viral persistence and the direction of future cure strategies.
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Affiliation(s)
- Edward F Kreider
- Perelman School of Medicine, University of Pennsylvania, Stemmler Hall Room 130-150, 3450 Hamilton Walk, Philadelphia, PA, 19104-6073, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, 502D Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104‑0673, USA.
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30
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Therapeutic efficacy of an Ad26/MVA vaccine with SIV gp140 protein and vesatolimod in ART-suppressed rhesus macaques. NPJ Vaccines 2022; 7:53. [PMID: 35585080 PMCID: PMC9117189 DOI: 10.1038/s41541-022-00477-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Developing an intervention that results in virologic control following discontinuation of antiretroviral therapy (ART) is a major objective of HIV-1 cure research. In this study, we investigated the therapeutic efficacy of a vaccine consisting of adenovirus serotype 26 (Ad26) and modified vaccinia Ankara (MVA) with or without an SIV Envelope (Env) gp140 protein with alum adjuvant in combination with the TLR7 agonist vesatolimod (GS-9620) in 36 ART-suppressed, SIVmac251-infected rhesus macaques. Ad26/MVA therapeutic vaccination led to robust humoral and cellular immune responses, and the Env protein boost increased antibody responses. Following discontinuation of ART, virologic control was observed in 5/12 animals in each vaccine group, compared with 0/12 animals in the sham control group. These data demonstrate therapeutic efficacy of Ad26/MVA vaccination with vesatolimod but no clear additional benefit of adding an Env protein boost. SIV-specific cellular immune responses correlated with virologic control. Our findings show partial efficacy of therapeutic vaccination following ART discontinuation in SIV-infected rhesus macaques.
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31
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Harper J, Ribeiro SP, Chan CN, Aid M, Deleage C, Micci L, Pino M, Cervasi B, Raghunathan G, Rimmer E, Ayanoglu G, Wu G, Shenvi N, Barnard RJ, Del Prete GQ, Busman-Sahay K, Silvestri G, Kulpa DA, Bosinger SE, Easley KA, Howell BJ, Gorman D, Hazuda DJ, Estes JD, Sekaly RP, Paiardini M. Interleukin-10 contributes to reservoir establishment and persistence in SIV-infected macaques treated with antiretroviral therapy. J Clin Invest 2022; 132:e155251. [PMID: 35230978 PMCID: PMC9012284 DOI: 10.1172/jci155251] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Interleukin-10 (IL-10) is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper (Tfh) cell differentiation and germinal center formation. In SIV-infected macaques, levels of IL-10 in plasma and lymph nodes (LNs) were induced by infection and not normalized with antiretroviral therapy (ART). During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including Tfh cells, and predicted the frequency of CD4+ Tfh cells and their cell-associated SIV-DNA content during ART, respectively. In ART-treated rhesus macaques, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B cell follicle in proximity to IL-10. Finally, we demonstrated that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques reduced B cell follicle maintenance and, by extension, LN memory CD4+ T cells, including Tfh cells and those expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.
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Affiliation(s)
- Justin Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Susan P. Ribeiro
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Luca Micci
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Discovery Oncology, Merck & Co., Inc., Boston, Massachusetts, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Barbara Cervasi
- Flow Cytometry Core, Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | | | - Eric Rimmer
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., South San Francisco, California, USA
| | - Gulesi Ayanoglu
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., South San Francisco, California, USA
| | - Guoxin Wu
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Neeta Shenvi
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Richard J.O. Barnard
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Kathleen Busman-Sahay
- 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
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kirk A. Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Bonnie J. Howell
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | | | - Daria J. Hazuda
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, 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
| | | | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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32
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White JA, Simonetti FR, Beg S, McMyn NF, Dai W, Bachmann N, Lai J, Ford WC, Bunch C, Jones JL, Ribeiro RM, Perelson AS, Siliciano JD, Siliciano RF. Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proc Natl Acad Sci U S A 2022; 119:e2120326119. [PMID: 35110411 PMCID: PMC8833145 DOI: 10.1073/pnas.2120326119] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4+ T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ∼3 mo, the decay slope changes, and CD4+ T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie F McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas Bachmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - William C Ford
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christina Bunch
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joyce L Jones
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ruy M Ribeiro
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - 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;
- HHMI, Baltimore, MD 21205
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33
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Shah S, Wong LM, Ellis K, Bodnar B, Saribas S, Ting J, Wei Z, Tang Y, Wang X, Wang H, Ling B, Margolis DM, Garcia JV, Hu W, Jiang G. Microglia-Specific Promoter Activities of HEXB Gene. Front Cell Neurosci 2022; 16:808598. [PMID: 35360489 PMCID: PMC8960132 DOI: 10.3389/fncel.2022.808598] [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: 11/03/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Adeno-associated virus (AAV)-mediated genetic targeting of microglia remains a challenge. Overcoming this hurdle is essential for gene editing in the central nervous system (CNS). Here, we characterized the minimal/native promoter of the HEXB gene, which is known to be specifically and stably expressed in the microglia during homeostatic and pathological conditions. Dual reporter and serial deletion assays identified the critical role of the natural 5' untranslated region (-97 bp related to the first ATG) in driving transcriptional activity of the mouse Hexb gene. The native promoter region of mouse, human, and monkey HEXB are located at -135, -134, and -170 bp to the first ATG, respectively. These promoters were highly active and specific in microglia with strong cross-species transcriptional activities, but did not exhibit activity in primary astrocytes. In addition, we identified a 135 bp promoter of CD68 gene that was highly active in microglia but not in astrocytes. Considering that HEXB is specifically expressed in microglia, these data suggest that the newly characterized microglia-specific HEXB minimal/native promoter can be an ideal candidate for microglia-targeting AAV gene therapy in the CNS.
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Affiliation(s)
- Sahil Shah
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Lilly M Wong
- University of North Carolina HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kendra Ellis
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Brittany Bodnar
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Sami Saribas
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Julia Ting
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Zhengyu Wei
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Yuyang Tang
- University of North Carolina HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Xianwei Wang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Hong Wang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Binhua Ling
- Southwest National Primate Research Center, Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - David M Margolis
- University of North Carolina HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, Microbiology and Immunology, Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Wenhui Hu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Guochun Jiang
- University of North Carolina HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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34
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Dashti A, Singh V, Chahroudi A. HIV Reservoirs: Modeling, Quantification, and Approaches to a Cure. Methods Mol Biol 2022; 2407:215-228. [PMID: 34985668 DOI: 10.1007/978-1-0716-1871-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biomedical research in animal models depends heavily on nonhuman primates (NHP) (Phillips et al., Am J Primatol 76(9):801-827, 2014). In their physiology, neurobiology, and, most importantly, their susceptibility to infectious diseases and subsequent immune responses, NHPs have many parallels with humans (Rhesus Macaque Genome Sequencing and Analysis Consortium et al., Science 316(5822):222-234, 2007). Different species of NHPs have served as important animal models for numerous infectious diseases spanning a wide range of pathogens (Gardner and Luciw, ILAR J 49(2):220-255, 2008). As a result of recognizing their utility in HIV research, NHPs have contributed to groundbreaking studies of disease pathogenesis, vaccination, and curative research (London et al., Lancet 2(8355):869-873, 1983; Henrickson et al., Lancet 1 (8321):388-390, 1983). Many African NHPs are considered natural hosts for SIV in which SIV infection is usually nonprogressive and does not cause acquired immunodeficiency syndrome (AIDS) (Chahroudi et al., Science 335(6073):1188-1193, 2012; Taaffe et al., J Virol 84(11):5476-5484, 2010). However, cross-species transmission of SIV strains to other NHPs or to humans (nonnatural hosts) leads to progressive disease and AIDS (Paiardini et al., Annu Rev Med 60:485-495, 2009). In particular, SIV infection of Asian rhesus macaques recapitulates many features of HIV infection in humans and therefore has become a widely used approach for contemporary HIV research into virus persistence and cure strategies (Gardner and Luciw, FASEB J 3(14):2593-2606, 1989). There are multiple factors that should be considered in HIV/SIV studies using NHPs including the particular monkey species and geographic background, age and sex, certain genetic properties, virus strain, route and dose of infection, interventional treatments, and prespecified study outcomes. Here, we discuss consideration of these factors to address specific questions in HIV cure research.
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Affiliation(s)
- Amir Dashti
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Vidisha Singh
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Ann Chahroudi
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA.
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35
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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: 23] [Impact Index Per Article: 7.7] [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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36
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Rahman SA, Yagnik B, Bally AP, Morrow KN, Wang S, Vanderford TH, Freeman GJ, Ahmed R, Amara RR. PD-1 blockade and vaccination provide therapeutic benefit against SIV by inducing broad and functional CD8 + T cells in lymphoid tissue. Sci Immunol 2021; 6:eabh3034. [PMID: 34516743 DOI: 10.1126/sciimmunol.abh3034] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Sheikh Abdul Rahman
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Bhrugu Yagnik
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Alexander P Bally
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Kristen N Morrow
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Shelly Wang
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gordon J Freeman
- Department of Medical Oncology and Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Rafi Ahmed
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Rama Rao Amara
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
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37
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Margolis DM. Measuring the Haystack's Needles. J Infect Dis 2021; 223:184-186. [PMID: 32823275 DOI: 10.1093/infdis/jiaa533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- David M Margolis
- Department of Medicine, Division of Infectious Diseases, University of North Carolina HIV Cure Center, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.,Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, 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: 24] [Impact Index Per Article: 8.0] [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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Advances in simian--human immunodeficiency viruses for nonhuman primate studies of HIV prevention and cure. Curr Opin HIV AIDS 2021; 15:275-281. [PMID: 32769631 DOI: 10.1097/coh.0000000000000645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Simian--human immunodeficiency viruses (SHIVs), chimeric viruses that encode HIV-1 Env within an SIV backbone, are key reagents for nonhuman primate studies of antibody-based vaccines, broadly neutralizing antibodies (bnAbs), and other Env-targeting reagents. Here, we discuss the provenance and characteristics of currently relevant SHIVs, novel technical advances, recent discoveries enabled by SHIV challenge studies, and the continued development of SHIVs for persistence and cure experiments. RECENT FINDINGS SHIV SF162P3, SHIV AD8EO, and transmitter/founder SHIVs with Env375 mutations are now common reagents in nonhuman primate studies, with increased use and validation establishing their properties and potential applications. Genetic barcoding of SIV and SHIV, which allows tracing of individual lineages and elucidation of viral kinetics from transmission through latency has expanded the experimental capacity of SHIV models. SHIV challenge studies have determined the neutralizing antibody titers that correlate with protection for passive and active immunization and enabled complementary human and nonhuman primate studies of vaccine development. SHIV models of latency continue to evolve, aided by descriptions of SHIV persistence on ART and the proviral landscape. SUMMARY Recent advances and more thorough characterization of SHIVs allow for expanded applications and greater confidence in experimental results.
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40
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Bricker KM, Chahroudi A, Mavigner M. New Latency Reversing Agents for HIV-1 Cure: Insights from Nonhuman Primate Models. Viruses 2021; 13:1560. [PMID: 34452425 PMCID: PMC8402914 DOI: 10.3390/v13081560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 01/30/2023] Open
Abstract
Antiretroviral therapy (ART) controls human immunodeficiency virus 1 (HIV-1) replication and prevents disease progression but does not eradicate HIV-1. The persistence of a reservoir of latently infected cells represents the main barrier to a cure. "Shock and kill" is a promising strategy involving latency reversing agents (LRAs) to reactivate HIV-1 from latently infected cells, thus exposing the infected cells to killing by the immune system or clearance agents. Here, we review advances to the "shock and kill" strategy made through the nonhuman primate (NHP) model, highlighting recently identified latency reversing agents and approaches such as mimetics of the second mitochondrial activator of caspase (SMACm), experimental CD8+ T cell depletion, immune checkpoint blockade (ICI), and toll-like receptor (TLR) agonists. We also discuss the advantages and limits of the NHP model for HIV cure research and methods developed to evaluate the efficacy of in vivo treatment with LRAs in NHPs.
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Affiliation(s)
- Katherine M. Bricker
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Emory + Children’s Center for Childhood Infections and Vaccines, Atlanta, GA 30322, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
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41
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Busman-Sahay K, Starke CE, Nekorchuk MD, Estes JD. Eliminating HIV reservoirs for a cure: the issue is in the tissue. Curr Opin HIV AIDS 2021; 16:200-208. [PMID: 34039843 PMCID: PMC8171814 DOI: 10.1097/coh.0000000000000688] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW Advances in antiretroviral therapy have saved numerous lives, converting a diagnosis with human immunodeficiency virus 1 (HIV-1) from a death sentence into the possibility for a (nearly) normal life in many instances. However, the obligation for lifelong adherence, increased risk of accumulated co-morbidities, and continued lack of uniform availability around the globe underscores the need for an HIV cure. Safe and scalable HIV cure strategies remain elusive, in large part due to the presence of viral reservoirs in which caches of infected cells remain hidden from immune elimination, primarily within tissues. Herein, we summarize some of the most exciting recent advances focused on understanding, quantifying, and ultimately targeting HIV tissue viral reservoirs. RECENT FINDINGS Current studies have underscored the differences between viral reservoirs in tissue compartments as compared to peripheral blood, in particular, the gastrointestinal (GI) tract. Additionally, several novel or modified techniques are showing promise in targeting the latent viral reservoir, including modifications in drug delivery platforms and techniques such as CRISPR. SUMMARY Elimination of tissue viral reservoirs is likely the key to generation of an effective HIV cure. Exciting studies have come out recently that reveal crucial insights into topics ranging from the basic biology of reservoir seeding to effective drug targeting. However, there are still many outstanding questions in the field about the relative importance of specific reservoirs, such as the GI tract, that may alter the final strategy pursued.
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Affiliation(s)
- Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon
| | - Carly E. Starke
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon
| | - Michael D. Nekorchuk
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon
- Division of Pathobiology & Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon
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42
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Rausch JW, Le Grice SFJ. Characterizing the Latent HIV-1 Reservoir in Patients with Viremia Suppressed on cART: Progress, Challenges, and Opportunities. Curr HIV Res 2021; 18:99-113. [PMID: 31889490 PMCID: PMC7475929 DOI: 10.2174/1570162x18666191231105438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Modern combination antiretroviral therapy (cART) can bring HIV-1 in blood plasma to level undetectable by standard tests, prevent the onset of acquired immune deficiency syndrome (AIDS), and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, cART is not curative, as within a few weeks of treatment cessation, HIV viremia in most patients rebounds to pre-cART levels. The primary source of this rebound, and the principal barrier to a cure, is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of resting memory CD4+ T cells. In this review, prevailing models for how the latent reservoir is established and maintained, residual viremia and viremic rebound upon withdrawal of cART, and the types and characteristics of cells harboring latent HIV-1 will be discussed. Selected technologies currently being used to advance our understanding of HIV latency will also be presented, as will a perspective on which areas of advancement are most essential for producing the next generation of HIV-1 therapeutics.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
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43
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Robust expansion of HIV CAR T cells following antigen boosting in ART-suppressed nonhuman primates. Blood 2021; 136:1722-1734. [PMID: 32614969 DOI: 10.1182/blood.2020006372] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/15/2020] [Indexed: 12/22/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cells targeting CD19+ hematologic malignancies have rapidly emerged as a promising, novel therapy. In contrast, results from the few CAR T-cell studies for infectious diseases such as HIV-1 have been less convincing. These challenges are likely due to the low level of antigen present in antiretroviral therapy (ART)-suppressed patients in contrast to those with hematologic malignancies. Using our well-established nonhuman primate model of ART-suppressed HIV-1 infection, we tested strategies to overcome these limitations and challenges. We first optimized CAR T-cell production to maintain central memory subsets, consistent with current clinical paradigms. We hypothesized that additional exogenous antigen might be required in an ART-suppressed setting to aid expansion and persistence of CAR T cells. Thus, we studied 4 simian/HIV-infected, ART-suppressed rhesus macaques infused with virus-specific CD4CAR T cells, followed by supplemental infusion of cell-associated HIV-1 envelope (Env). Env boosting led to significant and unprecedented expansion of virus-specific CAR+ T cells in vivo; after ART treatment interruption, viral rebound was significantly delayed compared with controls (P = .014). In 2 animals with declining CAR T cells, rhesusized anti-programmed cell death protein 1 (PD-1) antibody was administered to reverse PD-1-dependent immune exhaustion. Immune checkpoint blockade triggered expansion of exhausted CAR T cells and concordantly lowered viral loads to undetectable levels. These results show that supplemental cell-associated antigen enables robust expansion of CAR T cells in an antigen-sparse environment. To our knowledge, this is the first study to show expansion of virus-specific CAR T cells in infected, suppressed hosts, and delay/control of viral recrudescence.
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44
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Immonen TT, Fennessey CM, Lipkey L, Thorpe A, Del Prete GQ, Lifson JD, Davenport MP, Keele BF. Transient viral replication during analytical treatment interruptions in SIV infected macaques can alter the rebound-competent viral reservoir. PLoS Pathog 2021; 17:e1009686. [PMID: 34143853 PMCID: PMC8244872 DOI: 10.1371/journal.ppat.1009686] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/30/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Analytical treatment interruptions (ATIs) of antiretroviral therapy (ART) play a central role in evaluating the efficacy of HIV-1 treatment strategies targeting virus that persists despite ART. However, it remains unclear if ATIs alter the rebound-competent viral reservoir (RCVR), the virus population that persists during ART and from which viral recrudescence originates after ART discontinuation. To assess the impact of ATIs on the RCVR, we used a barcode sequence tagged SIV to track individual viral lineages through a series of ATIs in Rhesus macaques. We demonstrate that transient replication of individual rebounding lineages during an ATI can lead to their enrichment in the RCVR, increasing their probability of reactivating again after treatment discontinuation. These data establish that the RCVR can be altered by uncontrolled replication during ATI.
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Affiliation(s)
- Taina T. Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Abigail Thorpe
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, New South Wales, Australia
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
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Li H, Wang S, Lee FH, Roark RS, Murphy AI, Smith J, Zhao C, Rando J, Chohan N, Ding Y, Kim E, Lindemuth E, Bar KJ, Pandrea I, Apetrei C, Keele BF, Lifson JD, Lewis MG, Denny TN, Haynes BF, Hahn BH, Shaw GM. New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure. J Virol 2021; 95:JVI.00071-21. [PMID: 33658341 PMCID: PMC8139694 DOI: 10.1128/jvi.00071-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
Previously, we showed that substitution of HIV-1 Env residue 375-Ser by bulky aromatic residues enhances binding to rhesus CD4 and enables primary HIV-1 Envs to support efficient replication as simian-human immunodeficiency virus (SHIV) chimeras in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing SHIVs containing ten primary Envs corresponding to HIV-1 subtypes A, B, C, AE and AG. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4+ T cells, but only one replicated efficiently in primary rhesus cells. This was a subtype AE SHIV that naturally contained His at Env375. Replacement of wildtype Env375 residues by Trp, Tyr, Phe or His in the other nine SHIVs led to efficient replication in rhesus CD4+ T cells in vitro and in vivo Nine SHIVs containing optimized Env375 alleles were grown large-scale in primary rhesus CD4+ T cells to serve as challenge stocks in preclinical prevention trials. These virus stocks were genetically homogeneous, native-like in Env antigenicity and tier-2 neutralization sensitivity, and transmissible by rectal, vaginal, penile, oral or intravenous routes. To facilitate future SHIV constructions, we engineered a simplified second-generation design scheme and validated it in RMs. Overall, our findings demonstrate that SHIVs bearing primary Envs with bulky aromatic substitutions at Env375 consistently replicate in RMs, recapitulating many features of HIV-1 infection in humans. Such SHIVs are efficiently transmitted by mucosal routes common to HIV-1 infection and can be used to test vaccine efficacy in preclinical monkey trials.ImportanceSHIV infection of Indian rhesus macaques is an important animal model for studying HIV-1 transmission, prevention, immunopathogenesis and cure. Such research is timely, given recent progress with active and passive immunization and novel approaches to HIV-1 cure. Given the multifaceted roles of HIV-1 Env in cell tropism and virus entry, and as a target for neutralizing and non-neutralizing antibodies, Envs selected for SHIV construction are of paramount importance. Until recently, it has been impossible to strategically design SHIVs bearing clinically relevant Envs that replicate consistently in monkeys. This changed with the discovery that bulky aromatic substitutions at residue Env375 confer enhanced affinity to rhesus CD4. Here, we show that 10 new SHIVs bearing primary HIV-1 Envs with residue 375 substitutions replicated efficiently in RMs and could be transmitted efficiently across rectal, vaginal, penile and oral mucosa. These findings suggest an expanded role for SHIVs as a model of HIV-1 infection.
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Affiliation(s)
- Hui Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fang-Hua Lee
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ryan S Roark
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alex I Murphy
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica Smith
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chengyan Zhao
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Juliette Rando
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Neha Chohan
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yu Ding
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eunlim Kim
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emily Lindemuth
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine J Bar
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ivona Pandrea
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Levy CN, Hughes SM, Roychoudhury P, Reeves DB, Amstuz C, Zhu H, Huang ML, Wei Y, Bull ME, Cassidy NA, McClure J, Frenkel LM, Stone M, Bakkour S, Wonderlich ER, Busch MP, Deeks SG, Schiffer JT, Coombs RW, Lehman DA, Jerome KR, Hladik F. A highly multiplexed droplet digital PCR assay to measure the intact HIV-1 proviral reservoir. Cell Rep Med 2021; 2:100243. [PMID: 33948574 PMCID: PMC8080125 DOI: 10.1016/j.xcrm.2021.100243] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 01/16/2023]
Abstract
Quantifying the replication-competent HIV reservoir is essential for evaluating curative strategies. Viral outgrowth assays (VOAs) underestimate the reservoir because they fail to induce all replication-competent proviruses. Single- or double-region HIV DNA assays overestimate it because they fail to exclude many defective proviruses. We designed two triplex droplet digital PCR assays, each with 2 unique targets and 1 in common, and normalize the results to PCR-based T cell counts. Both HIV assays are specific, sensitive, and reproducible. Together, they estimate the number of proviruses containing all five primer-probe regions. Our 5-target results are on average 12.1-fold higher than and correlate with paired quantitative VOA (Spearman's ρ = 0.48) but estimate a markedly smaller reservoir than previous DNA assays. In patients on antiretroviral therapy, decay rates in blood CD4+ T cells are faster for intact than for defective proviruses, and intact provirus frequencies are similar in mucosal and circulating T cells.
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Affiliation(s)
- Claire N. Levy
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Sean M. Hughes
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chelsea Amstuz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Yulun Wei
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Marta E. Bull
- Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Noah A.J. Cassidy
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jan McClure
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lisa M. Frenkel
- Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mars Stone
- Vitalent Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of San Francisco, San Francisco, CA, USA
- School of Medicine, University of San Francisco, San Francisco, CA, USA
| | - Sonia Bakkour
- Vitalent Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of San Francisco, San Francisco, CA, USA
- School of Medicine, University of San Francisco, San Francisco, CA, USA
| | - Elizabeth R. Wonderlich
- Department of Infectious Disease Research, Southern Research, 431 Aviation Way, Frederick, MD, USA
| | - Michael P. Busch
- Vitalent Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of San Francisco, San Francisco, CA, USA
| | - Steven G. Deeks
- School of Medicine, University of San Francisco, San Francisco, CA, USA
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert W. Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dara A. Lehman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Florian Hladik
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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47
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Okoye AA, Duell DD, Fukazawa Y, Varco-Merth B, Marenco A, Behrens H, Chaunzwa M, Selseth AN, Gilbride RM, Shao J, Edlefsen PT, Geleziunas R, Pinkevych M, Davenport MP, Busman-Sahay K, Nekorchuk M, Park H, Smedley J, Axthelm MK, Estes JD, Hansen SG, Keele BF, Lifson JD, Picker LJ. CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification. J Clin Invest 2021; 131:141677. [PMID: 33630764 PMCID: PMC8262469 DOI: 10.1172/jci141677] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
To define the contribution of CD8+ T cell responses to control of SIV reactivation during and following antiretroviral therapy (ART), we determined the effect of long-term CD8+ T cell depletion using a rhesusized anti-CD8β monoclonal antibody on barcoded SIVmac239 dynamics on stable ART and after ART cessation in rhesus macaques (RMs). Among the RMs with full CD8+ T cell depletion in both blood and tissue, there were no significant differences in the frequency of viral blips in plasma, the number of SIV RNA+ cells and the average number of RNA copies/infected cell in tissue, and levels of cell-associated SIV RNA and DNA in blood and tissue relative to control-treated RMs during ART. Upon ART cessation, both CD8+ T cell-depleted and control RMs rebounded in fewer than 12 days, with no difference in the time to viral rebound or in either the number or growth rate of rebounding SIVmac239M barcode clonotypes. However, effectively CD8+ T cell-depleted RMs showed a stable, approximately 2-log increase in post-ART plasma viremia relative to controls. These results indicate that while potent antiviral CD8+ T cell responses can develop during ART-suppressed SIV infection, these responses effectively intercept post-ART SIV rebound only after systemic viral replication, too late to limit reactivation frequency or the early spread of reactivating SIV reservoirs.
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Affiliation(s)
- Afam A. Okoye
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Derick D. Duell
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Yoshinori Fukazawa
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Benjamin Varco-Merth
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Alejandra Marenco
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Hannah Behrens
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Morgan Chaunzwa
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Andrea N. Selseth
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Roxanne M. Gilbride
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jason Shao
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Paul T. Edlefsen
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Mykola Pinkevych
- Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, New South Wales, Australia
| | - Miles P. Davenport
- Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, New South Wales, Australia
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Haesun Park
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Michael K. Axthelm
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Scott G. Hansen
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Jeffery D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Louis J. Picker
- Vaccine and Gene Therapy Institute and
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
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48
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Immune Responses and Viral Persistence in Simian/Human Immunodeficiency Virus SHIV.C.CH848-Infected Rhesus Macaques. J Virol 2021; 95:JVI.02198-20. [PMID: 33568508 PMCID: PMC8104099 DOI: 10.1128/jvi.02198-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/01/2021] [Indexed: 01/16/2023] Open
Abstract
SHIVs have been extensively used in a nonhuman primate (NHP) model for HIV research. In this study, we investigated viral reservoirs in tissues and immune responses in an NHP model inoculated with newly generated transmitted/founder HIV-1 clade C-based SHIV.C.CH848. Chimeric simian/human immunodeficiency viruses (SHIVs) are widely used in nonhuman primate models to recapitulate human immunodeficiency virus (HIV) infection in humans, yet most SHIVs fail to establish persistent viral infection. We investigated immunological and virological events in rhesus macaques infected with the newly developed SHIV.C.CH848 (SHIVC) and treated with combined antiretroviral therapy (cART). Similar to HIV/simian immunodeficiency virus (SIV) infection, SHIV.C.CH848 infection established viral reservoirs in CD4+ T cells and myeloid cells, accompanied by productive infection and depletion of CD4+ T cells in systemic and lymphoid tissues throughout SHIV infection. Despite 6 months of cART-suppressed viral replication, integrated proviral DNA levels remained stable, especially in CD4+ T cells, and the viral rebound was also observed after ART interruption. Autologous neutralizing antibodies to the parental HIV-1 strain CH848 were detected, with limited viral evolution at 5 months postinfection. In comparison, heterogenous neutralizing antibodies in SHIV.C.CH848-infected macaques were not detected except for 1 (1 of 10) animal at 2 years postinfection. These findings suggest that SHIV.C.CH848, a novel class of transmitted/founder SHIVs, can establish sustained viremia and viral reservoirs in rhesus macaques with clinical immunodeficiency consequences, providing a valuable SHIV model for HIV research. IMPORTANCE SHIVs have been extensively used in a nonhuman primate (NHP) model for HIV research. In this study, we investigated viral reservoirs in tissues and immune responses in an NHP model inoculated with newly generated transmitted/founder HIV-1 clade C-based SHIV.C.CH848. The data show that transmitted founder (T/F) SHIVC infection of macaques more closely recapitulates the virological and clinical features of HIV infection, including persistent viremia and viral rebound once antiretroviral therapy is discontinued. These results suggest this CCR5-tropic, SHIVC strain is valuable for testing responses to HIV vaccines and therapeutics.
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49
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Swanstrom AE, Immonen TT, Oswald K, Pyle C, Thomas JA, Bosche WJ, Silipino L, Hull M, Newman L, Coalter V, Wiles A, Wiles R, Kiser J, Morcock DR, Shoemaker R, Fast R, Breed MW, Kramer J, Donohue D, Malys T, Fennessey CM, Trubey CM, Deleage C, Estes JD, Lifson JD, Keele BF, Del Prete GQ. Antibody-mediated depletion of viral reservoirs is limited in SIV-infected macaques treated early with antiretroviral therapy. J Clin Invest 2021; 131:142421. [PMID: 33465055 PMCID: PMC7954603 DOI: 10.1172/jci142421] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/13/2021] [Indexed: 12/22/2022] Open
Abstract
The effectiveness of virus-specific strategies, including administered HIV-specific mAbs, to target cells that persistently harbor latent, rebound-competent HIV genomes during combination antiretroviral therapy (cART) has been limited by inefficient induction of viral protein expression. To examine antibody-mediated viral reservoir targeting without a need for viral induction, we used an anti-CD4 mAb to deplete both infected and uninfected CD4+ T cells. Ten rhesus macaques infected with barcoded SIVmac239M received cART for 93 weeks starting 4 days after infection. During cART, 5 animals received 5 to 6 anti-CD4 antibody administrations and CD4+ T cell populations were then allowed 1 year on cART to recover. Despite profound CD4+ T cell depletion in blood and lymph nodes, time to viral rebound following cART cessation was not significantly delayed in anti-CD4-treated animals compared with controls. Viral reactivation rates, determined based on rebounding SIVmac239M clonotype proportions, also were not significantly different in CD4-depleted animals. Notably, antibody-mediated depletion was limited in rectal tissue and negligible in lymphoid follicles. These results suggest that, even if robust viral reactivation can be achieved, antibody-mediated viral reservoir depletion may be limited in key tissue sites.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Duncan Donohue
- DMS Applied Information and Management Sciences, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Tyler Malys
- DMS Applied Information and Management Sciences, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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50
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Persistence of viral RNA in lymph nodes in ART-suppressed SIV/SHIV-infected Rhesus Macaques. Nat Commun 2021; 12:1474. [PMID: 33674572 PMCID: PMC7935896 DOI: 10.1038/s41467-021-21724-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/04/2021] [Indexed: 01/01/2023] Open
Abstract
The establishment of a long-lived viral reservoir is the key obstacle for achieving an HIV-1 cure. However, the anatomic, virologic, and immunologic features of the viral reservoir in tissues during antiretroviral therapy (ART) remain poorly understood. Here we present a comprehensive necroscopic analysis of the SIV/SHIV viral reservoir in multiple lymphoid and non-lymphoid tissues from SIV/SHIV-infected rhesus macaques suppressed with ART for one year. Viral DNA is observed broadly in multiple tissues and is comparable in animals that had initiated ART at week 1 or week 52 of infection. In contrast, viral RNA is restricted primarily to lymph nodes. Ongoing viral RNA transcription is not the result of unsuppressed viral replication, as single-genome amplification and subsequent phylogenetic analysis do not show evidence of viral evolution. Gag-specific CD8+ T cell responses are predominantly observed in secondary lymphoid organs in animals chronically infected prior to ART and these responses are dominated by CD69+ populations. Overall, we observe that the viral reservoir in rhesus macaques is widely distributed across multiple tissue sites and that lymphoid tissues act as a site of persistent viral RNA transcription under conditions of long-term ART suppression. The existence of HIV reservoir and ongoing replication despite antiretroviral therapy (ART) represents a barrier for cure efforts. Here, using SIV/SHIV-infected rhesus macaque suppressed with ART for one year, the authors characterize multiple lymphoid and non-lymphoid tissues and show that while the viral reservoir exhibits a wide anatomic heterogeneity, persistent viral transcription is mainly restricted to secondary lymphoid organs.
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