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Semenova L, Wang Y, Falcinelli S, Archin N, Cooper-Volkheimer AD, Margolis DM, Goonetilleke N, Murdoch DM, Rudin CD, Browne EP. Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567386. [PMID: 38014340 PMCID: PMC10680759 DOI: 10.1101/2023.11.16.567386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Understanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host-reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A Leave-One-Covariate-Out (LOCO) inference approach identified specific HIV reservoir and clinical-demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical-demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, machine learning algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA. The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.
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Armani-Tourret M, Bone B, Tan TS, Sun W, Bellefroid M, Struyve T, Louella M, Yu XG, Lichterfeld M. Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure. Nat Rev Microbiol 2024; 22:328-344. [PMID: 38337034 PMCID: PMC11131351 DOI: 10.1038/s41579-024-01010-8] [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] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Successful approaches for eradication or cure of HIV-1 infection are likely to include immunological mechanisms, but remarkably little is known about how human immune responses can recognize and interact with the few HIV-1-infected cells that harbour genome-intact viral DNA, persist long term despite antiretroviral therapy and represent the main barrier to a cure. For a long time regarded as being completely shielded from host immune responses due to viral latency, these cells do, on closer examination with single-cell analytic techniques, display discrete footprints of immune selection, implying that human immune responses may be able to effectively engage and target at least some of these cells. The failure to eliminate rebound-competent virally infected cells in the majority of persons likely reflects the evolution of a highly selected pool of reservoir cells that are effectively camouflaged from immune recognition or rely on sophisticated approaches for resisting immune-mediated killing. Understanding the fine-tuned interplay between host immune responses and viral reservoir cells will help to design improved interventions that exploit the immunological vulnerabilities of HIV-1 reservoir cells.
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Affiliation(s)
- Marie Armani-Tourret
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Bone
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Toong Seng Tan
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Weiwei Sun
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Maxime Bellefroid
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tine Struyve
- HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Michael Louella
- Community Advisory Board, Delaney AIDS Research Enterprise (DARE), San Francisco, CA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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Liu Z, Julius P, Himwaze CM, Mucheleng’anga LA, Chapple AG, West JT, Wood C. Cannabis Use Associates With Reduced Proviral Burden and Inflammatory Cytokine in Tissues From Men With Clade C HIV-1 on Suppressive Antiretroviral Therapy. J Infect Dis 2024; 229:1306-1316. [PMID: 38243412 PMCID: PMC11095553 DOI: 10.1093/infdis/jiad575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/09/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Human immunodeficiency virus 1 (HIV-1) tissue reservoirs remain the main obstacle against an HIV cure. Limited information exists regarding cannabis's effects on HIV-1 infections in vivo, and the impact of cannabis use on HIV-1 parenchymal tissue reservoirs is unexplored. METHODS To investigate whether cannabis use alters HIV-1 tissue reservoirs, we systematically collected 21 postmortem brain and peripheral tissues from 20 men with subtype C HIV-1 and with suppressed viral load enrolled in Zambia, 10 of whom tested positive for cannabis use. The tissue distribution and copies of subtype C HIV-1 LTR, gag, env DNA and RNA, and the relative mRNA levels of cytokines IL-1β, IL-6, IL-10, and TGF-β1 were quantified using PCR-based approaches. Utilizing generalized linear mixed models we compared persons with HIV-1 and suppressed viral load, with and without cannabis use. RESULTS The odds of tissues harboring HIV-1 DNA and the viral DNA copies in those tissues were significantly lower in persons using cannabis. Moreover, the transcription levels of proinflammatory cytokines IL-1β and IL-6 in lymphoid tissues of persons using cannabis were also significantly lower. CONCLUSIONS Our findings suggested that cannabis use is associated with reduced sizes and inflammatory cytokine expression of subtype C HIV-1 reservoirs in men with suppressed viral load.
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Affiliation(s)
- Zhou Liu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center,New Orleans, Louisiana, USA
| | - Peter Julius
- Department of Pathology and Microbiology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Cordilia Maria Himwaze
- Department of Pathology and Microbiology, University of Zambia School of Medicine, Lusaka, Zambia
| | | | - Andrew G Chapple
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center,New Orleans, Louisiana, USA
| | - John T West
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center,New Orleans, Louisiana, USA
| | - Charles Wood
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center,New Orleans, Louisiana, USA
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Zhang Z, Reece MD, Roa S, Tyor W, Franklin DR, Letendre SL, Marconi VC, Anderson AM, Gavegnano C. The identification of intact HIV proviral DNA from human cerebrospinal fluid. Neurotherapeutics 2024; 21:e00373. [PMID: 38749843 DOI: 10.1016/j.neurot.2024.e00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 07/15/2024] Open
Abstract
We evaluated the HIV-1 DNA reservoir in peripheral blood mononuclear cells (PBMC) and cerebrospinal fluid (CSF) in people with HIV (PWH) and associations to cognitive dysfunction. Using the intact proviral DNA assay (IPDA), an emerging technique to identify provirus that may be the source of viral rebound, we assessed HIV DNA in CSF and PBMC in PWH regardless of antiretroviral therapy (ART). CSF was used as a sampling surrogate for the central nervous system (CNS) as opposed to tissue. IDPA results (3' defective, 5' defective, and intact HIV DNA) were analyzed by compartment (Wilcoxon signed rank; matched and unmatched pairs). Cognitive performance, measured via a battery of nine neuropsychological (NP) tests, were analyzed for correlation to HIV DNA (Spearman's rho). 11 CSF and 8 PBMC samples from PWH were evaluated both unmatched and matched. Total CSF HIV DNA was detectable in all participants and was significantly higher than in matched PBMCs (p = 0.0039). Intact CSF HIV DNA was detected in 7/11 participants and correlated closely with those in PBMCs but tended to be higher in CSF than in PBMC. CSF HIV DNA did not correlate with global NP performance, but higher values did correlate with worse executive function (p = 0.0440). Intact HIV DNA is frequently present in the CSF of PWH regardless of ART. This further supports the presence of an HIV CNS reservoir and provides a method to study CNS reservoirs during HIV cure studies. Larger studies are needed to evaluate relationships with CNS clinical outcomes.
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Affiliation(s)
- Zhan Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Atlanta VA Medical Center, Atlanta, GA, USA
| | - Monica D Reece
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sebastian Roa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - William Tyor
- Atlanta VA Medical Center, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Donald R Franklin
- Department of Psychiatry, University of California at San Diego School of Medicine, La Jolla, CA, USA
| | - Scott L Letendre
- Department of Medicine, Division of Infectious Diseases, University of California at San Diego School of Medicine, La Jolla, CA, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA; Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Albert M Anderson
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Christina Gavegnano
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA; Center for the Study of Human Health, Emory College, Atlanta, GA, USA; Harvard Medical School, Center for Bioethics, Boston, MA, USA.
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Fombellida-Lopez C, Berkhout B, Darcis G, Pasternak AO. Persistent HIV-1 transcription during ART: time to reassess its significance? Curr Opin HIV AIDS 2024; 19:124-132. [PMID: 38502547 PMCID: PMC10990031 DOI: 10.1097/coh.0000000000000849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), HIV-1 reservoirs persist and reignite viral replication if therapy is interrupted. Persistence of the viral reservoir in people with HIV-1 (PWH) is the main obstacle to an HIV-1 cure. The reservoirs are not transcriptionally silent, and viral transcripts can be detected in most ART-treated individuals. Here, we review the recent progress in the characterization of persistent HIV-1 transcription during ART. RECENT FINDINGS Evidence from several studies indicates that, although cell-associated unspliced (US) HIV-1 RNA is abundantly expressed in ART-treated PWH, intact full-length US transcripts are rare and most US RNA is derived from defective proviruses. The transcription- and translation-competent defective proviruses, previously considered irrelevant, are increasingly being linked to residual HIV-1 pathogenesis under suppressive ART. Recent data suggest a continuous crosstalk between the residual HIV-1 activity under ART and the immune system. Persistent HIV-1 transcription on ART, despite being mostly derived from defective proviruses, predicts viral rebound upon therapy interruption, suggesting its role as an indicator of the strength of the host antiviral immune response that is shaping the viral rebound. SUMMARY In light of the recent findings, the significance of persistent HIV-1 transcription during ART for the long-term health of PWH and the cure research should be reassessed.
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Affiliation(s)
- Céline Fombellida-Lopez
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gilles Darcis
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
- Department of General Internal Medicine and Infectious Diseases, University Hospital of Liège, Liège, Belgium
| | - Alexander O. Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Lee SK, Sondgeroth A, Xu Y, Warren J, Zhou S, Gilleece M, Hauser BM, Gay CL, Kuruc JD, Archin NM, Eron JJ, Margolis DM, Goonetilleke N, Swanstrom R. Sequence Analysis of Inducible, Replication-Competent Virus Reveals No Evidence of HIV-1 Evolution During Suppressive Antiviral Therapy, Indicating a Lack of Ongoing Viral Replication. Open Forum Infect Dis 2024; 11:ofae212. [PMID: 38756763 PMCID: PMC11097118 DOI: 10.1093/ofid/ofae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/14/2024] [Indexed: 05/18/2024] Open
Abstract
Background Persistence of HIV-1 in reservoirs necessitates life-long antiretroviral therapy (ART). There are conflicting data using genetic analysis on whether persistence includes an actively replicating reservoir with strong evidence arguing against replication. Methods We investigated the possibility of ongoing viral evolution during suppressive therapy by comparing near full-length viral genomic sequences using phylogenetic analysis of viral RNA in plasma before therapy initiation early after infection and from virus induced to grow from the latent reservoir after a period of suppressive ART. We also focused our analysis on evidence of selective pressure by drugs in the treatment regimen and at sites of selective pressure by the adaptive immune response. Results Viral genomes induced to grow from the latent reservoir from 10 participants with up to 9 years on suppressive ART were highly similar to the nearly homogeneous sequences in plasma taken early after infection at ART initiation. This finding was consistent across the entire genome and when the analysis focused on sites targeted by the drug regimen and by host selective pressure of antibody and cytotoxic T cells. The lack of viral evolution away from pretherapy sequences in spite of demonstrated selective pressure is most consistent with a lack of viral replication during reservoir persistence. Conclusions These results do not support ongoing viral replication as a mechanism of HIV-1 persistence during suppressive ART.
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Affiliation(s)
- Sook-Kyung Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amy Sondgeroth
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yinyan Xu
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joanna Warren
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maria Gilleece
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Blake M Hauser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Cynthia L Gay
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - JoAnn D Kuruc
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancie M Archin
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M Margolis
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nilu Goonetilleke
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
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Bone B, Lichterfeld M. "Block and lock" viral integration sites in persons with drug-free control of HIV-1 infection. Curr Opin HIV AIDS 2024; 19:110-115. [PMID: 38457193 DOI: 10.1097/coh.0000000000000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
PURPOSE OF REVIEW Elite controllers (ECs) and Posttreatment controllers (PTCs) represent a small subset of individuals who are capable of maintaining drug-free control of HIV plasma viral loads despite the persistence of a replication-competent viral reservoir. This review aims to curate recent experimental studies evaluating viral reservoirs that distinguish EC/PTC and may contribute to their ability to maintain undetectable viral loads in the absence of antiretroviral therapy. RECENT FINDINGS Recent studies on ECs have demonstrated that integration sites of intact proviruses in EC/PTC are markedly biased towards heterochromatin regions; in contrast, intact proviruses in accessible and permissive chromatin were profoundly underrepresented. Of note, no such biases were noted when CD4 + T cells from EC were infected directly ex vivo, suggesting that the viral reservoir profile in EC is not related to altered integration site preferences during acute infection, but instead represents the result of immune-mediated selection mechanisms that can eliminate proviruses in transcriptionally-active euchromatin regions while promoting preferential persistence of intact proviruses in nonpermissive genome regions. Proviral transcription in such "blocked and locked" regions may be restricted through epigenetic mechanisms, protecting them from immune-recognition but presumably limiting their ability to drive viral rebound. While the exact immune mechanisms driving this selection process remain undefined, recent single-cell analytic approaches support the hypothesis that HIV reservoir cells are subject to immune selection pressure by host factors. SUMMARY A "blocked and locked" viral reservoir profile may constitute a structural virological correlate of a functional cure of HIV-1 infection. Further research into the immunological mechanism promoting HIV-1 reservoir selection and evolution in EC/PTC is warranted and could inform foreseeable cure strategies.
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Affiliation(s)
- Benjamin Bone
- Infectious Disease Division, Brigham Women's Hospital, Boston
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham Women's Hospital, Boston
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
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8
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Gay CL, Hanley PJ, Falcinelli SD, Kuruc JD, Pedersen SM, Kirchherr J, Raines SLM, Motta CM, Lazarski C, Chansky P, Tanna J, Shibli A, Datar A, McCann CD, Sili U, Ke R, Eron JJ, Archin N, Goonetilleke N, Bollard CM, Margolis DM. The Effects of Human Immunodeficiency Virus Type 1 (HIV-1) Antigen-Expanded Specific T-Cell Therapy and Vorinostat on Persistent HIV-1 Infection in People With HIV on Antiretroviral Therapy. J Infect Dis 2024; 229:743-752. [PMID: 38349333 PMCID: PMC10938201 DOI: 10.1093/infdis/jiad423] [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: 05/04/2023] [Accepted: 09/29/2023] [Indexed: 03/16/2024] Open
Abstract
BACKGROUND The histone deacetylase inhibitor vorinostat (VOR) can reverse human immunodeficiency virus type 1 (HIV-1) latency in vivo and allow T cells to clear infected cells in vitro. HIV-specific T cells (HXTCs) can be expanded ex vivo and have been safely administered to people with HIV (PWH) on antiretroviral therapy. METHODS Six PWH received infusions of 2 × 107 HXTCs/m² with VOR 400 mg, and 3 PWH received infusions of 10 × 107 HXTCs/m² with VOR. The frequency of persistent HIV by multiple assays including quantitative viral outgrowth assay (QVOA) of resting CD4+ T cells was measured before and after study therapy. RESULTS VOR and HXTCs were safe, and biomarkers of serial VOR effect were detected, but enhanced antiviral activity in circulating cells was not evident. After 2 × 107 HXTCs/m² with VOR, 1 of 6 PWH exhibited a decrease in QVOA, and all 3 PWH exhibited such declines after 10 × 107 HXTCs/m² and VOR. However, most declines did not exceed the 6-fold threshold needed to definitively attribute decline to the study intervention. CONCLUSIONS These modest effects provide support for the strategy of HIV latency reversal and reservoir clearance, but more effective interventions are needed to yield the profound depletion of persistent HIV likely to yield clinical benefit. Clinical Trials Registration. NCT03212989.
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Affiliation(s)
- Cynthia L Gay
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Medicine, University of North Carolina at Chapel Hill
| | - Patrick J Hanley
- Center for Cancer and Immunology Research, Children's National Health System
- Pediatrics and GW Cancer Center, The George Washington University, Washington, District of Columbia
| | - Shane D Falcinelli
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Medicine, University of North Carolina at Chapel Hill
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | - JoAnn D Kuruc
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Medicine, University of North Carolina at Chapel Hill
| | - Susan M Pedersen
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Medicine, University of North Carolina at Chapel Hill
| | - Jennifer Kirchherr
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Medicine, University of North Carolina at Chapel Hill
| | | | - Cecilia M Motta
- Center for Cancer and Immunology Research, Children's National Health System
| | - Chris Lazarski
- Center for Cancer and Immunology Research, Children's National Health System
- Pediatrics and GW Cancer Center, The George Washington University, Washington, District of Columbia
| | - Pamela Chansky
- Center for Cancer and Immunology Research, Children's National Health System
| | - Jay Tanna
- Center for Cancer and Immunology Research, Children's National Health System
| | - Abeer Shibli
- Center for Cancer and Immunology Research, Children's National Health System
| | - Anushree Datar
- Center for Cancer and Immunology Research, Children's National Health System
| | - Chase D McCann
- Center for Cancer and Immunology Research, Children's National Health System
- Pediatrics and GW Cancer Center, The George Washington University, Washington, District of Columbia
| | - Uluhan Sili
- Center for Cancer and Immunology Research, Children's National Health System
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico
| | - Joseph J Eron
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Nancie Archin
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Medicine, University of North Carolina at Chapel Hill
| | - Nilu Goonetilleke
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Health System
- Pediatrics and GW Cancer Center, The George Washington University, Washington, District of Columbia
| | - David M Margolis
- UNC HIV Cure Center, University of North Carolina at Chapel Hill
- Department of Medicine, University of North Carolina at Chapel Hill
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
- Department of Epidemiology, University of North Carolina at Chapel Hill
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9
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Armani-Tourret M, Gao C, Hartana CA, Sun W, Carrere L, Vela L, Hochroth A, Bellefroid M, Sbrolla A, Shea K, Flynn T, Roseto I, Rassadkina Y, Lee C, Giguel F, Malhotra R, Bushman FD, Gandhi RT, Yu XG, Kuritzkes DR, Lichterfeld M. Selection of epigenetically privileged HIV-1 proviruses during treatment with panobinostat and interferon-α2a. Cell 2024; 187:1238-1254.e14. [PMID: 38367616 PMCID: PMC10903630 DOI: 10.1016/j.cell.2024.01.037] [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: 06/14/2023] [Revised: 11/26/2023] [Accepted: 01/24/2024] [Indexed: 02/19/2024]
Abstract
CD4+ T cells with latent HIV-1 infection persist despite treatment with antiretroviral agents and represent the main barrier to a cure of HIV-1 infection. Pharmacological disruption of viral latency may expose HIV-1-infected cells to host immune activity, but the clinical efficacy of latency-reversing agents for reducing HIV-1 persistence remains to be proven. Here, we show in a randomized-controlled human clinical trial that the histone deacetylase inhibitor panobinostat, when administered in combination with pegylated interferon-α2a, induces a structural transformation of the HIV-1 reservoir cell pool, characterized by a disproportionate overrepresentation of HIV-1 proviruses integrated in ZNF genes and in chromatin regions with reduced H3K27ac marks, the molecular target sites for panobinostat. By contrast, proviruses near H3K27ac marks were actively selected against, likely due to increased susceptibility to panobinostat. These data suggest that latency-reversing treatment can increase the immunological vulnerability of HIV-1 reservoir cells and accelerate the selection of epigenetically privileged HIV-1 proviruses.
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Affiliation(s)
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ciputra Adijaya Hartana
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - WeiWei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Leah Carrere
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Liliana Vela
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | | | - Amy Sbrolla
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katrina Shea
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Theresa Flynn
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabelle Roseto
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Carole Lee
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francoise Giguel
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rajeev Malhotra
- Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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10
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Buchholtz NVEJ, Nühn MM, de Jong TCM, Stienstra TAT, Reddy K, Ndung'u T, Ndhlovu ZM, Fisher K, Palmer S, Wensing AMJ, Symons J, Nijhuis M. Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C. Virol J 2024; 21:36. [PMID: 38297379 PMCID: PMC10832250 DOI: 10.1186/s12985-024-02300-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
INTRODUCTION HIV reservoir quantification is essential for evaluation of HIV curative strategies and may provide valuable insights about reservoir dynamics during antiretroviral therapy. The Intact Proviral DNA Assay (IPDA) provides the unique opportunity to quantify the intact and defective reservoir. The current IPDA is optimized for HIV-1 subtype B, the dominant subtype in resource-rich settings. However, subtype C is dominant in Sub-Saharan Africa, jointly accounting for around 60% of the pandemic. We developed an assay capable of quantifying intact and defective proviral HIV-1 DNA of subtype B and C. METHODS Primer and probe sequences were strategically positioned at conserved regions in psi and env and adapted to subtype B&C. In silico analysis of 752 subtype B and 697 subtype C near-full length genome sequences (nFGS) was performed to predict the specificity and sensitivity. Gblocks were used to determine the limit of blank (LoB), limit of detection (LoD), and different annealing temperatures were tested to address impact of sequence variability. RESULTS The in silico analysis showed that the HIV-1 B&C IPDA correctly identified 100% of the intact subtype B, and 86% of the subtype C sequences. In contrast, the original IPDA identified 86% and 12% of these subtype B and C sequences as intact. Furthermore, the HIV-1 B&C IPDA correctly identified hypermutated (87% and 88%) and other defective sequences (73% and 66%) for subtype B and C with comparable specificity as the original IPDA for subtype B (59% and 63%). Subtype B cis-acting sequences were more frequently identified as intact by the HIV-1 B&C IPDA compared to the original IPDA (39% and 2%). The LoB for intact proviral DNA copies was 0, and the LoD for intact proviral DNA copies was 6 (> 95% certainty) at 60 °C. Quantification of 2-6 copies can be performed with > 80% certainty. Lowering the annealing temperature to 55 °C slightly lowered the specificity but prevented exclusion of samples with single mutations in the primer/probe region. CONCLUSIONS We developed a robust and sensitive assay for the quantification of intact and defective HIV-1 subtype B and C proviral DNA, making this a suitable tool to monitor the impact of (large-scale) curative interventions.
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Affiliation(s)
- N V E J Buchholtz
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M M Nühn
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T C M de Jong
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T A T Stienstra
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - K Reddy
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - T Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA, 01238, USA
- Division of Infection and Immunity, University College London, London, UK
| | - Z M Ndhlovu
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - K Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - S Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - A M J Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
- ha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J Symons
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands.
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
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11
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Peterson JJ, Lewis CA, Burgos SD, Manickam A, Xu Y, Rowley AA, Clutton G, Richardson B, Zou F, Simon JM, Margolis DM, Goonetilleke N, Browne EP. A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV-infected cells. Cell Chem Biol 2023; 30:1617-1633.e9. [PMID: 38134881 PMCID: PMC10754471 DOI: 10.1016/j.chembiol.2023.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/23/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
A long-lived latent reservoir of HIV-1-infected CD4 T cells persists with antiretroviral therapy and prevents cure. We report that the emergence of latently infected primary CD4 T cells requires the activity of histone deacetylase enzymes HDAC1/2 and HDAC3. Data from targeted HDAC molecules, an HDAC3-directed PROTAC, and CRISPR-Cas9 knockout experiments converge on a model where either HDAC1/2 or HDAC3 targeting can prevent latency, whereas all three enzymes must be targeted to achieve latency reversal. Furthermore, HDACi treatment targets features of memory T cells that are linked to proviral latency and persistence. Latency prevention is associated with increased H3K9ac at the proviral LTR promoter region and decreased H3K9me3, suggesting that this epigenetic switch is a key proviral silencing mechanism that depends on HDAC activity. These findings support further mechanistic work on latency initiation and eventual clinical studies of HDAC inhibitors to interfere with latency initiation.
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Affiliation(s)
- Jackson J Peterson
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Catherine A Lewis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Samuel D Burgos
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Ashokkumar Manickam
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Yinyan Xu
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Allison A Rowley
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Genevieve Clutton
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Brian Richardson
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Fei Zou
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Jeremy M Simon
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC 27514, USA; UNC Neuroscience Center, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA; Department of Medicine, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Edward P Browne
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA.
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12
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. mBio 2023; 14:e0241723. [PMID: 37971267 PMCID: PMC10746175 DOI: 10.1128/mbio.02417-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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13
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Barton K, Ferguson JM, Deveson IW, Falcinelli SD, James KS, Kirchherr J, Ramirez C, Gay CL, Hammond JM, Bevear B, Carswell SL, Margolis DM, Smith MA, Adimora AA, Archin NM. HIVepsilon-seq-scalable characterization of intact persistent proviral HIV reservoirs in women. J Virol 2023; 97:e0070523. [PMID: 37843370 PMCID: PMC10688329 DOI: 10.1128/jvi.00705-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The lack of a reliable method to accurately detect when replication-competent HIV has been cleared is a major challenge in developing a cure. This study introduces a new approach called the HIVepsilon-seq (HIVε-seq) assay, which uses long-read sequencing technology and bioinformatics to scrutinize the HIV genome at the nucleotide level, distinguishing between defective and intact HIV. This study included 30 participants on antiretroviral therapy, including 17 women, and was able to discriminate between defective and genetically intact viruses at the single DNA strand level. The HIVε-seq assay is an improvement over previous methods, as it requires minimal sample, less specialized lab equipment, and offers a shorter turnaround time. The HIVε-seq assay offers a promising new tool for researchers to measure the intact HIV reservoir, advancing efforts towards finding a cure for this devastating disease.
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Affiliation(s)
- Kirston Barton
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- The Kirby Institute, University of New South Wales, Randwick, New South Wales, Australia
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, New South Wales, Australia
| | - James M. Ferguson
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ira W. Deveson
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Shane D. Falcinelli
- Department of Microbiology, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Katherine S. James
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Catalina Ramirez
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Cynthia L. Gay
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jillian M. Hammond
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Brent Bevear
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Shaun L. Carswell
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- National Institute of Water and Atmospheric Research, Auckland, New Zealand
| | - David M. Margolis
- Department of Microbiology, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Martin A. Smith
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
- CHU Sainte-Justine Research Centre, Montreal, Canada
| | - Adaora A. Adimora
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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14
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Falcinelli SD, Cooper-Volkheimer AD, Semenova L, Wu E, Richardson A, Ashokkumar M, Margolis DM, Archin NM, Rudin CD, Murdoch D, Browne EP. Impact of Cannabis Use on Immune Cell Populations and the Viral Reservoir in People With HIV on Suppressive Antiretroviral Therapy. J Infect Dis 2023; 228:1600-1609. [PMID: 37606598 PMCID: PMC10681869 DOI: 10.1093/infdis/jiad364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV) infection remains incurable due to the persistence of a viral reservoir despite antiretroviral therapy (ART). Cannabis (CB) use is prevalent amongst people with HIV (PWH), but the impact of CB on the latent HIV reservoir has not been investigated. METHODS Peripheral blood cells from a cohort of PWH who use CB and a matched cohort of PWH who do not use CB on ART were evaluated for expression of maturation/activation markers, HIV-specific T-cell responses, and intact proviral DNA. RESULTS CB use was associated with increased abundance of naive T cells, reduced effector T cells, and reduced expression of activation markers. CB use was also associated with reduced levels of exhausted and senescent T cells compared to nonusing controls. HIV-specific T-cell responses were unaffected by CB use. CB use was not associated with intact or total HIV DNA frequency in CD4 T cells. CONCLUSIONS This analysis is consistent with the hypothesis that CB use reduces activation, exhaustion, and senescence in the T cells of PWH, and does not impair HIV-specific CD8 T-cell responses. Longitudinal and interventional studies with evaluation of CB exposure are needed to fully evaluate the impact of CB use on the HIV reservoir.
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Affiliation(s)
- Shane D Falcinelli
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Lesia Semenova
- Department of Computer Science, Duke University, Durham, North Carolina, USA
| | - Ethan Wu
- Department of Computer Science, Duke University, Durham, North Carolina, USA
| | | | - Manickam Ashokkumar
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancie M Archin
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cynthia D Rudin
- Department of Computer Science, Duke University, Durham, North Carolina, USA
| | - David Murdoch
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Edward P Browne
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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15
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Więcek K, Chen HC. Understanding latent HIV-1 reservoirs through host genomics approaches. iScience 2023; 26:108342. [PMID: 38026212 PMCID: PMC10665824 DOI: 10.1016/j.isci.2023.108342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Genetically intact HIV-1 proviruses are a major concern with regard to curing infection because they cause viral rebound after the cessation of antiretroviral therapy. However, intact proviruses are not prevalent in HIV-1 reservoirs. As such, it is essential to precisely determine the position of these proviruses before putting forward a better antiretroviral cure. Recently, a revised HIV-1 deeply latent reservoir concept has been proposed, stating that the progress of the establishment of HIV-1 reservoirs is influenced by immune-mediated selection during the course of infection. This selection force leads to the persistence of genetically intact proviruses as those with the best fit to avoid clearance. This hypothesis refreshes our understanding of HIV-1 latent reservoirs. For this reason, we reviewed current studies relevant to this theme and provide our perspectives to reinforce the overall understanding of HIV-1 latency in the context of the host genome.
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Affiliation(s)
- Kamil Więcek
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
| | - Heng-Chang Chen
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
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16
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Singh K, Natarajan V, Dewar R, Rupert A, Badralmaa Y, Zhai T, Winchester N, Scrimieri F, Smith M, Davis I, Lallemand P, Giglietti A, Hensien J, Buerkert T, Goshu B, Rehm CA, Hu Z, Lane HC, Imamichi H. Long-term persistence of transcriptionally active 'defective' HIV-1 proviruses: implications for persistent immune activation during antiretroviral therapy. AIDS 2023; 37:2119-2130. [PMID: 37555786 PMCID: PMC10615727 DOI: 10.1097/qad.0000000000003667] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/10/2023]
Abstract
OBJECTIVES People with HIV-1 (PWH) on effective antiretroviral therapy (ART) continue to exhibit chronic systemic inflammation, immune activation, and persistent elevations in markers of HIV-1 infection [including HIV-DNA, cell-associated HIV-RNA (CA HIV-RNA), and antibodies to HIV-1 proteins] despite prolonged suppression of plasma HIV-RNA levels less than 50 copies/ml. Here, we investigated the hypothesis that nonreplicating but transcriptionally and translationally competent 'defective' HIV-1 proviruses may be one of drivers of these phenomena. DESIGN A combined cohort of 23 viremic and virologically suppressed individuals on ART were studied. METHODS HIV-DNA, CA HIV-RNA, western blot score (measure of anti-HIV-1 antibodies as a surrogate for viral protein expression in vivo ), and key biomarkers of inflammation and coagulation (IL-6, hsCRP, TNF-alpha, tissue factor, and D-dimer) were measured in peripheral blood and analyzed using a combined cross-sectional and longitudinal approaches. Sequences of HIV-DNA and CA HIV-RNA obtained via 5'-LTR-to-3'-LTR PCR and single-genome sequencing were also analyzed. RESULTS We observed similar long-term persistence of multiple, unique, transcriptionally active 'defective' HIV-1 provirus clones (average: 11 years., range: 4-20 years) and antibody responses against HIV-1 viral proteins among all ART-treated participants evaluated. A direct correlation was observed between the magnitude of HIV-1 western blot score and the levels of transcription of 'defective' HIV-1 proviruses ( r = 0.73, P < 0.01). Additional correlations were noted between total CD8 + T-cell counts and HIV-DNA ( r = 0.52, P = 0.01) or CA HIV-RNA ( r = 0.65, P < 0.01). CONCLUSION These findings suggest a novel interplay between transcription and translation of 'defective' HIV-1 proviruses and the persistent immune activation seen in the setting of treated chronic HIV-1 infection.
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Affiliation(s)
- Kanal Singh
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Ven Natarajan
- Frederick National Laboratory for Cancer Research, Frederick
| | - Robin Dewar
- Frederick National Laboratory for Cancer Research, Frederick
| | - Adam Rupert
- Frederick National Laboratory for Cancer Research, Frederick
| | - Yuden Badralmaa
- Frederick National Laboratory for Cancer Research, Frederick
| | - Tracey Zhai
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Nicole Winchester
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | | | - Mindy Smith
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Ivery Davis
- Frederick National Laboratory for Cancer Research, Frederick
| | | | - Aude Giglietti
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Jack Hensien
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Thomas Buerkert
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Bruktawit Goshu
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Catherine A. Rehm
- Clinical Research Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH
| | - Zonghui Hu
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - H. Clifford Lane
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
| | - Hiromi Imamichi
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda
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17
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Dwivedi AK, Gornalusse GG, Siegel DA, Barbehenn A, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Reppetti J, Vo PM, Levy CN, Roychoudhury P, Jerome KR, Hladik F, Henrich TJ, Deeks SG, Lee SA. A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size. PLoS Pathog 2023; 19:e1011114. [PMID: 38019897 PMCID: PMC10712869 DOI: 10.1371/journal.ppat.1011114] [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: 01/11/2023] [Revised: 12/11/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). There have been few cohort-based studies evaluating host genomic or transcriptomic predictors of the HIV reservoir. We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 ART-suppressed people with HIV (PWH). After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, P3H3 and NBL1, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (KCNJ2, GJB2), inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q = 0.006), IL-1/NRLP3 inflammasome (q = 0.008), and IL-10 (q = 0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-α protein associations achieving statistical significance (p<0.05). Plasma IL-10 was also significantly inversely associated with HIV DNA (p = 0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. To our knowledge, this is the largest host transcriptomic study of the HIV reservoir. Our findings suggest that host gene expression may vary in response to the transcriptionally active reservoir and that changes in cellular proliferation genes may influence the size of the HIV reservoir. These findings add important data to the limited host genetic HIV reservoir studies to date.
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Affiliation(s)
- Ashok K. Dwivedi
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Germán G. Gornalusse
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - David A. Siegel
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Alton Barbehenn
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Cassandra Thanh
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Rebecca Hoh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Kristen S. Hobbs
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Tony Pan
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Erica A. Gibson
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Jeffrey Martin
- Department of Biostatistics & Epidemiology, University of California San Francisco, California, United States of America
| | - Frederick Hecht
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Christopher Pilcher
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Jeffrey Milush
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Michael P. Busch
- Vitalant Blood Bank, San Francisco, California, United States of America
| | - Mars Stone
- Vitalant Blood Bank, San Francisco, California, United States of America
| | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Julieta Reppetti
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
- Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO- Houssay), Buenos Aires, Argentina
| | - Phuong M. Vo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Claire N. Levy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Florian Hladik
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Timothy J. Henrich
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Steven G. Deeks
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Sulggi A. Lee
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
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18
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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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19
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Sanz M, Weideman AMK, Ward AR, Clohosey ML, Garcia-Recio S, Selitsky SR, Mann BT, Iannone MA, Whitworth CP, Chitrakar A, Garrido C, Kirchherr J, Coffey AR, Tsai YH, Samir S, Xu Y, Copertino D, Bosque A, Jones BR, Parker JS, Hudgens MG, Goonetilleke N, Soriano-Sarabia N. Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1. Front Immunol 2023; 14:1219250. [PMID: 37744358 PMCID: PMC10516574 DOI: 10.3389/fimmu.2023.1219250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.
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Affiliation(s)
- Marta Sanz
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Ann Marie K. Weideman
- Biostatistics Core, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Adam R. Ward
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
- Department of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Matthew L. Clohosey
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sara R. Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Brendan T. Mann
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Marie Anne Iannone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Chloe P. Whitworth
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alisha Chitrakar
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Carolina Garrido
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jennifer Kirchherr
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alisha R. Coffey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yi- Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shahryar Samir
- Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yinyan Xu
- Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Dennis Copertino
- Department of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Alberto Bosque
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Brad R. Jones
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
- Department of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Michael G. Hudgens
- Biostatistics Core, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nilu Goonetilleke
- Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Natalia Soriano-Sarabia
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
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20
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Reeves DB, Gaebler C, Oliveira TY, Peluso MJ, Schiffer JT, Cohn LB, Deeks SG, Nussenzweig MC. Impact of misclassified defective proviruses on HIV reservoir measurements. Nat Commun 2023; 14:4186. [PMID: 37443365 PMCID: PMC10345136 DOI: 10.1038/s41467-023-39837-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Most proviruses persisting in people living with HIV (PWH) on antiretroviral therapy (ART) are defective. However, rarer intact proviruses almost always reinitiate viral rebound if ART stops. Therefore, assessing therapies to prevent viral rebound hinges on specifically quantifying intact proviruses. We evaluated the same samples from 10 male PWH on ART using the two-probe intact proviral DNA assay (IPDA) and near full length (nfl) Q4PCR. Both assays admitted similar ratios of intact to total HIV DNA, but IPDA found ~40-fold more intact proviruses. Neither assay suggested defective proviruses decay over 10 years. However, the mean intact half-lives were different: 108 months for IPDA and 65 months for Q4PCR. To reconcile this difference, we modeled additional longitudinal IPDA data and showed that decelerating intact decay could arise from very long-lived intact proviruses and/or misclassified defective proviruses: slowly decaying defective proviruses that are intact in IPDA probe locations (estimated up to 5%, in agreement with sequence library based predictions). The model also demonstrates how misclassification can lead to underestimated efficacy of therapies that exclusively reduce intact proviruses. We conclude that sensitive multi-probe assays combined with specific nfl-verified assays would be optimal to document absolute and changing levels of intact HIV proviruses.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Laboratory of Translational Immunology of Viral Infections, Department of Infectious Diseases, Charité -Universitätsmedizin, Berlin, Germany
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lillian B Cohn
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
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21
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Gandhi RT, Bosch RJ, Mar H, Laird GM, Halvas EK, Hovind L, Collier AC, Riddler SA, Martin A, Ritter K, McMahon DK, Eron JJ, Cyktor JC, Mellors JW. Varied Patterns of Decay of Intact Human Immunodeficiency Virus Type 1 Proviruses Over 2 Decades of Antiretroviral Therapy. J Infect Dis 2023; 227:1376-1380. [PMID: 36763044 PMCID: PMC10474937 DOI: 10.1093/infdis/jiad039] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Fourteen people with human immunodeficiency virus type 1 had longitudinal measurements of intact, defective, and total proviral DNA over the course of two decades of antiretroviral therapy. Three patterns of intact proviral DNA decay were revealed: (1) biphasic decline with markedly slower second-phase decline, (2) initial decline that transitions to a zero-slope plateau, and (3) initial decline followed by later increases in intact proviral DNA. Defective proviral DNA levels were essentially stable. Mechanisms of slowing or reversal of second-phase decay of intact proviral DNA may include the inability to clear cells with intact but transcriptionally silent proviruses and clonal expansion of cells with intact proviruses.
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Affiliation(s)
- Rajesh T Gandhi
- Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Hanna Mar
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Elias K Halvas
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Laura Hovind
- Frontier Science and Technology Research Foundation, Amherst, New York, USA
| | - Ann C Collier
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sharon A Riddler
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | - Deborah K McMahon
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Joshua C Cyktor
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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22
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Bottanelli M, Ceccarelli D, Lolatto R, Galli L, Guffanti M, Dell'Acqua R, Ponta G, Mori G, Castagna A, Muccini C. Risk of Cardiovascular Diseases or Mortality in People With Higher Values of HIV-1 DNA. J Acquir Immune Defic Syndr 2023; 93:e6-e8. [PMID: 36989135 DOI: 10.1097/qai.0000000000003192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Affiliation(s)
- Martina Bottanelli
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Ceccarelli
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Riccardo Lolatto
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Galli
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monica Guffanti
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaele Dell'Acqua
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giacomo Ponta
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Mori
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Castagna
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Muccini
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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23
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536611. [PMID: 37090500 PMCID: PMC10120704 DOI: 10.1101/2023.04.12.536611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
| | | | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Experimental Medicine Program, University of British Columbia, Vancouver, BC
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby BC
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
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24
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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: 13] [Impact Index Per Article: 13.0] [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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25
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Siegel DA, Thanh C, Wan E, Hoh R, Hobbs K, Pan T, Gibson EA, Kroetz DL, Martin J, Hecht F, Pilcher C, Martin M, Carrington M, Pillai S, Busch MP, Stone M, Levy CN, Huang ML, Roychoudhury P, Hladik F, Jerome KR, Kiem HP, Henrich TJ, Deeks SG, Lee SA. Host variation in type I interferon signaling genes (MX1), C-C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size. AIDS 2023; 37:477-488. [PMID: 36695358 PMCID: PMC9894159 DOI: 10.1097/qad.0000000000003428] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/28/2022] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Prior genomewide association studies have identified variation in major histocompatibility complex (MHC) class I alleles and C-C chemokine receptor type 5 gene (CCR5Δ32) as genetic predictors of viral control, especially in 'elite' controllers, individuals who remain virally suppressed in the absence of therapy. DESIGN Cross-sectional genomewide association study. METHODS We analyzed custom whole exome sequencing and direct human leukocyte antigen (HLA) typing from 202 antiretroviral therapy (ART)-suppressed HIV+ noncontrollers in relation to four measures of the peripheral CD4+ T-cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T-cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression. RESULTS Previously reported 'protective' host genetic mutations related to viral setpoint (e.g. among elite controllers) were found to predict smaller HIV reservoir size. The HLA 'protective' B∗57:01 was associated with significantly lower HIV usRNA (q = 3.3 × 10-3), and among the largest subgroup, European ancestry individuals, the CCR5Δ32 deletion was associated with smaller HIV tDNA (P = 4.3 × 10-3) and usRNA (P = 8.7 × 10-3). In addition, genomewide analysis identified several single nucleotide polymorphisms in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q = 0.02), and the direction of these associations paralleled MX1 gene eQTL expression. CONCLUSIONS We observed a significant association between previously reported 'protective' MHC class I alleles and CCR5Δ32 with the HIV reservoir size in noncontrollers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.
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Affiliation(s)
- David A. Siegel
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | | | | | - Rebecca Hoh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Kristen Hobbs
- Department of Medicine, Division of Experimental Medicine
| | - Tony Pan
- Department of Medicine, Division of Experimental Medicine
| | | | | | - Jeffrey Martin
- Department of Biostatistics & Epidemiology, University of California San Francisco, California
| | - Frederick Hecht
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Christopher Pilcher
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Mars Stone
- Vitalant Blood Bank, San Francisco, California
| | | | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hans-Peter Kiem
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Steven G. Deeks
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Sulggi A. Lee
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
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26
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Sanz M, Weideman AMK, Ward AR, Clohosey ML, Garcia-Recio S, Selitsky SR, Mann BT, Iannone MA, Whitworth CP, Chitrakar A, Garrido C, Kirchherr J, Coffey AR, Tsai YH, Samir S, Xu Y, Copertino D, Bosque A, Jones BR, Parker JS, Hudgens MG, Goonetilleke N, Soriano-Sarabia N. Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527421. [PMID: 36798291 PMCID: PMC9934553 DOI: 10.1101/2023.02.07.527421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.
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Affiliation(s)
- Marta Sanz
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Ann Marie K. Weideman
- Department of Biostatistics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Adam R. Ward
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
- Department of Infectious Diseases, Weill Cornell Medicine, New York, USA
| | - Matthew L. Clohosey
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Sara R. Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Brendan T. Mann
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Marie Anne Iannone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Chloe P. Whitworth
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Alisha Chitrakar
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Carolina Garrido
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Alisha R. Coffey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Shahryar Samir
- Microbiology & Immunology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Yinyan Xu
- Microbiology & Immunology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Dennis Copertino
- Department of Infectious Diseases, Weill Cornell Medicine, New York, USA
| | - Alberto Bosque
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Brad R. Jones
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
- Department of Infectious Diseases, Weill Cornell Medicine, New York, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Michael G. Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Nilu Goonetilleke
- Microbiology & Immunology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Natalia Soriano-Sarabia
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
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27
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Sun W, Gao C, Hartana CA, Osborn MR, Einkauf KB, Lian X, Bone B, Bonheur N, Chun TW, Rosenberg ES, Walker BD, Yu XG, Lichterfeld M. Phenotypic signatures of immune selection in HIV-1 reservoir cells. Nature 2023; 614:309-317. [PMID: 36599977 PMCID: PMC9908552 DOI: 10.1038/s41586-022-05538-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 11/08/2022] [Indexed: 01/06/2023]
Abstract
Human immunodeficiency virus 1 (HIV-1) reservoir cells persist lifelong despite antiretroviral treatment1,2 but may be vulnerable to host immune responses that could be exploited in strategies to cure HIV-1. Here we used a single-cell, next-generation sequencing approach for the direct ex vivo phenotypic profiling of individual HIV-1-infected memory CD4+ T cells from peripheral blood and lymph nodes of people living with HIV-1 and receiving antiretroviral treatment for approximately 10 years. We demonstrate that in peripheral blood, cells harbouring genome-intact proviruses and large clones of virally infected cells frequently express ensemble signatures of surface markers conferring increased resistance to immune-mediated killing by cytotoxic T and natural killer cells, paired with elevated levels of expression of immune checkpoint markers likely to limit proviral gene transcription; this phenotypic profile might reduce HIV-1 reservoir cell exposure to and killing by cellular host immune responses. Viral reservoir cells harbouring intact HIV-1 from lymph nodes exhibited a phenotypic signature primarily characterized by upregulation of surface markers promoting cell survival, including CD44, CD28, CD127 and the IL-21 receptor. Together, these results suggest compartmentalized phenotypic signatures of immune selection in HIV-1 reservoir cells, implying that only small subsets of infected cells with optimal adaptation to their anatomical immune microenvironment are able to survive during long-term antiretroviral treatment. The identification of phenotypic markers distinguishing viral reservoir cells may inform future approaches for strategies to cure and eradicate HIV-1.
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Affiliation(s)
- Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin Bone
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD, USA
| | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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28
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Koofhethile CK, Rinaldi S, Rassadkina Y, Dinh VB, Gao C, Pallikkuth S, Garcia-Broncano P, de Armas LR, Pahwa R, Cotugno N, Vaz P, Lain MG, Palma P, Yu XG, Shapiro R, Pahwa S, Lichterfeld M. HIV-1 reservoir evolution in infants infected with clade C from Mozambique. Int J Infect Dis 2023; 127:129-136. [PMID: 36476348 PMCID: PMC9892347 DOI: 10.1016/j.ijid.2022.11.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The persistence of HIV-1-infected cells during antiretroviral therapy is well documented but may be modulated by early initiation of antiretroviral therapy in infants. METHODS Here, we longitudinally analyzed the proviral landscape in nine infants with vertical HIV-1 infection from Mozambique over a median period of 24 months, using single-genome, near full-length, next-generation proviral sequencing. RESULTS We observed a rapid decline in the frequency of intact proviruses, leading to a disproportional under-representation of intact HIV-1 sequences within the total number of HIV-1 DNA sequences after 12-24 months of therapy. In addition, proviral integration site profiling in one infant demonstrated clonal expansion of infected cells harboring intact proviruses and indicated that viral rebound was associated with an integration site profile dominated by intact proviruses integrated into genic and accessible chromatin locations. CONCLUSION Together, these results permit rare insight into the evolution of the HIV-1 reservoir in infants infected with HIV-1 and suggest that the rapid decline of intact proviruses, relative to defective proviruses, may be attributed to a higher vulnerability of genome-intact proviruses to antiviral immunity. Technologies to analyze combinations of intact proviral sequences and corresponding integration sites permit a high-resolution analysis of HIV-1 reservoir cells after early antiretroviral treatment initiation in infants.
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Affiliation(s)
- Catherine K Koofhethile
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA; Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | | | | | - Nicola Cotugno
- Academic Department of Pediatrics, Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Paula Vaz
- Fundação Ariel Glaser contra o SIDA Pediátrico, Maputo, Mozambique
| | | | - Paolo Palma
- Academic Department of Pediatrics, Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy; Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Roger Shapiro
- Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.
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29
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Dwivedi AK, Siegel DA, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Levy CN, Roychoudhury P, Hladik F, Jerome KR, Henrich TJ, Deeks SG, Lee SA. Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523535. [PMID: 36712077 PMCID: PMC9882059 DOI: 10.1101/2023.01.10.523535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective antiretroviral therapy (ART). Most prior host genetic HIV studies have focused on identifying DNA polymorphisms (e.g., CCR5Δ32 , MHC class I alleles) associated with viral load among untreated "elite controllers" (~1% of HIV+ individuals who are able to control virus without ART). However, there have been few studies evaluating host genetic predictors of viral control for the majority of people living with HIV (PLWH) on ART. We performed host RNA sequencing and HIV reservoir quantification (total DNA, unspliced RNA, intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. Multivariate models included covariates for timing of ART initiation, nadir CD4+ count, age, sex, and ancestry. Lower HIV total DNA (an estimate of the total reservoir) was associated with upregulation of tumor suppressor genes NBL1 (q=0.012) and P3H3 (q=0.012). Higher HIV unspliced RNA (an estimate of residual HIV transcription) was associated with downregulation of several host genes involving inflammasome ( IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9 , CXCL3, CXCL10 ) and innate immune ( TLR7 ) signaling, as well as novel associations with potassium ( KCNJ2 ) and gap junction ( GJB2 ) channels, all q<0.05. Gene set enrichment analyses identified significant associations with TLR4/microbial translocation (q=0.006), IL-1β/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. HIV intact DNA (an estimate of the "replication-competent" reservoir) demonstrated trends with thrombin degradation ( PLGLB1 ) and glucose metabolism ( AGL ) genes, but data were (HIV intact DNA detected in only 42% of participants). Our findings demonstrate that among treated PLWH, that inflammation, innate immune responses, bacterial translocation, and tumor suppression/cell proliferation host signaling play a key role in the maintenance of the HIV reservoir during ART. Further data are needed to validate these findings, including functional genomic studies, and expanded epidemiologic studies in female, non-European cohorts. Author Summary Although lifelong HIV antiretroviral therapy (ART) suppresses virus, the major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective ART, "the HIV reservoir." HIV eradication strategies have focused on eliminating residual virus to allow for HIV remission, but HIV cure trials to date have thus far failed to show a clinically meaningful reduction in the HIV reservoir. There is an urgent need for a better understanding of the host-viral dynamics during ART suppression to identify potential novel therapeutic targets for HIV cure. This is the first epidemiologic host gene expression study to demonstrate a significant link between HIV reservoir size and several well-known immunologic pathways (e.g., IL-1β, TLR7, TNF-α signaling pathways), as well as novel associations with potassium and gap junction channels (Kir2.1, connexin 26). Further data are needed to validate these findings, including functional genomic studies and expanded epidemiologic studies in female, non-European cohorts.
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30
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Lian X, Seiger KW, Parsons EM, Gao C, Sun W, Gladkov GT, Roseto IC, Einkauf KB, Osborn MR, Chevalier JM, Jiang C, Blackmer J, Carrington M, Rosenberg ES, Lederman MM, McMahon DK, Bosch RJ, Jacobson JM, Gandhi RT, Peluso MJ, Chun TW, Deeks SG, Yu XG, Lichterfeld M. Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy. Cell Host Microbe 2023; 31:83-96.e5. [PMID: 36596305 PMCID: PMC9839361 DOI: 10.1016/j.chom.2022.12.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/08/2022] [Accepted: 11/30/2022] [Indexed: 01/03/2023]
Abstract
HIV-1 establishes a life-long reservoir of virally infected cells which cannot be eliminated by antiretroviral therapy (ART). Here, we demonstrate a markedly altered viral reservoir profile of long-term ART-treated individuals, characterized by large clones of intact proviruses preferentially integrated in heterochromatin locations, most prominently in centromeric satellite/micro-satellite DNA. Longitudinal evaluations suggested that this specific reservoir configuration results from selection processes that promote the persistence of intact proviruses in repressive chromatin positions, while proviruses in permissive chromosomal locations are more likely to be eliminated. A bias toward chromosomal integration sites in heterochromatin locations was also observed for intact proviruses in study participants who maintained viral control after discontinuation of antiretroviral therapy. Together, these results raise the possibility that antiviral selection mechanisms during long-term ART may induce an HIV-1 reservoir structure with features of deep latency and, possibly, more limited abilities to drive rebound viremia upon treatment interruptions.
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Affiliation(s)
- Xiaodong Lian
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kyra W Seiger
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elizabeth M Parsons
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ce Gao
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Gregory T Gladkov
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Kevin B Einkauf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matthew R Osborn
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Joshua M Chevalier
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Chenyang Jiang
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jane Blackmer
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Rajesh T Gandhi
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
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31
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Schiffer JT, Levy C, Hughes SM, Pandey U, Padullo M, Jerome KR, Zhu H, Puckett K, Helgeson E, Harrington RD, Hladik F. Stable HIV Reservoir Despite Prolonged Low-Dose Mycophenolate to Limit CD4+ T-cell Proliferation. Open Forum Infect Dis 2022; 9:ofac620. [PMID: 36519118 PMCID: PMC9745781 DOI: 10.1093/ofid/ofac620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/15/2022] [Indexed: 10/14/2023] Open
Abstract
Background The HIV reservoir of latently infected CD4+ T cells represents the barrier to cure. CD4+ T-cell proliferation is a mechanism that sustains the reservoir even during prolonged antiretroviral therapy (ART). Blocking proliferation may therefore deplete the reservoir. Methods We conducted an unblinded, uncontrolled clinical trial of mycophenolate, a T-cell antiproliferative compound, in people with HIV on chronic suppressive ART. Study drug dose selection was based on calibration to an observed ex vivo antiproliferative effect. The primary outcome was clinically significant reduction (>0.25 log10) in the HIV reservoir, measured by total and intact HIV DNA per million T cells in blood over 48 weeks. Results Five participants enrolled in the trial. Four participants took mycophenolate mofetil (MMF). One had a per-protocol switch to enteric-coated mycophenolate sodium (Myfortic) due to nausea but left the study for personal reasons. One participant developed finger cellulitis, but there were no opportunistic infections. In the 4 participants who completed the protocol, there was no clinically significant reduction in total or intact HIV DNA. There was no change in blood CD4+ T-cell subset composition within the HIV reservoir or the entire CD4+ T-cell population, although total CD4+ T cells decreased slightly in all 4 participants. An ex vivo antiproliferative effect was observed using participant serum obtained 1 hour after dosing, but this effect was severely diminished at drug trough. Conclusions Mycophenolate given over 48 weeks did not reduce the volume or composition of the HIV reservoir. Clinical Trials registration NCT03262441.
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Affiliation(s)
- Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Claire Levy
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Sean M Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Urvashi Pandey
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Mel Padullo
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Haiying Zhu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Katrina Puckett
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Eric Helgeson
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Florian Hladik
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
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32
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Khetan P, Liu Y, Dhummakupt A, Persaud D. Advances in Pediatric HIV-1 Cure Therapies and Reservoir Assays. Viruses 2022; 14:v14122608. [PMID: 36560612 PMCID: PMC9787749 DOI: 10.3390/v14122608] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
Significant advances in the field of HIV-1 therapeutics to achieve antiretroviral treatment (ART)-free remission and cure for persons living with HIV-1 are being made with the advent of broadly neutralizing antibodies and very early ART in perinatal infection. The need for HIV-1 remission and cure arises due to the inability of ART to eradicate the major reservoir for HIV-1 in resting memory CD4+ T cells (the latent reservoir), and the strict adherence to lifelong treatment. To measure the efficacy of these cure interventions on reservoir size and to dissect reservoir dynamics, assays that are sensitive and specific to intact proviruses are critical. In this review, we provided a broad overview of some of the key interventions underway to purge the reservoir in adults living with HIV-1 and ones under study in pediatric populations to reduce and control the latent reservoir, primarily focusing on very early treatment in combination with broadly neutralizing antibodies. We also summarized assays currently in use to measure HIV-1 reservoirs and their feasibility and considerations for studies in children.
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Affiliation(s)
- Priya Khetan
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yufeng Liu
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Adit Dhummakupt
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Deborah Persaud
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Correspondence: ; Tel.: +1-443-287-3735
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33
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Liu Z, Julius P, Kang G, West JT, Wood C. Subtype C HIV-1 reservoirs throughout the body in ART-suppressed individuals. JCI Insight 2022; 7:162604. [PMID: 36278485 PMCID: PMC9714794 DOI: 10.1172/jci.insight.162604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
Subtype B HIV-1 reservoirs have been intensively investigated, but reservoirs in other subtypes and how they respond to antiretroviral therapy (ART) is substantially less established. To characterize subtype C HIV-1 reservoirs, we implemented postmortem frozen, as well as formalin fixed paraffin embedded (FFPE) tissue sampling of central nervous system (CNS) and peripheral tissues. HIV-1 LTR, gag, envelope (env) DNA and RNA was quantified using genomic DNA and RNA extracted from frozen tissues. RNAscope was used to localize subtype C HIV-1 DNA and RNA in FFPE tissue. Despite uniform viral load suppression in our cohort, PCR results showed that subtype C HIV-1 proviral copies vary both in magnitude and tissue distribution, with detection primarily in secondary lymphoid tissues. Interestingly, the appendix harbored proviruses in all subjects. Unlike subtype B, subtype C provirus was rarely detectable in the CNS, and there was no detectable HIV-1 RNA. HIV-1 RNA was detected in peripheral lymphoid tissues of 6 out of 8 ART-suppressed cases. In addition to active HIV-1 expression in lymphoid tissues, RNAscope revealed HIV RNA detection in CD4-expressing cells in the appendix, suggesting that this tissue was a previously unreported potential treatment-resistant reservoir for subtype C HIV-1.
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Affiliation(s)
- Zhou Liu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
| | - Peter Julius
- Department of Pathology and Microbiology, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Guobin Kang
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
| | - John T. West
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
| | - Charles Wood
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
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34
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Cochrane CR, Angelovich TA, Byrnes SJ, Waring E, Guanizo AC, Trollope GS, Zhou J, Vue J, Senior L, Wanicek E, Eddine JJ, Gartner MJ, Jenkins TA, Gorry PR, Brew BJ, Lewin SR, Estes JD, Roche M, Churchill MJ. Intact HIV Proviruses Persist in the Brain Despite Viral Suppression with ART. Ann Neurol 2022; 92:532-544. [PMID: 35867351 PMCID: PMC9489665 DOI: 10.1002/ana.26456] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Human immunodeficiency virus (HIV) persistence in blood and tissue reservoirs, including the brain, is a major barrier to HIV cure and possible cause of comorbid disease. However, the size and replication competent nature of the central nervous system (CNS) reservoir is unclear. Here, we used the intact proviral DNA assay (IPDA) to provide the first quantitative assessment of the intact and defective HIV reservoir in the brain of people with HIV (PWH). METHODS Total, intact, and defective HIV proviruses were measured in autopsy frontal lobe tissue from viremic (n = 18) or virologically suppressed (n = 12) PWH. Total or intact/defective proviruses were measured by detection of HIV pol or the IPDA, respectively, through use of droplet digital polymerase chain reaction (ddPCR). HIV-seronegative individuals were included as controls (n = 6). RESULTS Total HIV DNA was present at similar levels in brain tissues from untreated viremic and antiretroviral (ART)-suppressed individuals (median = 22.3 vs 26.2 HIV pol copies/106 cells), reflecting a stable CNS reservoir of HIV that persists despite therapy. Furthermore, 8 of 10 viremic and 6 of 9 virally suppressed PWH also harbored intact proviruses in the CNS (4.63 vs 12.7 intact copies/106 cells). Viral reservoirs in CNS and matched lymphoid tissue were similar in the composition of intact and/or defective proviruses, albeit at lower levels in the brain. Importantly, CNS resident CD68+ myeloid cells in virally suppressed individuals harbored HIV DNA, directly showing the presence of a CNS resident HIV reservoir. INTERPRETATION Our results demonstrate the first evidence for an intact, potentially replication competent HIV reservoir in the CNS of virally suppressed PWH. ANN NEUROL 2022;92:532-544.
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Affiliation(s)
- Catherine R. Cochrane
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of MedicineThe Royal Melbourne Hospital, The University of MelbourneMelbourneVICAustralia
| | - Thomas A. Angelovich
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Life SciencesBurnet InstituteMelbourneVICAustralia,Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Sarah J. Byrnes
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Emily Waring
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of MedicineThe Royal Melbourne Hospital, The University of MelbourneMelbourneVICAustralia
| | - Aleks C. Guanizo
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Gemma S. Trollope
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of MedicineThe Royal Melbourne Hospital, The University of MelbourneMelbourneVICAustralia
| | - Jingling Zhou
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Judith Vue
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Lachlan Senior
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Emma Wanicek
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Janna Jamal Eddine
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Matthew J. Gartner
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Trisha A. Jenkins
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Paul R. Gorry
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of Infectious DiseasesAlfred Hospital and Monash UniversityMelbourneVICAustralia,Department of Microbiology and ImmunologyThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Bruce J. Brew
- Peter Duncan Neurosciences Unit, Departments of Neurology and Immunology St Vincent's HospitalSydney, University of New South Wales and University of Notre DameSydneyNew South WalesAustralia
| | - Sharon R. Lewin
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia,Department of Infectious DiseasesAlfred Hospital and Monash UniversityMelbourneVICAustralia,Victorian Infectious Diseases ServiceRoyal Melbourne Hospital at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon National Primate Research CentreOregon Health & Science UniversityPortlandORUSA
| | - Michael Roche
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Melissa J. Churchill
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Life SciencesBurnet InstituteMelbourneVICAustralia,Departments of Microbiology and MedicineMonash UniversityMelbourneVICAustralia
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Lichterfeld M, Gao C, Yu XG. An ordeal that does not heal: understanding barriers to a cure for HIV-1 infection. Trends Immunol 2022; 43:608-616. [PMID: 35905706 PMCID: PMC9346997 DOI: 10.1016/j.it.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 12/23/2022]
Abstract
With more than 38 million people living with HIV-1 (PLWH) worldwide, developing a cure for HIV-1 remains a major global health priority. Lifelong persistence of HIV-1 is frequently attributed to a pool of stable, transcriptionally silent HIV-1 proviruses, which are unaffected by currently available antiretroviral therapy (ART) or host immune activity. In this opinion article, we propose a more dynamic interpretation of HIV-1 reservoir cell biology and argue that HIV-1 proviruses frequently display residual viral transcriptional activity, making them vulnerable to longitudinal immune-mediated selection processes. Such mechanisms may, over extended periods of ART, induce an attenuated viral reservoir profile characterized by intact proviruses preferentially integrated into heterochromatin locations. We suggest that intensifying and accelerating naturally occurring selection mechanisms might represent a promising strategy for finding a potential cure for HIV-1 infection.
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Affiliation(s)
- Mathias Lichterfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Ce Gao
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA.
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36
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Hartana CA, Garcia-Broncano P, Rassadkina Y, Lian X, Jiang C, Einkauf KB, Maswabi K, Ajibola G, Moyo S, Mohammed T, Maphorisa C, Makhema J, Yuki Y, Martin M, Bennett K, Jean-Philippe P, Viard M, Hughes MD, Powis KM, Carrington M, Lockman S, Gao C, Yu XG, Kuritzkes DR, Shapiro R, Lichterfeld M. Immune correlates of HIV-1 reservoir cell decline in early-treated infants. Cell Rep 2022; 40:111126. [PMID: 35858580 PMCID: PMC9314543 DOI: 10.1016/j.celrep.2022.111126] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/13/2022] [Accepted: 06/30/2022] [Indexed: 11/03/2022] Open
Abstract
Initiation of antiretroviral therapy (ART) in infected neonates within hours after birth limits viral reservoir seeding but does not prevent long-term HIV-1 persistence. Here, we report parallel assessments of HIV-1 reservoir cells and innate antiviral immune responses in a unique cohort of 37 infected neonates from Botswana who started ART extremely early, frequently within hours after birth. Decline of genome-intact HIV-1 proviruses occurs rapidly after initiation of ART and is associated with an increase in natural killer (NK) cell populations expressing the cytotoxicity marker CD57 and with a decrease in NK cell subsets expressing the inhibitory marker NKG2A. Immune perturbations in innate lymphoid cells, myeloid dendritic cells, and monocytes detected at birth normalize after rapid institution of antiretroviral therapy but do not notably influence HIV-1 reservoir cell dynamics. These results suggest that HIV-1 reservoir cell seeding and evolution in early-treated neonates is markedly influenced by antiviral NK cell immune responses.
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Affiliation(s)
- Ciputra Adijaya Hartana
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pilar Garcia-Broncano
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kenneth Maswabi
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Gbolahan Ajibola
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Terence Mohammed
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Joseph Makhema
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 20892, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 20892, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kara Bennett
- Bennett Statistical Consulting, Inc., Ballston Lake, NY 12019, USA
| | | | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 20892, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael D Hughes
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kathleen M Powis
- Harvard Medical School, Boston, MA 02115, USA; Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Medicine and Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 20892, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Roger Shapiro
- Harvard Medical School, Boston, MA 02115, USA; Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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37
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Hu W, Li YJ, Zhen C, Wang YY, Huang HH, Zou J, Zheng YQ, Huang GC, Meng SR, Jin JH, Li J, Zhou MJ, Fu YL, Zhang P, Li XY, Yang T, Wang XW, Yang XH, Song JW, Fan X, Jiao YM, Xu RN, Zhang JY, Zhou CB, Yuan JH, Huang L, Qin YQ, Wu FY, Shi M, Wang FS, Zhang C. CCL5-Secreting Virtual Memory CD8+ T Cells Inversely Associate With Viral Reservoir Size in HIV-1-Infected Individuals on Antiretroviral Therapy. Front Immunol 2022; 13:897569. [PMID: 35720272 PMCID: PMC9204588 DOI: 10.3389/fimmu.2022.897569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Recent studies highlighted that CD8+ T cells are necessary for restraining reservoir in HIV-1-infected individuals who undergo antiretroviral therapy (ART), whereas the underlying cellular and molecular mechanisms remain largely unknown. Here, we enrolled 60 virologically suppressed HIV-1-infected individuals, to assess the correlations of the effector molecules and phenotypic subsets of CD8+ T cells with HIV-1 DNA and cell-associated unspliced RNA (CA usRNA). We found that the levels of HIV-1 DNA and usRNA correlated positively with the percentage of CCL4+CCL5- CD8+ central memory cells (TCM) while negatively with CCL4-CCL5+ CD8+ terminally differentiated effector memory cells (TEMRA). Moreover, a virtual memory CD8+ T cell (TVM) subset was enriched in CCL4-CCL5+ TEMRA cells and phenotypically distinctive from CCL4+ TCM subset, supported by single-cell RNA-Seq data. Specifically, TVM cells showed superior cytotoxicity potentially driven by T-bet and RUNX3, while CCL4+ TCM subset displayed a suppressive phenotype dominated by JUNB and CREM. In viral inhibition assays, TVM cells inhibited HIV-1 reactivation more effectively than non-TVM CD8+ T cells, which was dependent on CCL5 secretion. Our study highlights CCL5-secreting TVM cells subset as a potential determinant of HIV-1 reservoir size. This might be helpful to design CD8+ T cell-based therapeutic strategies for cure of the disease.
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Affiliation(s)
- Wei Hu
- Medical School of Chinese People's Liberation Army (PLA), Beijing, China.,Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yan-Jun Li
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Cheng Zhen
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - You-Yuan Wang
- Medical School of Chinese People's Liberation Army (PLA), Beijing, China.,Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Hui-Huang Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jun Zou
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Yan-Qing Zheng
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Gui-Chan Huang
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Si-Run Meng
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Jie-Hua Jin
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jing Li
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ming-Ju Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yu-Long Fu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Peng Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xiao-Yu Li
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Tao Yang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xiu-Wen Wang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xiu-Han Yang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Wen Song
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xing Fan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yan-Mei Jiao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ruo-Nan Xu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ji-Yuan Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Chun-Bao Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Hong Yuan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Lei Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ya-Qin Qin
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Feng-Yao Wu
- Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Ming Shi
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Fu-Sheng Wang
- Medical School of Chinese People's Liberation Army (PLA), Beijing, China.,Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China.,Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Chao Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China.,Guangxi Acquired Immune Deficiency Syndrome (AIDS) Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
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Bosch RJ, Gandhi RT, Mar H, Eron JJ, Cyktor JC, McMahon DK, Mellors JW. Associations Between Multiple Measures of HIV-1 Persistence in Persons on Suppressive Antiretroviral Therapy. J Infect Dis 2022; 225:2163-2166. [PMID: 35137129 PMCID: PMC9200144 DOI: 10.1093/infdis/jiac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/03/2022] [Indexed: 02/06/2023] Open
Abstract
Clinical research to achieve antiretroviral therapy-free remission requires quantitative assays of the HIV-1 reservoir. Intact proviral DNA (IPD) measurement has greater throughput than the quantitative viral outgrowth assay (QVOA). In 25 individuals with well-documented long-term viral suppression, IPD levels and infectious units per million CD4+ T cells by QVOA strongly correlated (r = 0.59, P = .002), and IPD correlated with total cell-associated HIV-1 DNA and cell-associated HIV-1 RNA (r = 0.62 and r = 0.59, P ≤ .002). IPD may provide an accessible marker of inducible replication-competent virus, total numbers of infected cells, and cellular expression of HIV-1 RNA.
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Affiliation(s)
- Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Rajesh T Gandhi
- Infectious Diseases Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanna Mar
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Joshua C Cyktor
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah K McMahon
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Gaebler C, Nogueira L, Stoffel E, Oliveira TY, Breton G, Millard KG, Turroja M, Butler A, Ramos V, Seaman MS, Reeves JD, Petroupoulos CJ, Shimeliovich I, Gazumyan A, Jiang CS, Jilg N, Scheid JF, Gandhi R, Walker BD, Sneller MC, Fauci A, Chun TW, Caskey M, Nussenzweig MC. Prolonged viral suppression with anti-HIV-1 antibody therapy. Nature 2022; 606:368-374. [PMID: 35418681 PMCID: PMC9177424 DOI: 10.1038/s41586-022-04597-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/28/2022] [Indexed: 01/26/2023]
Abstract
HIV-1 infection remains a public health problem with no cure. Anti-retroviral therapy (ART) is effective but requires lifelong drug administration owing to a stable reservoir of latent proviruses integrated into the genome of CD4+ T cells1. Immunotherapy with anti-HIV-1 antibodies has the potential to suppress infection and increase the rate of clearance of infected cells2,3. Here we report on a clinical study in which people living with HIV received seven doses of a combination of two broadly neutralizing antibodies over 20 weeks in the presence or absence of ART. Without pre-screening for antibody sensitivity, 76% (13 out of 17) of the volunteers maintained virologic suppression for at least 20 weeks off ART. Post hoc sensitivity analyses were not predictive of the time to viral rebound. Individuals in whom virus remained suppressed for more than 20 weeks showed rebound viraemia after one of the antibodies reached serum concentrations below 10 µg ml-1. Two of the individuals who received all seven antibody doses maintained suppression after one year. Reservoir analysis performed after six months of antibody therapy revealed changes in the size and composition of the intact proviral reservoir. By contrast, there was no measurable decrease in the defective reservoir in the same individuals. These data suggest that antibody administration affects the HIV-1 reservoir, but additional larger and longer studies will be required to define the precise effect of antibody immunotherapy on the reservoir.
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Affiliation(s)
- Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Elina Stoffel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Columbia University Irving Medical Center, New York, NY, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Allison Butler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Caroline S Jiang
- Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA
| | - Nikolaus Jilg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Johannes F Scheid
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Rajesh Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael C Sneller
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anthony Fauci
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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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: 13] [Impact Index Per Article: 6.5] [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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Moldt B, Günthard HF, Workowski KA, Little SJ, Eron JJ, Overton ET, Lehmann C, Rokx C, Kozal MJ, Gandhi RT, Braun DL, Parvangada A, Li J, Martin R, Selzer L, Cox S, Margot N, Liu H, Slamowitz D, Makadzange T, Collins SE, Geleziunas R, Callebaut C. Evaluation of HIV-1 reservoir size and broadly neutralizing antibody susceptibility in acute antiretroviral therapy-treated individuals. AIDS 2022; 36:205-214. [PMID: 34586088 DOI: 10.1097/qad.0000000000003088] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Persistence of the viral reservoir is the main barrier to curing HIV. Initiation of ART during acute HIV infection can limit the size and diversity of the reservoir. In depth characterization of the reservoir in individuals who initiate ART during acute infection will be critical for clinical trial design and cure strategies. METHODS Four cohorts with participants who initiated ART during acute infection or during chronic infection were enrolled in a cross-sectional, noninterventional study. Viral reservoir was evaluated by the Intact Proviral DNA Assay (IPDA), the Total HIV DNA Assay (THDA) and the Quantitative Viral Outgrowth Assay (QVOA). Viral diversity and susceptibility to V3-glycan bNAbs were determined by genotyping of the viral envelope gene. RESULTS Participants who initiated ART during the acute Fiebig I-IV stages had lower level of total HIV DNA than participants who initiated ART during chronic infection whereas no difference was observed in intact HIV DNA or outgrowth virus. Participants who initiated ART during Fiebig I-IV also had lower viral diversity and appeared to have higher susceptibility to bNAbs than participants initiating ART during chronic infection. CONCLUSION Individuals initiating ART during Fiebig I-IV had small viral reservoirs, low viral diversity, and high susceptibility to bNAbs, and would be an optimal target population for proof-of-concept HIV cure trials.
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Affiliation(s)
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kimberly A Workowski
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia
| | - Susan J Little
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California
| | - Joseph J Eron
- Division of Infectious Diseases, University of North Carolina at Chapel Hill School of Medicine, North Carolina
| | - Edgar T Overton
- Division of Infectious Diseases, University of Alabama at Birmingham School of Medicine, Alabama, USA
| | - Clara Lehmann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne
- German Center for Infection Research, Partner Site Bonn-Cologne
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Casper Rokx
- Department of Internal Medicine, and
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Rajesh T Gandhi
- Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusett, USA
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Jiani Li
- Gilead Sciences, Inc., California, USA
| | | | | | | | | | - Hui Liu
- Gilead Sciences, Inc., California, USA
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Miller JS, Davis ZB, Helgeson E, Reilly C, Thorkelson A, Anderson J, Lima NS, Jorstad S, Hart GT, Lee JH, Safrit JT, Wong H, Cooley S, Gharu L, Chung H, Soon-Shiong P, Dobrowolski C, Fletcher CV, Karn J, Douek DC, Schacker TW. Safety and virologic impact of the IL-15 superagonist N-803 in people living with HIV: a phase 1 trial. Nat Med 2022; 28:392-400. [DOI: 10.1038/s41591-021-01651-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/30/2021] [Indexed: 12/26/2022]
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Lian X, Gao C, Sun X, Jiang C, Einkauf KB, Seiger KW, Chevalier JM, Yuki Y, Martin M, Hoh R, Peluso MJ, Carrington M, Ruiz-Mateos E, Deeks SG, Rosenberg ES, Walker BD, Lichterfeld M, Yu XG. Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers. Sci Transl Med 2021; 13:eabl4097. [PMID: 34910552 PMCID: PMC9202005 DOI: 10.1126/scitranslmed.abl4097] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Increasing evidence suggests that durable drug-free control of HIV-1 replication is enabled by effective cellular immune responses that may induce an attenuated viral reservoir configuration with a weaker ability to drive viral rebound. Here, we comprehensively tracked effects of antiviral immune responses on intact and defective proviral sequences from elite controllers (ECs), analyzing both classical escape mutations and HIV-1 chromosomal integration sites as biomarkers of antiviral immune selection pressure. We observed that, within ECs, defective proviruses were commonly located in permissive genic euchromatin positions, which represented an apparent contrast to autologous intact proviruses that were frequently located in heterochromatin regions; this suggests differential immune selection pressure on intact versus defective proviruses in ECs. In comparison to individuals receiving antiretroviral therapy, intact and defective proviruses from ECs showed reduced frequencies of escape mutations in cytotoxic T cell epitopes and antibody contact regions, possibly due to the small and poorly inducible reservoir that may be insufficient to drive effective viral escape in ECs. About 15% of ECs harbored nef deletions in intact proviruses, consistent with increased viral vulnerability to host immunity in the setting of nef dysfunction. Together, these results suggest a distinct signature of immune footprints in proviral sequences from ECs.
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Affiliation(s)
- Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kevin B. Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kyra W. Seiger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Joshua M. Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rebecca Hoh
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Michael J. Peluso
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ezequiel Ruiz-Mateos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville 41013, Spain
| | - Steven G. Deeks
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Eric S. Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
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Kuniholm J, Armstrong E, Bernabe B, Coote C, Berenson A, Patalano SD, Olson A, He X, Lin NH, Fuxman Bass JI, Henderson AJ. Intragenic proviral elements support transcription of defective HIV-1 proviruses. PLoS Pathog 2021; 17:e1009982. [PMID: 34962974 PMCID: PMC8746790 DOI: 10.1371/journal.ppat.1009982] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/10/2022] [Accepted: 12/07/2021] [Indexed: 11/18/2022] Open
Abstract
HIV-1 establishes a persistent proviral reservoir by integrating into the genome of infected host cells. Current antiretroviral treatments do not target this persistent population of proviruses which include latently infected cells that upon treatment interruption can be reactivated to contribute to HIV-1 rebound. Deep sequencing of persistent HIV proviruses has revealed that greater than 90% of integrated HIV genomes are defective and unable to produce infectious virions. We hypothesized that intragenic elements in the HIV genome support transcription of aberrant HIV-1 RNAs from defective proviruses that lack long terminal repeats (LTRs). Using an intact provirus detection assay, we observed that resting CD4+ T cells and monocyte-derived macrophages (MDMs) are biased towards generating defective HIV-1 proviruses. Multiplex reverse transcription droplet digital PCR identified env and nef transcripts which lacked 5' untranslated regions (UTR) in acutely infected CD4+ T cells and MDMs indicating transcripts are generated that do not utilize the promoter within the LTR. 5'UTR-deficient env transcripts were also identified in a cohort of people living with HIV (PLWH) on ART, suggesting that these aberrant RNAs are produced in vivo. Using 5' rapid amplification of cDNA ends (RACE), we mapped the start site of these transcripts within the Env gene. This region bound several cellular transcription factors and functioned as a transcriptional regulatory element that could support transcription and translation of downstream HIV-1 RNAs. These studies provide mechanistic insights into how defective HIV-1 proviruses are persistently expressed to potentially drive inflammation in PLWH.
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Affiliation(s)
- Jeffrey Kuniholm
- Boston University School of Medicine, Department of Microbiology, Boston, Massachusetts, United States of America
| | - Elise Armstrong
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Brandy Bernabe
- Boston University School of Medicine Graduate Medical Sciences, Boston, Massachusetts, United States of America
| | - Carolyn Coote
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Anna Berenson
- Boston University, Department of Biology, Boston, Massachusetts, United States of America
| | - Samantha D. Patalano
- Boston University, Department of Biology, Boston, Massachusetts, United States of America
| | - Alex Olson
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Xianbao He
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Nina H. Lin
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Juan I. Fuxman Bass
- Boston University, Department of Biology, Boston, Massachusetts, United States of America
| | - Andrew J. Henderson
- Boston University School of Medicine, Department of Microbiology, Boston, Massachusetts, United States of America
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
- Boston University School of Medicine Graduate Medical Sciences, Boston, Massachusetts, United States of America
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HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy. mBio 2021; 12:e0249021. [PMID: 34781741 PMCID: PMC8693448 DOI: 10.1128/mbio.02490-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Curing HIV will require eliminating the reservoir of integrated, replication-competent proviruses that persist despite antiretroviral therapy (ART). Understanding the burden, genetic diversity, and longevity of persisting proviruses in diverse individuals with HIV is critical to this goal, but these characteristics remain understudied in some groups. Among them are viremic controllers—individuals who naturally suppress HIV to low levels but for whom therapy is nevertheless recommended. We reconstructed within-host HIV evolutionary histories from longitudinal single-genome amplified viral sequences in four viremic controllers who eventually initiated ART and used this information to characterize the age and diversity of proviruses persisting on therapy. We further leveraged these within-host proviral age distributions to estimate rates of proviral turnover prior to ART. This is an important yet understudied metric, since pre-ART proviral turnover dictates reservoir composition at ART initiation (and thereafter), which is when curative interventions, once developed, would be administered. Despite natural viremic control, all participants displayed significant within-host HIV evolution pretherapy, where overall on-ART proviral burden and diversity broadly reflected the extent of viral replication and diversity pre-ART. Consistent with recent studies of noncontrollers, the proviral pools of two participants were skewed toward sequences that integrated near ART initiation, suggesting dynamic proviral turnover during untreated infection. In contrast, proviruses recovered from the other two participants dated to time points that were more evenly spread throughout infection, suggesting slow or negligible proviral decay following deposition. HIV cure strategies will need to overcome within-host proviral diversity, even in individuals who naturally controlled HIV replication before therapy.
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Ismail SD, Riou C, Joseph SB, Archin NM, Margolis DM, Perelson AS, Cassidy T, Abrahams MR, Moeser M, Council OD, McKinnon LR, Osman F, Karim QA, Abdool Karim SS, Swanstrom R, Williamson C, Garrett NJ, Burgers WA. Immunological Correlates of the HIV-1 Replication-Competent Reservoir Size. Clin Infect Dis 2021; 73:1528-1531. [PMID: 34181706 PMCID: PMC8528395 DOI: 10.1093/cid/ciab587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 12/28/2022] Open
Abstract
Understanding what shapes the latent human immunodeficiency virus type 1 (HIV-1) reservoir is critical for developing strategies for cure. We measured frequency of persistent HIV-1 infection after 5 years of suppressive antiretroviral therapy initiated during chronic infection. Pretreatment CD8+ T-cell activation, nadir CD4 count, and CD4:CD8 ratio predicted reservoir size.
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Affiliation(s)
- Sherazaan D Ismail
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Catherine Riou
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town,South Africa
| | - Sarah B Joseph
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancie M Archin
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,USA
| | - David M Margolis
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tyler Cassidy
- Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Melissa-Rose Abrahams
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Matthew Moeser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Olivia D Council
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lyle R McKinnon
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Farzana Osman
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Ronald Swanstrom
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolyn Williamson
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town,South Africa
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel J Garrett
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Wendy A Burgers
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town,South Africa
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Lungu C, Banga R, Gruters RA, Procopio FA. Inducible HIV-1 Reservoir Quantification: Clinical Relevance, Applications and Advancements of TILDA. Front Microbiol 2021; 12:686690. [PMID: 34211450 PMCID: PMC8239294 DOI: 10.3389/fmicb.2021.686690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/21/2021] [Indexed: 01/07/2023] Open
Abstract
The presence of a stable HIV-1 reservoir persisting over time despite effective antiretroviral suppression therapy precludes a cure for HIV-1. Characterizing and quantifying this residual reservoir is considered an essential prerequisite to develop and validate curative strategies. However, a sensitive, reproducible, cost-effective, and easily executable test is still needed. The quantitative viral outgrowth assay is considered the gold standard approach to quantify the reservoir in HIV-1-infected patients on suppressive ART, but it has several limitations. An alternative method to quantify the viral reservoir following the reactivation of latent HIV-1 provirus detects multiply-spliced tat/rev RNA (msRNA) molecules by real-time PCR [tat/rev induced limiting dilution assay (TILDA)]. This article provides a perspective overview of the clinical relevance, various applications, recent advancements of TILDA, and how the assay has contributed to our understanding of the HIV-1 reservoir.
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Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Riddhima Banga
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A. Procopio
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland,*Correspondence: Francesco A. Procopio,
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48
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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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49
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Gaebler C, Falcinelli SD, Stoffel E, Read J, Murtagh R, Oliveira TY, Ramos V, Lorenzi JCC, Kirchherr J, James KS, Allard B, Baker C, Kuruc JD, Caskey M, Archin NM, Siliciano RF, Margolis DM, Nussenzweig MC. Sequence Evaluation and Comparative Analysis of Novel Assays for Intact Proviral HIV-1 DNA. J Virol 2021; 95:e01986-20. [PMID: 33361426 PMCID: PMC8094944 DOI: 10.1128/jvi.01986-20] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
The HIV proviral reservoir is the major barrier to cure. The predominantly replication-defective proviral landscape makes the measurement of virus that is likely to cause rebound upon antiretroviral therapy (ART)-cessation challenging. To address this issue, novel assays to measure intact HIV proviruses have been developed. The intact proviral DNA assay (IPDA) is a high-throughput assay that uses two probes to exclude the majority of defective proviruses and determine the frequency of intact proviruses, albeit without sequence confirmation. Quadruplex PCR with four probes (Q4PCR) is a lower-throughput assay that uses limiting dilution long-distance PCR amplification followed by quantitative PCR (qPCR) and near-full-length genome sequencing (nFGS) to estimate the frequency of sequence-confirmed intact proviruses and provide insight into their clonal composition. To explore the advantages and limitations of these assays, we compared IPDA and Q4PCR measurements from 39 ART-suppressed people living with HIV. We found that IPDA and Q4PCR measurements correlated with one another, but frequencies of intact proviral DNA differed by approximately 19-fold. This difference may be in part due to inefficiencies in long-distance PCR amplification of proviruses in Q4PCR, leading to underestimates of intact proviral frequencies. In addition, nFGS analysis within Q4PCR explained that some of this difference is explained by proviruses that are classified as intact by IPDA but carry defects elsewhere in the genome. Taken together, this head-to-head comparison of novel intact proviral DNA assays provides important context for their interpretation in studies to deplete the HIV reservoir and shows that together the assays bracket true reservoir size.IMPORTANCE The intact proviral DNA assay (IPDA) and quadruplex PCR (Q4PCR) represent major advances in accurately quantifying and characterizing the replication-competent HIV reservoir. This study compares the two novel approaches for measuring intact HIV proviral DNA in samples from 39 antiretroviral therapy (ART)-suppressed people living with HIV, thereby informing ongoing efforts to deplete the HIV reservoir in cure-related trials.
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Affiliation(s)
- Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Shane D Falcinelli
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Elina Stoffel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Jenna Read
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ross Murtagh
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Jennifer Kirchherr
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Katherine S James
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Brigitte Allard
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Caroline Baker
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - JoAnn D Kuruc
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Nancie M Archin
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - David M Margolis
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
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