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Tincati C, Bono V, Cannizzo ES, Tosi D, Savi F, Falcinella C, Casabianca A, Orlandi C, Luigiano C, Augello M, Rusconi S, Muscatello A, Bandera A, Calcagno A, Gori A, Nozza S, Marchetti G. Primary HIV infection features colonic damage and neutrophil inflammation yet containment of microbial translocation. AIDS 2024; 38:623-632. [PMID: 38016163 PMCID: PMC10942218 DOI: 10.1097/qad.0000000000003799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/20/2023] [Accepted: 11/18/2023] [Indexed: 11/30/2023]
Abstract
INTRODUCTION Impairment of the gastrointestinal barrier leads to microbial translocation and peripheral immune activation, which are linked to disease progression. Data in the setting of primary HIV/SIV infection suggest that gut barrier damage is one of the first events of the pathogenic cascade, preceding mucosal immune dysfunction and microbial translocation. We assessed gut structure and immunity as well as microbial translocation in acutely and chronically-infected, combination antiretroviral therapy (cART)-naive individuals. METHODS Fifteen people with primary HIV infection (P-HIV) and 13 with chronic HIV infection (C-HIV) c-ART-naive participants were cross-sectionally studied. Gut biopsies were analysed in terms of gut reservoirs (total, integrated and unintegrated HIV DNA); tight junction proteins (E-cadherin, Zonula Occludens-1), CD4 + expression, neutrophil myeloperoxidase (histochemical staining); collagen deposition (Masson staining). Flow cytometry was used to assess γδ T-cell frequency (CD3 + panγδ+Vδ1+/Vδ2+). In plasma, we measured microbial translocation (LPS, sCD14, EndoCAb) and gut barrier function (I-FABP) markers (ELISA). RESULTS P-HIV displayed significantly higher tissue HIV DNA, yet neutrophil infiltration and collagen deposition in the gut were similar in the two groups. In contrast, microbial translocation markers were significantly lower in P-HIV compared with C-HIV. A trend to higher mucosal E-cadherin, and gut γδ T-cells was also observed in P-HIV. CONCLUSION Early HIV infection features higher HIV DNA in the gut, yet comparable mucosal alterations to those observed in chronic infection. In contrast, microbial translocation is contained in primary HIV infection, likely because of a partial preservation of E-cadherin and mucosal immune subsets, namely γδ T-cells.
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Affiliation(s)
- Camilla Tincati
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan
| | - Valeria Bono
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan
| | | | - Delfina Tosi
- Pathology Unit, Department of Health Sciences, ASST Santi Paolo e Carlo, University of Milan, Milan
| | - Federica Savi
- Pathology Unit, Department of Health Sciences, ASST Santi Paolo e Carlo, University of Milan, Milan
| | - Camilla Falcinella
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan
| | - Anna Casabianca
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Fano
| | - Chiara Orlandi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Fano
| | | | - Matteo Augello
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan
| | - Stefano Rusconi
- UOC Malattie Infettive, Ospedale Civile di Legnano, Department of Biomedical and Clinical Biosciences, University of Milan
| | - Antonio Muscatello
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan
| | - Andrea Calcagno
- Unit of Infectious Diseases Unit, Department of Medical Sciences, University of Turin, Turin
| | - Andrea Gori
- Clinic of Infectious Diseases, Department of Pathophysiology and Transplantation, ASST Fatebenefratelli Sacco University of Milan
| | - Silvia Nozza
- Infectious Diseases Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan
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Roux H, Chomont N. Measuring Human Immunodeficiency Virus Reservoirs: Do We Need to Choose Between Quantity and Quality? J Infect Dis 2024; 229:635-643. [PMID: 37665978 PMCID: PMC10938203 DOI: 10.1093/infdis/jiad381] [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: 06/15/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023] Open
Abstract
The persistence of latent viral genomes in people receiving antiretroviral therapy (ART) is the main obstacle to a cure for human immunodeficiency virus (HIV) infection. Viral reservoirs can be defined as cells harboring HIV genomes that have the ability to produce infectious virions. Precise quantification of the cellular reservoirs of HIV is challenging because these cells are rare, heterogeneous, and outnumbered by a larger number of cells carrying defective genomes. In addition, measuring the inducibility of these proviruses requires functional assays and remains technically difficult. The recent development of single-cell and single-viral genome approaches revealed additional layers of complexity: the cell subsets that harbor proviruses are heterogeneous and their ability to be induced is variable. A substantial fraction of intact HIV genomes may be permanently silenced after years of ART, revealing the underappreciated importance of induction assays. As such, a simple approach that would assess simultaneously the genetic intactness and the inducibility of the reservoir is still lacking. In this study, we review recent advances in the development of methods to quantify and characterize persistently infected cells, and we discuss how these findings can inform the design of future assays aimed at measuring the size of the intact and inducible HIV reservoir.
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Affiliation(s)
- Hélène Roux
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
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Vanegas-Torres CA, Schindler M. HIV-1 Vpr Functions in Primary CD4 + T Cells. Viruses 2024; 16:420. [PMID: 38543785 PMCID: PMC10975730 DOI: 10.3390/v16030420] [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: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 05/23/2024] Open
Abstract
HIV-1 encodes four accesory proteins in addition to its structural and regulatory genes. Uniquely amongst them, Vpr is abundantly present within virions, meaning it is poised to exert various biological effects on the host cell upon delivery. In this way, Vpr contributes towards the establishment of a successful infection, as evidenced by the extent to which HIV-1 depends on this factor to achieve full pathogenicity in vivo. Although HIV infects various cell types in the host organism, CD4+ T cells are preferentially targeted since they are highly permissive towards productive infection, concomitantly bringing about the hallmark immune dysfunction that accompanies HIV-1 spread. The last several decades have seen unprecedented progress in unraveling the activities Vpr possesses in the host cell at the molecular scale, increasingly underscoring the importance of this viral component. Nevertheless, it remains controversial whether some of these advances bear in vivo relevance, since commonly employed cellular models significantly differ from primary T lymphocytes. One prominent example is the "established" ability of Vpr to induce G2 cell cycle arrest, with enigmatic physiological relevance in infected primary T lymphocytes. The objective of this review is to present these discoveries in their biological context to illustrate the mechanisms whereby Vpr supports HIV-1 infection in CD4+ T cells, whilst identifying findings that require validation in physiologically relevant models.
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Affiliation(s)
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany;
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Ram A, Rascon Velasco V, Mchantaf G, Avettand-Fénoël V, Viard JP. Factors associated with unquantifiable total HIV-1 DNA in peripheral blood in persons living with HIV: An observational study. J Virus Erad 2024; 10:100370. [PMID: 38596322 PMCID: PMC11002866 DOI: 10.1016/j.jve.2024.100370] [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: 03/14/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Background The human immunodeficiency virus type 1 (HIV-1) cannot be eradicated even with suppressive antiretroviral therapy because its retrotranscribed genome integrates into the DNA of host cells, creating a long-term reservoir. Quantification of total HIV-1 DNA in peripheral blood is a biomarker of this reservoir that can predict progression of the infection, treatment response, and HIV-1-related complications. A deeper understanding of the reservoir may help develop a cures. Objective This study aimed to characterize persons living with HIV-1 (PLWH) with unquantifiable total HIV-1 DNA in blood (below the quantification threshold) and identify associated factors. Methods We have conducted a retrospective observational study. During the study period, all PLWH who had total leukocyte-associated HIV-1 DNA measured by quantitative PCR were included. We have isolated a population of participants with HIV-1 DNA levels below the quantification threshold (40 copies/106 leukocytes). Results Out of 1094 patients analysed, 62 had unquantifiable and 1032 quantifiable HIV-1 DNA levels in blood. We have found that those with unquantifiable HIV-1 DNA had a higher CD4 T cell nadir (p = 0.006) and a lower viral load zenith (p < 0.001). Multivariate analyses showed that initiation of treatment in primary infection was the only protective factor against HIV-1 DNA quantifiability, the odds of HIV-1 DNA quantifiability decreased by 82% in those treated within 30 days of infection, after controlling for other factors. Conclusion Our research highlights the importance of an early start of anti-retroviral therapy to limit the size of the HIV-1 reservoir, as receiving treatment during primary infection was found as the only protective factor against quantifiability of HIV-1 DNA in blood.
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Affiliation(s)
- Aurélie Ram
- Service d’Immuno-infectiologie, Hôpital Hôtel-Dieu, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Vanessa Rascon Velasco
- Service d’Immuno-infectiologie, Hôpital Hôtel-Dieu, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Gilbert Mchantaf
- Laboratoire de Virologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, School of Medicine, France
- Inserm U1016, CNRS UMR8104, Equipe Retrovirus, Infection, Latence, Institut Cochin, Paris, France
| | - Véronique Avettand-Fénoël
- Laboratoire de Virologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, School of Medicine, France
- Inserm U1016, CNRS UMR8104, Equipe Retrovirus, Infection, Latence, Institut Cochin, Paris, France
| | - Jean-Paul Viard
- Service d’Immuno-infectiologie, Hôpital Hôtel-Dieu, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, School of Medicine, France
- Inserm U1016, CNRS UMR8104, Equipe Retrovirus, Infection, Latence, Institut Cochin, Paris, France
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Ratouit P, Malet I, Soulie C, Denis J, Legrand R, Teyssou E, Marcelin AG, Calvez V, Guiraud V. HIV-1 resistance mutations to integrase inhibitors impair both integration and reverse transcription steps. Int J Antimicrob Agents 2024; 63:107026. [PMID: 37926272 DOI: 10.1016/j.ijantimicag.2023.107026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/09/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Affiliation(s)
- Pauline Ratouit
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France.
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Jerome Denis
- AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Biochimie Endocrinienne et Oncologie, Paris, France
| | - Ronan Legrand
- AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Biochimie Endocrinienne et Oncologie, Paris, France
| | - Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Vincent Guiraud
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
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Rial-Crestelo D, Pinto-Martínez A, Navarro-Soler R, Pulido F. Deep Sequencing on Proviral DNA: More Questions than Answers. J Acquir Immune Defic Syndr 2023; 94:e1. [PMID: 37256638 DOI: 10.1097/qai.0000000000003230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- David Rial-Crestelo
- HIV Unit, Hospital, University Hospital 12 de Octubre, Madrid, Spain; and
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | | | | | - Federico Pulido
- HIV Unit, Hospital, University Hospital 12 de Octubre, Madrid, Spain; and
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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7
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Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev 2022; 35:e0005222. [PMID: 36102816 PMCID: PMC9769561 DOI: 10.1128/cmr.00052-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, California, USA
| | - Daniele Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Charles Walworth
- LabCorp-Monogram Biosciences, South San Francisco, California, USA
| | - Maria M. Santoro
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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8
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Wang X, Vincent E, Siddiqui S, Turnbull K, Lu H, Blair R, Wu X, Watkins M, Ziani W, Shao J, Doyle-Meyers LA, Russell-Lodrigue KE, Bohm RP, Veazey RS, Xu H. Early treatment regimens achieve sustained virologic remission in infant macaques infected with SIV at birth. Nat Commun 2022; 13:4823. [PMID: 35973985 PMCID: PMC9381774 DOI: 10.1038/s41467-022-32554-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 08/04/2022] [Indexed: 01/28/2023] Open
Abstract
Early antiretroviral therapy (ART) in HIV-infected infants generally fails to achieve a sustained state of ART-free virologic remission, even after years of treatment. Our studies show that viral reservoir seeding is different in neonatal macaques intravenously exposed to SIV at birth, in contrast to adults. Furthermore, one month of ART including an integrase inhibitor, initiated at day 3, but not day 4 or 5 post infection, efficiently and rapidly suppresses viremia to undetectable levels. Intervention initiated at day 3 post infection and continued for 9 months achieves a sustained virologic remission in 4 of 5 infants. Collectively, an early intervention strategy within a key timeframe and regimen may result in viral remission or successful post-exposure prophylaxis for neonatal SIV infection, which may be clinically relevant for optimizing treatment strategies for HIV-infected or exposed infants.
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Affiliation(s)
- Xiaolei Wang
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Eunice Vincent
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Summer Siddiqui
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Katherine Turnbull
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Robert Blair
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Meagan Watkins
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Widade Ziani
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Jiasheng Shao
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Lara A Doyle-Meyers
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Kasi E Russell-Lodrigue
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Rudolf P Bohm
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Huanbin Xu
- Tulane National Primate Research Center, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA, 70433, USA.
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Beliakova-Bethell N, Manousopoulou A, Deshmukh S, Mukim A, Richman DD, Garbis SD, Spina CA. Integrated proteomics and transcriptomics analyses identify novel cell surface markers of HIV latency. Virology 2022; 573:50-58. [PMID: 35714458 PMCID: PMC10427345 DOI: 10.1016/j.virol.2022.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
Elimination of the latent HIV cell reservoir may be possible, if the molecular identity of latently infected cells were fully elucidated. We conducted comprehensive molecular profiling, at the protein and RNA levels, of primary T cells latently infected with HIV in vitro. Isobaric labelling quantitative proteomics and RNA sequencing identified 1453 proteins and 618 genes, altered in latently infected cells compared to mock-infected controls (p < 0.05). Biomarker selection was based on results from integrated data analysis. Relative enrichment for latently infected cells was monitored using flow cytometric sorting and the HIV integrant assay. Antibodies against selected proteins, encoded by CEACAM1 and PLXNB2, enabled enrichment of latently infected cells from cell mixtures by 3-10 fold (5.8 average, p < 0.001), comparable to levels obtained with biomarkers reported previously. Individual biomarkers are likely linked to subsets of latently infected cells, and an extended antibody panel will be required to inclusively target the latent HIV reservoir.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA.
| | - Antigoni Manousopoulou
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK; Proteas Bioanalytics Inc., BioLabs at the Lundquist Institute, Torrance, CA, USA
| | | | - Amey Mukim
- University of California at San Diego, CA, USA
| | - Douglas D Richman
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA
| | - Spiros D Garbis
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK; Proteas Bioanalytics Inc., BioLabs at the Lundquist Institute, Torrance, CA, USA
| | - Celsa A Spina
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA
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10
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Soto PC, Terry VH, Lewinski MK, Deshmukh S, Beliakova-Bethell N, Spina CA. HIV-1 latency is established preferentially in minimally activated and non-dividing cells during productive infection of primary CD4 T cells. PLoS One 2022; 17:e0271674. [PMID: 35895672 PMCID: PMC9328514 DOI: 10.1371/journal.pone.0271674] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Latently infected CD4 T cells form a stable reservoir of HIV that leads to life-long viral persistence; the mechanisms involved in establishment of this latency are not well understood. Three scenarios have been proposed: 1) an activated, proliferating cell becomes infected and reverts back to a resting state; 2) an activated cell becomes infected during its return to resting; or 3) infection is established directly in a resting cell. The aim of this study was, therefore, to investigate the relationship between T cell activation and proliferation and the establishment of HIV latency. Isolated primary CD4 cells were infected at different time points before or after TCR-induced stimulation. Cell proliferation within acutely infected cultures was tracked using CFSE viable dye over 14 days; and cell subsets that underwent varying degrees of proliferation were isolated at end of culture by flow cytometric sorting. Recovered cell subpopulations were analyzed for the amount of integrated HIV DNA, and the ability to produce virus, upon a second round of cell stimulation. We show that cell cultures exposed to virus, prior to stimulus addition, contained the highest levels of integrated and replication-competent provirus after returning to quiescence; whereas, cells infected during the height of cell proliferation retained the least. Cells that did not divide or exhibited limited division, following virus exposure and stimulation contained greater amounts of integrated and inducible HIV than did cells that had divided many times. Based on these results, co-culture experiments were conducted to demonstrate that latent infection could be established directly in non-dividing cells via cell-to-cell transmission from autologous productively infected cells. Together, the findings from our studies implicate the likely importance of direct infection of sub-optimally activated T cells in establishment of latently infected reservoirs in vivo, especially in CD4 lymphocytes that surround productive viral foci within immune tissue microenvironments.
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Affiliation(s)
- Paula C. Soto
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Valeri H. Terry
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
| | - Mary K. Lewinski
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Savitha Deshmukh
- Veterans Medical Research Foundation, San Diego, California, United States of America
| | - Nadejda Beliakova-Bethell
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Celsa A. Spina
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
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11
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Alidjinou E, Robineau O, Huleux T, Meybeck A, Hober D, Ajana F, Bocket L. Difficulty in reaching viral suppression in a long-term treated HIV-1 patient: role of the reservoir rather than drug resistance? Infect Dis Now 2022; 52:315-317. [PMID: 35283341 DOI: 10.1016/j.idnow.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/28/2021] [Accepted: 03/04/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Ek Alidjinou
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie ULR 3610, F-59000 Lille, France.
| | - O Robineau
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - T Huleux
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - A Meybeck
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - D Hober
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie ULR 3610, F-59000 Lille, France
| | - F Ajana
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - L Bocket
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie ULR 3610, F-59000 Lille, France
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12
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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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13
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Quantification of Total HIV DNA as a Marker to Measure Viral Reservoir: Methods and Potential Implications for Clinical Practice. Diagnostics (Basel) 2021; 12:diagnostics12010039. [PMID: 35054206 PMCID: PMC8774405 DOI: 10.3390/diagnostics12010039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
The focus of this review is to examine the importance of quantifying total HIV DNA to target the HIV reservoir and the clinical implications and challenges involved in its future application in clinical practice. Despite intrinsic limitations, the quantification of total HIV DNA is currently the most widely used marker for exploring the HIV reservoir. As it allows estimating all forms of HIV DNA in the infected cells, total HIV DNA load is the biomarker of the HIV reservoir that provides most of the insights into HIV pathogenesis. The clinical role of total HIV-DNA in both untreated and treated patients is extensively supported by important lines of evidence. Thus, predictive models that include total HIV DNA load together with other variables could constitute a prognostic tool for use in clinical practice. To date, however, this marker has been primarily used in experimental evaluations. The main challenge is technical. Although the implementation of droplet digital PCR could improve analytical performance over real-time PCR, the lack of standardization has made cross-comparisons of the data difficult. An effort by investigators to compare protocols is needed. Furthermore, the main effort now should be to involve the biomedical industry in the development of certified assays for in vitro diagnostics use.
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14
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Zhang L, Wang J, von Kleist M. Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes. PLoS Comput Biol 2021; 17:e1009295. [PMID: 34941864 PMCID: PMC8741042 DOI: 10.1371/journal.pcbi.1009295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/07/2022] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Pre-exposure prophylaxis (PrEP) is an important pillar to prevent HIV transmission. Because of experimental and clinical shortcomings, mathematical models that integrate pharmacological, viral- and host factors are frequently used to quantify clinical efficacy of PrEP. Stochastic simulations of these models provides sample statistics from which the clinical efficacy is approximated. However, many stochastic simulations are needed to reduce the associated sampling error. To remedy the shortcomings of stochastic simulation, we developed a numerical method that allows predicting the efficacy of arbitrary prophylactic regimen directly from a viral dynamics model, without sampling. We apply the method to various hypothetical dolutegravir (DTG) prophylaxis scenarios. The approach is verified against state-of-the-art stochastic simulation. While the method is more accurate than stochastic simulation, it is superior in terms of computational performance. For example, a continuous 6-month prophylactic profile is computed within a few seconds on a laptop computer. The method’s computational performance, therefore, substantially expands the horizon of feasible analysis in the context of PrEP, and possibly other applications. Pre-exposure prophylaxis (PrEP) is an important tool to prevent HIV transmission. However, experimental identification of parameters that determine prophylactic efficacy is extremely difficult. Clues about these parameters could prove essential for the design of next-generation PrEP compounds. Integrative mathematical models can fill this void: Based on stochastic simulation, a sample statistic can be generated, from which the prophylactic efficacy is estimated. However, for this sample statistic to be accurate, many simulations need to be performed. Here, we introduce a numerical method to directly compute the prophylactic efficacy from a viral dynamics model, without the need for sampling. Based on several examples with dolutegravir (DTG) -based short- and long-term PrEP, as well as post-exposure prophylaxis we demonstrate the correctness of the new method and its outstanding computational performance. Due to the method’s computational performance, a number of analyses, including formal sensitivity analysis, are becoming feasible with the proposed method.
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Affiliation(s)
- Lanxin Zhang
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
| | - Junyu Wang
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
| | - Max von Kleist
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
- * E-mail:
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15
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Systemic and Intestinal Viral Reservoirs in CD4+ T Cell Subsets in Primary SIV Infection. Viruses 2021; 13:v13122398. [PMID: 34960667 PMCID: PMC8704255 DOI: 10.3390/v13122398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV reservoir size in target CD4+ T cells during primary infection remains unknown. Here, we sorted peripheral and intestinal CD4+ T cells and quantified the levels of cell-associated SIV RNA and DNA in rhesus macaques within days of SIVmac251 inoculation. As a major target cell of HIV/SIV, CD4+ T cells in both tissues contained a large amount of SIV RNA and DNA at day 8–13 post-SIV infection, in which productive SIV RNA highly correlated with the levels of cell-associated SIV DNA. Memory CD4+ T cells had much higher viral RNA and DNA than naïve subsets, yet memory CD4+ T cells co-expressing CCR5 had no significant reservoir size compared with those that were CCR5-negative in blood and intestine. Collectively, memory CD4+ T cells appear to be the major targets for primary infection, and viral reservoirs are equally distributed in systemic and lymphoid compartments in acutely SIV-infected macaques.
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16
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Rausch JW, Le Grice SFJ. Characterizing the Latent HIV-1 Reservoir in Patients with Viremia Suppressed on cART: Progress, Challenges, and Opportunities. Curr HIV Res 2021; 18:99-113. [PMID: 31889490 PMCID: PMC7475929 DOI: 10.2174/1570162x18666191231105438] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Modern combination antiretroviral therapy (cART) can bring HIV-1 in blood plasma to level undetectable by standard tests, prevent the onset of acquired immune deficiency syndrome (AIDS), and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, cART is not curative, as within a few weeks of treatment cessation, HIV viremia in most patients rebounds to pre-cART levels. The primary source of this rebound, and the principal barrier to a cure, is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of resting memory CD4+ T cells. In this review, prevailing models for how the latent reservoir is established and maintained, residual viremia and viremic rebound upon withdrawal of cART, and the types and characteristics of cells harboring latent HIV-1 will be discussed. Selected technologies currently being used to advance our understanding of HIV latency will also be presented, as will a perspective on which areas of advancement are most essential for producing the next generation of HIV-1 therapeutics.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
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17
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Leyre L, Kroon E, Vandergeeten C, Sacdalan C, Colby DJ, Buranapraditkun S, Schuetz A, Chomchey N, de Souza M, Bakeman W, Fromentin R, Pinyakorn S, Akapirat S, Trichavaroj R, Chottanapund S, Manasnayakorn S, Rerknimitr R, Wattanaboonyoungcharoen P, Kim JH, Tovanabutra S, Schacker TW, O'Connell R, Valcour VG, Phanuphak P, Robb ML, Michael N, Trautmann L, Phanuphak N, Ananworanich J, Chomont N. Abundant HIV-infected cells in blood and tissues are rapidly cleared upon ART initiation during acute HIV infection. Sci Transl Med 2021; 12:12/533/eaav3491. [PMID: 32132218 DOI: 10.1126/scitranslmed.aav3491] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/19/2019] [Accepted: 01/21/2020] [Indexed: 12/15/2022]
Abstract
The timing and location of the establishment of the viral reservoir during acute HIV infection remain unclear. Using longitudinal blood and tissue samples obtained from HIV-infected individuals at the earliest stage of infection, we demonstrate that frequencies of infected cells reach maximal values in gut-associated lymphoid tissue and lymph nodes as early as Fiebig stage II, before seroconversion. Both tissues displayed higher frequencies of infected cells than blood until Fiebig stage III, after which infected cells were equally distributed in all compartments examined. Initiation of antiretroviral therapy (ART) at Fiebig stages I to III led to a profound decrease in the frequency of infected cells to nearly undetectable level in all compartments. The rare infected cells that persisted were preferentially found in the lymphoid tissues. Initiation of ART at later stages (Fiebig stages IV/V and chronic infection) induced only a modest reduction in the frequency of infected cells. Quantification of HIV DNA in memory CD4+ T cell subsets confirmed the unstable nature of most of the infected cells at Fiebig stages I to III and the emergence of persistently infected cells during the transition to Fiebig stage IV. Our results indicate that although a large pool of cells is infected during acute HIV infection, most of these early targets are rapidly cleared upon ART initiation. Therefore, infected cells present after peak viremia have a greater ability to persist.
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Affiliation(s)
- Louise Leyre
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Eugène Kroon
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | | | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Donn J Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | | | - Alexandra Schuetz
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA
| | - Nitiya Chomchey
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Mark de Souza
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Wendy Bakeman
- Vaccine and Gene Therapy Institute of Florida, FL 34987, USA
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Suteeraporn Pinyakorn
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA
| | - Siriwat Akapirat
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Rapee Trichavaroj
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | | | | | | | | | - Jerome H Kim
- International Vaccine Institute, Seoul 08826, Korea
| | - Sodsai Tovanabutra
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA
| | - Timothy W Schacker
- Department of Medicine, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert O'Connell
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA
| | - Victor G Valcour
- University of California San Francisco, San Francisco, CA 94117, USA
| | - Praphan Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Merlin L Robb
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA
| | - Nelson Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA
| | - Lydie Trautmann
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Jintanat Ananworanich
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research Silver Spring, MD 20910, USA.,Department of Global Health, University of Amsterdam, Amsterdam, Netherlands
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H2X 0A9, Canada.
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18
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Wang X, Xu H. Residual Proviral Reservoirs: A High Risk for HIV Persistence and Driving Forces for Viral Rebound after Analytical Treatment Interruption. Viruses 2021; 13:335. [PMID: 33670027 PMCID: PMC7926539 DOI: 10.3390/v13020335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Antiretroviral therapy (ART) has dramatically suppressed human immunodeficiency virus (HIV) replication and become undetectable viremia. However, a small number of residual replication-competent HIV proviruses can still persist in a latent state even with lifelong ART, fueling viral rebound in HIV-infected patient subjects after treatment interruption. Therefore, the proviral reservoirs distributed in tissues in the body represent a major obstacle to a cure for HIV infection. Given unavailable HIV vaccine and a failure to eradicate HIV proviral reservoirs by current treatment, it is crucial to develop new therapeutic strategies to eliminate proviral reservoirs for ART-free HIV remission (functional cure), including a sterilizing cure (eradication of HIV reservoirs). This review highlights recent advances in the establishment and persistence of HIV proviral reservoirs, their detection, and potential eradication strategies.
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Affiliation(s)
| | - Huanbin Xu
- Tulane National Primate Research Center, Division of Comparative Pathology, Tulane University School of Medicine, 18703 Three Rivers Road, Covington, LA 70433, USA;
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19
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Horn C, Augustin M, Ercanoglu MS, Heger E, Knops E, Bondet V, Duffy D, Chon SH, Nierhoff D, Oette M, Schäfer H, Vivaldi C, Held K, Anderson J, Geldmacher C, Suárez I, Rybniker J, Klein F, Fätkenheuer G, Müller-Trutwin M, Lehmann C. HIV DNA reservoir and elevated PD-1 expression of CD4 T-cell subsets particularly persist in the terminal ileum of HIV-positive patients despite cART. HIV Med 2021; 22:397-408. [PMID: 33421299 DOI: 10.1111/hiv.13031] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/23/2020] [Accepted: 11/04/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Despite its importance as an HIV anatomic sanctuary, little is known about the characteristics of the HIV reservoir in the terminal ileum (TI). In blood, the immune checkpoint inhibitor programmed-death-1 (PD-1) has been linked to the HIV reservoir and T-cell immune dysfunction. We thus evaluated PD-1 expression and cell-associated HIV DNA in memory CD4 T-cell subsets from TI, peripheral blood (PB) and rectum (RE) of untreated and treated HIV-positive patients to identify associations between PD-1 and HIV reservoir in other sites. METHODS Using mononuclear cells from PB, TI and RE of untreated HIV-positive (N = 6), treated (n = 18) HIV-positive and uninfected individuals (n = 16), we identified and sorted distinct memory CD4 T-cell subsets by flow cytometry, quantified their cell-associated HIV DNA using quantitative PCR and assessed PD-1 expression levels using geometric mean fluorescence intensity. Combined HIV-1 RNA in situ hybridization and immunohistochemistry was performed on ileal biopsy sections. RESULTS Combined antiretroviral therapy (cART)-treated patients with undetectable HIV RNA and significantly lower levels of HIV DNA in PB showed particularly high PD-1 expression in PB and TI, and high HIV DNA levels in TI, irrespective of clinical characteristics. By contrast, in treatment-naïve patients HIV DNA levels in memory CD4 T-cell subsets were high in PB and TI. CONCLUSION Elevated PD-1 expression on memory CD4 T-cells in PB and TI despite treatment points to continuous immune dysfunction and underlines the importance of evaluating immunotherapy in reversing HIV latency and T-cell reconstitution. As HIV DNA particularly persists in TI despite cART, investigating samples from TI is crucial in understanding HIV immunopathogenesis.
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Affiliation(s)
- C Horn
- Division of Infectious Diseases, Department I of Internal Medicine, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Cologne, Germany
| | - M Augustin
- Division of Infectious Diseases, Department I of Internal Medicine, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Cologne, Germany
| | - M S Ercanoglu
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - E Heger
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - E Knops
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - V Bondet
- Immunobiology of Dendritic Cells Unit, Inserm U1223, Institut Pasteur, Paris Cedex 15, France
| | - D Duffy
- Immunobiology of Dendritic Cells Unit, Inserm U1223, Institut Pasteur, Paris Cedex 15, France
| | - S-H Chon
- Department of General, Visceral Surgery and Cancer Surgery, University Hospital Cologne, Cologne, Germany
| | - D Nierhoff
- Clinic for Gastroenterology and Hepatology, University Hospital of Cologne, Cologne, Germany
| | - M Oette
- Clinic for Coloproctology, PanKlinik, Cologne, Germany
| | - H Schäfer
- Clinic for Coloproctology, PanKlinik, Cologne, Germany
| | - C Vivaldi
- Clinic for Coloproctology, PanKlinik, Cologne, Germany
| | - K Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - J Anderson
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - C Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - I Suárez
- Division of Infectious Diseases, Department I of Internal Medicine, University of Cologne, Cologne, Germany
| | - J Rybniker
- Division of Infectious Diseases, Department I of Internal Medicine, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Cologne, Germany
| | - F Klein
- German Center for Infection Research (DZIF), Cologne, Germany.,Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - G Fätkenheuer
- Division of Infectious Diseases, Department I of Internal Medicine, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Cologne, Germany
| | - M Müller-Trutwin
- Unité HIV, Inflammation & Persistence, Institut Pasteur, Paris Cedex 15, France
| | - C Lehmann
- Division of Infectious Diseases, Department I of Internal Medicine, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Cologne, Germany
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20
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Thorball CW, Borghesi A, Bachmann N, Von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Roth V, Kok YL, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Schmid P, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ, Fellay J. Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment. J Acquir Immune Defic Syndr 2020; 85:517-524. [PMID: 33136754 DOI: 10.1097/qai.0000000000002473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The primary hurdle for the eradication of HIV-1 is the establishment of a latent viral reservoir early after primary infection. Here, we investigated the potential influence of human genetic variation on the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. SETTING Genome-wide association study and exome sequencing study to look for host genetic determinants of HIV-1 reservoir measurements in patients enrolled in the Swiss HIV Cohort Study, a nation-wide prospective observational study. METHODS We measured total HIV-1 DNA in peripheral blood mononuclear cells from study participants, as a proxy for the reservoir size at 3 time points over a median of 5.4 years, and searched for associations between human genetic variation and 2 phenotypic readouts: the reservoir size at the first time point and its decay rate over the study period. We assessed the contribution of common genetic variants using genome-wide genotyping data from 797 patients with European ancestry enrolled in the Swiss HIV Cohort Study and searched for a potential impact of rare variants and exonic copy number variants using exome sequencing data generated in a subset of 194 study participants. RESULTS Genome-wide and exome-wide analyses did not reveal any significant association with the size of the HIV-1 reservoir or its decay rate on suppressive antiretroviral treatment. CONCLUSIONS Our results point to a limited influence of human genetics on the size of the HIV-1 reservoir and its long-term dynamics in successfully treated individuals.
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Affiliation(s)
- Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chantal Von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital of Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland; and
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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21
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Extremely low viral reservoir in treated chronically HIV-1-infected individuals. EBioMedicine 2020; 57:102830. [PMID: 32580136 PMCID: PMC7317241 DOI: 10.1016/j.ebiom.2020.102830] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Small viral reservoirs are found predominantly in HIV-1 controllers and individuals treated during acute/early HIV-1 infection. However, other HIV+ individuals could naturally also harbour low viral reservoirs. METHODS We screened 451 HIV-1-infected treated-individuals with suppressed plasma viremia for at least 3 years and stored cryopreserved peripheral blood mononuclear cells (PBMCs). Total HIV-DNA was analysed in PBMCs with ddPCR. Individuals with <50 HIV-DNA copies/106 PBMCs constitute the 'Low Viral Reservoir Treated' cohort (LoViReT). Longitudinal samples were obtained from 12 chronically treated LoViReT and compared to 13 controls (>50 HIV-DNA copies/106 PBMCs) to analyse total HIV-DNA, T-cell and NK-cell populations, HIV-1 specific antibodies, and plasma inflammation markers. FINDINGS We found that 9.3% of the individuals screened had <50 HIV-DNA copies/106 PBMCs. At least 66% initiated cART during the chronic phase of HIV-1 infection (cp-LoViReT). Cp-LoViReT harboured lower levels of HIV-DNA before cART and after treatment introduction the decays were greater compared to controls. They displayed a marked decline in quantity and avidity in HIV-specific antibodies after initiation of cART. Cp-LoViReT had fewer CD8+ TTM and TEMRA in the absence of cART, and higher CD8+ TN after 18 months on therapy. INTERPRETATION Treated chronically HIV-1-infected LoViReT represent a new phenotype of individuals characterized by an intrinsically reduced viral reservoir, less impaired CD8+ T-cell compartment before cART, and low circulating HIV-1 antigens despite being treated in the chronic phase of infection. The identification of this unique group of individuals is of great interest for the design of future eradication studies. FUNDING MSD Spain.
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22
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Infrequent HIV Infection of Circulating Monocytes during Antiretroviral Therapy. J Virol 2019; 94:JVI.01174-19. [PMID: 31597764 DOI: 10.1128/jvi.01174-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022] Open
Abstract
Whereas human immunodeficiency virus (HIV) persists in tissue macrophages during antiretroviral therapy (ART), the role of circulating monocytes as HIV reservoirs remains controversial. Three magnetic bead selection methods and flow cytometry cell sorting were compared for their capacity to yield pure CD14+ monocyte populations. Cell sorting by flow cytometry provided the purest population of monocytes (median CD4+ T-cell contamination, 0.06%), and the levels of CD4+ T-cell contamination were positively correlated with the levels of integrated HIV DNA in the monocyte populations. Using cell sorting by flow cytometry, we assessed longitudinally the infection of monocytes and other cell subsets in a cohort of 29 Thai HIV-infected individuals. Low levels of HIV DNA were detected in a minority of monocyte fractions obtained before and after 1 year of ART (27% and 33%, respectively), whereas HIV DNA was readily detected in CD4+ T cells from all samples. Additional samples (2 to 5 years of ART) were obtained from 5 individuals in whom monocyte infection was previously detected. Whereas CD4+ T cells were infected at high levels at all time points, monocyte infection was inconsistent and absent in at least one longitudinal sample from 4/5 individuals. Our results indicate that infection of monocytes is infrequent and highlight the importance of using flow cytometry cell sorting to minimize contamination by CD4+ T cells.IMPORTANCE The role of circulating monocytes as persistent HIV reservoirs during ART is still controversial. Several studies have reported persistent infection of monocytes in virally suppressed individuals; however, others failed to detect HIV in this subset. These discrepancies are likely explained by the diversity of the methods used to isolate monocytes and to detect HIV infection. In this study, we show that only flow cytometry cell sorting yields a highly pure population of monocytes largely devoid of CD4 contaminants. Using this approach in a longitudinal cohort of HIV-infected individuals before and during ART, we demonstrate that HIV is rarely found in monocytes from untreated and treated HIV-infected individuals. This study highlights the importance of using methods that yield highly pure populations of cells as flow cytometry cell sorting to minimize and control for CD4+ T-cell contamination.
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23
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Strouvelle VP, Braun DL, Vongrad V, Scherrer AU, Kok YL, Kouyos RD, Stöckle M, Rauch A, Darling K, Hoffmann M, Metzner KJ, Günthard HF. No Effect of Pegylated Interferon-α on Total HIV-1 DNA Load in HIV-1/HCV Coinfected Patients. J Infect Dis 2019. [PMID: 29528417 DOI: 10.1093/infdis/jiy131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pegylated interferon-alpha (pIFN-α) is suggested to lower human immunodeficiency virus type-1 (HIV-1) DNA load in antiretroviral therapy (ART)-treated patients. We studied kinetics of HIV-1 DNA levels in 40 HIV-1/hepatitis C virus (HCV) coinfected patients, treated with pIFN-α for HCV and categorized into 3 groups according to start of ART: chronic HIV-1 infection (n = 22), acute HIV-1 infection (n = 8), no-ART (n = 10). Total HIV-1 DNA levels in 247 peripheral blood mononuclear cell samples were stable before, during, and after pIFN-α treatment in all groups. Our results question the benefit of pIFN-α as an immunotherapeutic agent for reducing the HIV-1 reservoir.
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Affiliation(s)
- Victoria P Strouvelle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Valentina Vongrad
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Yik Lim Kok
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Marcel Stöckle
- Department of Infectious Diseases and Hospital Hygiene, University Hospital Basel, University of Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Switzerland
| | - Katharine Darling
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Kantonal Hospital St Gallen, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
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24
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Bachmann N, von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Kok YL, Thorball CW, Borghesi A, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Hoffmann M, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ. Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nat Commun 2019; 10:3193. [PMID: 31324762 PMCID: PMC6642170 DOI: 10.1038/s41467-019-10884-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies. Here, Bachmann et al. provide data on long-term dynamics of the HIV-1 reservoir in 1,057 individuals on suppressive antiretroviral therapy and show that in 26.6% of individuals the reservoir increases. Viral blips and low-level viremia are significantly associated with a slower reservoir decay.
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Affiliation(s)
- Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Chantal von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4057 Basel, Switzerland
| | | | - Jaques Fellay
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital, 1011, Lausanne, Switzerland
| | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Alessandro Borghesi
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, 27100, Italy
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, 4001, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, 3010, Bern, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, 9007, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital, 6900, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland. .,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland.
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
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25
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Bon I, Calza L, Musumeci G, Longo S, Bertoldi A, D'Urbano V, Gibellini D, Magistrelli E, Viale PL, Re MC. Impact of Different Antiretroviral Strategies on Total HIV-DNA Level in Virologically Suppressed HIV-1 Infected Patients. Curr HIV Res 2019; 15:448-455. [PMID: 29210661 PMCID: PMC5876918 DOI: 10.2174/1570162x16666171206121026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/02/2017] [Accepted: 11/28/2017] [Indexed: 01/11/2023]
Abstract
Background: Total HIV-DNA load in peripheral blood cell (PBMCs) reflects the global viral reservoir that seems not to be affected by antiretroviral treatment. However, some studies report-ed a different permeability of different drugs in cellular compartments. Objective: To investigate the relation between the amount of total HIV-1 DNA and different treatment strategies. Methods: Total HIV-1 DNA was quantified by real time PCR in PBMCs collected from 161 patients with long-term undetectable HIV-RNA receiving different therapy schedules (3-drug regimens or 2-drug regimen containing Raltegravir as integrase inhibitor). Results: Overall, HIV patients who started therapy with a median pre-ART CD4+ cell count >400 cells/mm3 and HIV viral load of 3 log10 copies/ml, achieved a lower amount of HIV total DNA. No significant correlation was found in DNA size when patients were stratified on the basis of different therapeutic protocols. However, HIV DNA load analysis, when only performed in HIV patients with a median pre-ART CD4+ cell count >200 cells/mm3 and HIV viral load < 3 log10 copies/ml, showed a significative DNA decrease in Raltegravir treated group with respect to the NNRTIs-treated group. Conclusion: The data emphasize that HIV-DNA level represents a predictive factor in long-term sup-pressive therapy patients. In addition, the diminished reservoir, only observed in patients treated with the NRTI-sparing regimen RAL plus PI/r before immunological and virological derangement, sug-gests that latest generation drugs, such as integrase inhibitors, might represent an optimal chance in the management of HIV infection.
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Affiliation(s)
- Isabella Bon
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Leonardo Calza
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Giuseppina Musumeci
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Serena Longo
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Alessia Bertoldi
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Vanessa D'Urbano
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Davide Gibellini
- Unit of Microbiology Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Eleonora Magistrelli
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Pier Luigi Viale
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Maria Carla Re
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy.,Interuniversity Consortium, National Institute of Biostructures and Biosystems (INBB), Rome, Italy
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26
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Beliakova-Bethell N, Mukim A, White CH, Deshmukh S, Abewe H, Richman DD, Spina CA. Histone deacetylase inhibitors induce complex host responses that contribute to differential potencies of these compounds in HIV reactivation. J Biol Chem 2019; 294:5576-5589. [PMID: 30745362 PMCID: PMC6462528 DOI: 10.1074/jbc.ra118.005185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/07/2019] [Indexed: 12/23/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors (HDACis) have been widely tested in clinical trials for their ability to reverse HIV latency but have yielded only limited success. One HDACi, suberoylanilide hydroxamic acid (SAHA), exhibits off-target effects on host gene expression predicted to interfere with induction of HIV transcription. Romidepsin (RMD) has higher potency and specificity for class I HDACs implicated in maintaining HIV provirus in the latent state. More robust HIV reactivation has indeed been achieved with RMD use ex vivo than with SAHA; however, reduction of viral reservoir size has not been observed in clinical trials. Therefore, using RNA-Seq, we sought to compare the effects of SAHA and RMD on gene expression in primary CD4+ T cells. Among the genes whose expression was modulated by both HDACi agents, we identified genes previously implicated in HIV latency. Two genes, SMARCB1 and PARP1, whose modulation by SAHA and RMD is predicted to inhibit HIV reactivation, were evaluated in the major maturation subsets of CD4+ T cells and were consistently either up- or down-regulated by both HDACi compounds. Our results indicate that despite having different potencies and HDAC specificities, SAHA and RMD modulate an overlapping set of genes, implicated in HIV latency regulation. Some of these genes merit exploration as additional targets to improve the therapeutic outcomes of "shock and kill" strategies. The overall complexity of HDACi-induced responses among host genes with predicted stimulatory or inhibitory effects on HIV expression likely contributes to differential HDACi potencies and dictates the outcome of HIV reactivation.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Amey Mukim
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
| | - Cory H White
- the University of California San Diego, La Jolla, California 92093
| | - Savitha Deshmukh
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
| | - Hosiana Abewe
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Douglas D Richman
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Celsa A Spina
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
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27
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Duwal S, Seeler D, Dickinson L, Khoo S, von Kleist M. The Utility of Efavirenz-based Prophylaxis Against HIV Infection. A Systems Pharmacological Analysis. Front Pharmacol 2019; 10:199. [PMID: 30918485 PMCID: PMC6424904 DOI: 10.3389/fphar.2019.00199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
Pre-exposure prophylaxis (PrEP) is considered one of the five “pillars” by UNAIDS to reduce HIV transmission. Moreover, it is a tool for female self-protection against HIV, making it highly relevant to sub-Saharan regions, where women have the highest infection burden. To date, Truvada is the only medication for PrEP. However, the cost of Truvada limits its uptake in resource-constrained countries. Similarly, several currently investigated, patent-protected compounds may be unaffordable in these regions. We set out to explore the potential of the patent-expired antiviral efavirenz (EFV) as a cost-efficient PrEP alternative. A population pharmacokinetic model utilizing data from the ENCORE1 study was developed. The model was refined for metabolic autoinduction. We then explored EFV cellular uptake mechanisms, finding that it is largely determined by plasma protein binding. Next, we predicted the prophylactic efficacy of various EFV dosing schemes after exposure to HIV using a stochastic simulation framework. We predicted that plasma concentrations of 11, 36, 1287 and 1486ng/mL prevent 90% sexual transmissions with wild type and Y181C, K103N and G190S mutants, respectively. Trough concentrations achieved after 600 mg once daily dosing (median: 2017 ng/mL, 95% CI:445–9830) and after reduced dose (400 mg) efavirenz (median: 1349ng/mL, 95% CI: 297–6553) provided complete protection against wild-type virus and the Y181C mutant, and median trough concentrations provided about 90% protection against the K103N and G190S mutants. As reduced dose EFV has a lower toxicity profile, we predicted the reduction in HIV infection when 400 mg EFV-PrEP was poorly adhered to, when it was taken “on demand” and as post-exposure prophylaxis (PEP). Once daily EFV-PrEP provided 99% protection against wild-type virus, if ≥50% of doses were taken. PrEP “on demand” provided complete protection against wild-type virus and prevented ≥81% infections in the mutants. PEP could prevent >98% infection with susceptible virus when initiated within 24 h after virus exposure and continued for at least 9 days. We predict that 400 mg oral EFV may provide superior protection against wild-type HIV. However, further studies are warranted to evaluate EFV as a cost-efficient alternative to Truvada. Predicted prophylactic concentrations may guide release kinetics of EFV long-acting formulations for clinical trial design.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics and Computer Science, Systems Pharmacology and Disease Control, Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Daniel Seeler
- Department of Mathematics and Computer Science, Systems Pharmacology and Disease Control, Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Laura Dickinson
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Saye Khoo
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Max von Kleist
- Department of Mathematics and Computer Science, Systems Pharmacology and Disease Control, Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
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28
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Duwal S, Dickinson L, Khoo S, von Kleist M. Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis. PLoS Comput Biol 2019; 15:e1006740. [PMID: 30699105 PMCID: PMC6370240 DOI: 10.1371/journal.pcbi.1006740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/11/2019] [Accepted: 12/20/2018] [Indexed: 11/21/2022] Open
Abstract
Currently, there is no effective vaccine to halt HIV transmission. However, pre-exposure prophylaxis (PrEP) with the drug combination Truvada can substantially decrease HIV transmission in individuals at risk. Despite its benefits, Truvada-based PrEP is expensive and needs to be taken once-daily, which often leads to inadequate adherence and incomplete protection. These deficits may be overcome by next-generation PrEP regimen, including currently investigated long-acting formulations, or patent-expired drugs. However, poor translatability of animal- and ex vivo/in vitro experiments, and the necessity to conduct long-term (several years) human trials involving considerable sample sizes (N>1000 individuals) are major obstacles to rationalize drug-candidate selection. We developed a prophylaxis modelling tool that mechanistically considers the mode-of-action of all available drugs. We used the tool to screen antivirals for their prophylactic utility and identify lower bound effective concentrations that can guide dose selection in PrEP trials. While in vitro measurable drug potency usually guides PrEP trial design, we found that it may over-predict PrEP potency for all drug classes except reverse transcriptase inhibitors. While most drugs displayed graded concentration-prophylaxis profiles, protease inhibitors tended to switch between none- and complete protection. While several treatment-approved drugs could be ruled out as PrEP candidates based on lack-of-prophylactic efficacy, darunavir, efavirenz, nevirapine, etravirine and rilpivirine could more potently prevent infection than existing PrEP regimen (Truvada). Notably, some drugs from this candidate set are patent-expired and currently neglected for PrEP repurposing. A next step is to further trim this candidate set by ruling out compounds with ominous safety profiles, to assess different administration schemes in silico and to test the remaining candidates in human trials. Pre-exposure prophylaxis (PrEP) is a novel, promising strategy to halt HIV transmission. PrEP with Truvada can substantially decrease the risk of infection. However, individuals often inadequately adhere to the once-daily regimen and the drug is expensive. These shortcomings may be overcome by next-generation PrEP compounds, including long-acting formulations. However, poor translatability of animal- and ex vivo/in vitro experiments, and difficulties in conducting long-term trials involving considerable sample sizes (N > 1000 individuals) make drug-candidate selection and optimization of administration schemes costly and often infeasible. We developed a simulation tool that mechanistically considers the mode-of-action of all antivirals. We used the tool to screen all available antivirals for their prophylactic utility and identified lower bound effective concentrations for designing PrEP dosing regimen in clinical trials. We found that in vitro measured drug potency may over-predict PrEP potency, for all antiviral classes except reverse transcriptase inhibitors. We could rule out a number of antivirals for PrEP repurposing and predicted that darunavir, efavirenz, nevirapine, etravirine and rilpivirine provide complete protection at clinically relevant concentrations. Further trimming of this candidate set by compound-safety and by assessing different implementation schemes is envisaged.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics & Computer Science, Freie Universität Berlin, Germany
- * E-mail: (SD); (MvK)
| | - Laura Dickinson
- Institute of Translational Medicine, University of Liverpool, United Kingdom
| | - Saye Khoo
- Institute of Translational Medicine, University of Liverpool, United Kingdom
| | - Max von Kleist
- Department of Mathematics & Computer Science, Freie Universität Berlin, Germany
- * E-mail: (SD); (MvK)
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29
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Rochat MA, Schlaepfer E, Kuster SP, Li D, Audige A, Ivic S, Fahrny A, Speck RF. Monitoring HIV DNA and cellular activation markers in HIV-infected humanized mice under cART. Virol J 2018; 15:191. [PMID: 30558630 PMCID: PMC6296118 DOI: 10.1186/s12985-018-1101-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
Background The major obstacle to cure of HIV type-1 infection is the presence of the HIV reservoir, hidden from the immune system and insensitive to combined antiretroviral therapy (cART). Eradication approaches have been hindered by the difficulty for accurately monitoring its size in vivo, especially in the lymphoid organs. Humanized mouse models are a valuable tool for systematically assess the efficacy of therapeutic interventions in reducing the HIV reservoir. Nonetheless, persistence of the HIV reservoir over time, in the presence of cART, has yet to be analyzed in this in vivo model. Findings We found that the proviral DNA as well as the total DNA were very stable in the spleen and mesenteric lymph node irrespective of the length of cART. Notably, the amount of proviral DNA was very similar in the spleen and lymph node. Furthermore, we observed a correlation between the percentage of splenic human CD4+ T-cells with total HIV DNA, between the number of human CD38 + CD8+ T-cells in the spleen with the amount of integrated HIV DNA, and eventually between the hCD4/hCD8 ratio in the spleen with integrated as well as total HIV DNA implying that the CD8+ T cells influence the size of the HIV reservoir. Conclusions Here, we demonstrated the stability of this reservoir in humanized mice irrespective of the length of cART, confirming the relevancy of this model for HIV latency eradication investigations. Notably, we also found correlates between the frequency of CD4+ T-cells, their activation status and viral parameters, which were analogous to the ones in HIV-infected patients. Thus, hu-mice represent a very valuable HIV latency model.
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Affiliation(s)
- Mary-Aude Rochat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Erika Schlaepfer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Stefan P Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Duo Li
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Annette Audige
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Sandra Ivic
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Audrey Fahrny
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Roberto F Speck
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland.
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Quantitation of Integrated HIV Provirus by Pulsed-Field Gel Electrophoresis and Droplet Digital PCR. J Clin Microbiol 2018; 56:JCM.01158-18. [PMID: 30232127 DOI: 10.1128/jcm.01158-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/12/2018] [Indexed: 12/19/2022] Open
Abstract
We utilized pulsed-field gel electrophoresis (PFGE) to purify high-molecular-weight DNA from HIV-infected cells. This purification, in combination with our previously described droplet digital PCR (ddPCR) assay, was used to develop a method to quantify proviral integrated HIV DNA free of lower-molecular-weight species of HIV DNA. Episomal 2-long-terminal-repeat (2-LTR) circles were completely cleared from HIV DNA samples. Technical replicates of the complete assay, starting with the same specimens, resulted in no statistical differences in quantification of integrated HIV gag sequences in cellular DNA from cells from HIV-infected subjects after prolonged treatment with antiretroviral therapy (ART). The PFGE ddPCR assay was compared to the Alu-gag quantitative PCR (qPCR) assay, the most widely used assay to measure proviral integrated HIV DNA. Spearman's rho nonparametric correlation determined PFGE ddPCR results to be positively correlated with Alu-gag qPCR results (r = 0.7052; P = 0.0273). In summary, PFGE ddPCR is a sensitive, reproducible, and robust method to measure proviral integrated HIV DNA and is theoretically more accurate than previously described assays, because it is a direct measure of integrated HIV DNA.
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Moragas M, Distefano M, Mecikovsky D, Arazi Caillaud S, Cernadas C, Bologna R, Aulicino P, Mangano A. Impact of the time to achieve viral control on the dynamics of circulating HIV-1 reservoir in vertically infected children with long-term sustained virological suppression: A longitudinal study. PLoS One 2018; 13:e0205579. [PMID: 30352067 PMCID: PMC6198963 DOI: 10.1371/journal.pone.0205579] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/27/2018] [Indexed: 12/22/2022] Open
Abstract
Objective Determine the decay rate of HIV-1 DNA reservoir in vertically infected children during sustained viral suppression (VS) and how it is affected by the age at VS. Methods This study included 37 HIV-1 vertically infected children on suppressive antiretroviral therapy for at least 4 years. Children were grouped according to the age of antiretroviral therapy initiation (≤0.5 or >0.5 yrs) and to the age at VS (≤1.5, between >1.5 and 4, and >4 years). Decay of cell-associated HIV-1 DNA (CA-HIV-DNA) level and 2-long terminal repeats (2-LTR) circles frequency were analyzed over 4 years of viral suppression using piecewise linear mixed-effects model with two splines and logistic regression, respectively. Results CA-HIV-DNA in peripheral blood mononuclear cells had a significant decay during the first two years of VS [-0.26 (95% CI: -0.43, -0.09) log10 copies per one million cells (cpm)/year], and subsequently reached a plateau [-0.06 (95% CI: -0.15, 0.55) log10 cpm/year]. The initial decay was higher in children who achieved VS by 1.5 years of age compared to those who achieved VS between >1.5 and 4 years and those after 4 years of age: -0.51 (95% CI:-0.94, -0.07), -0.35 (95% CI:-0.83, 0.14), and -0.21 (95% CI:-0.39, -0.02) log10cpm PBMC/year, respectively. The 2-LTR circles frequency decayed significantly, from 82.9% at pre-VS to 37.5% and 28.1% at 2 and 4 years of VS, respectively (P = .0009). Conclusions These data highlight that achieving VS during the first 18 months of life limit the establishment of HIV-1 reservoirs, reinforcing the clinical benefit of very early effective therapy in children.
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Affiliation(s)
- Matías Moragas
- Laboratorio de BiologíaCelular y Retrovirus-CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Maximiliano Distefano
- Laboratorio de BiologíaCelular y Retrovirus-CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Debora Mecikovsky
- Servicio de Epidemiología e Infectología, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Solange Arazi Caillaud
- Servicio de Epidemiología e Infectología, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Cernadas
- DirecciónAsociada de Docencia e Investigación, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Aulicino
- Laboratorio de BiologíaCelular y Retrovirus-CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de BiologíaCelular y Retrovirus-CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan”, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail: ,
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Anderson EM, Maldarelli F. The role of integration and clonal expansion in HIV infection: live long and prosper. Retrovirology 2018; 15:71. [PMID: 30352600 PMCID: PMC6199739 DOI: 10.1186/s12977-018-0448-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/15/2018] [Indexed: 02/07/2023] Open
Abstract
Integration of viral DNA into the host genome is a central event in the replication cycle and the pathogenesis of retroviruses, including HIV. Although most cells infected with HIV are rapidly eliminated in vivo, HIV also infects long-lived cells that persist during combination antiretroviral therapy (cART). Cells with replication competent HIV proviruses form a reservoir that persists despite cART and such reservoirs are at the center of efforts to eradicate or control infection without cART. The mechanisms of persistence of these chronically infected long-lived cells is uncertain, but recent research has demonstrated that the presence of the HIV provirus has enduring effects on infected cells. Cells with integrated proviruses may persist for many years, undergo clonal expansion, and produce replication competent HIV. Even proviruses with defective genomes can produce HIV RNA and may contribute to ongoing HIV pathogenesis. New analyses of HIV infected cells suggest that over time on cART, there is a shift in the composition of the population of HIV infected cells, with the infected cells that persist over prolonged periods having proviruses integrated in genes associated with regulation of cell growth. In several cases, strong evidence indicates the presence of the provirus in specific genes may determine persistence, proliferation, or both. These data have raised the intriguing possibility that after cART is introduced, a selection process enriches for cells with proviruses integrated in genes associated with cell growth regulation. The dynamic nature of populations of cells infected with HIV during cART is not well understood, but is likely to have a profound influence on the composition of the HIV reservoir with critical consequences for HIV eradication and control strategies. As such, integration studies will shed light on understanding viral persistence and inform eradication and control strategies. Here we review the process of HIV integration, the role that integration plays in persistence, clonal expansion of the HIV reservoir, and highlight current challenges and outstanding questions for future research.
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Affiliation(s)
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD, 21702, USA.
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Thomas J, Ruggiero A, Procopio FA, Pantaleo G, Paxton WA, Pollakis G. Comparative analysis and generation of a robust HIV-1 DNA quantification assay. J Virol Methods 2018; 263:24-31. [PMID: 30326210 DOI: 10.1016/j.jviromet.2018.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 12/18/2022]
Abstract
HIV-1 infection cannot be cured due to the presence of the latent reservoir (LR). Novel cure or treatment strategies, such as "shock and kill" or therapeutic vaccination, aim to reduce or eradicate the LR. Cure strategies utilise robust DNA quantification assays to measure the change in the LR in low copy scenarios. No standard assay exists, which impedes the reliable comparison of results from different therapy and vaccine trials and HIV-1 total DNA quantification methods have not been previously compared. The HIV-1 long terminal repeat (LTR) has been shown to be the best target for DNA quantification. We have analysed two HIV-1 quantification assays, both able to differentiate between the variant HIV-1 DNA forms via the use of pre-amplification and primers targeting LTR. We identify a strong correlation (r=0.9759, P<0.0001) between assays which is conserved in low copy samples (r=0.8220, P<0.0001) indicating that these assays may be used interchangeably. The RvS assay performed significantly (P=0.0021) better than the CV assay when quantifying HIV-1 total DNA in patient CD4+ T lymphocytes. Sequence analysis demonstrated that viral diversity can limit DNA quantification, however in silico analysis of the primers indicated that within the target region nucleotide miss-matches appear infrequently. Further in silico analysis using up to-date sequence information led to the improvement of primers and enabled us to establish a more broadly specific assay with significantly higher HIV-1 DNA quantification capacity in patient samples (p=0.0057, n=17).
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Francesco A Procopio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom.
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Hong F, Jacobs JL, Aga E, Cillo AR, Fyne E, Koontz DL, Zheng L, Mellors JW. Associations between HIV-1 DNA copy number, proviral transcriptional activity, and plasma viremia in individuals off or on suppressive antiretroviral therapy. Virology 2018; 521:51-57. [PMID: 29879542 PMCID: PMC6279608 DOI: 10.1016/j.virol.2018.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
Abstract
The relationships between HIV-1 DNA copy number, proviral transcriptional activity, and residual plasma viremia in individuals off and on ART are not well defined. To address this, we performed a cross-sectional study of 12 viremic donors and 23 ART-treated virologically suppressed (plasma HIV-1 RNA<20 copies/ml) donors. We report a strong association between HIV-1 DNA copy number and HIV-1 transcriptional activity in blood that persists on suppressive ART, but not between transcriptional activity and the levels of persistent viremia on ART. The latter finding contrasts with that in viremic donors and suggests that most HIV transcription in donors on suppressive ART does not result in virion production. This uncoupling of proviral transcription and viremia warrants closer investigation.
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Affiliation(s)
- Feiyu Hong
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Jana L Jacobs
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Evgenia Aga
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Anthony R Cillo
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Elizabeth Fyne
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Dianna L Koontz
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States
| | - Lu Zheng
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - John W Mellors
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, 3550 Terrace Street, Scaife Hall, Suite 818, Pittsburgh, PA 15261, United States.
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Mortier V, Demecheleer E, Staelens D, Schauvliege M, Dauwe K, Dinakis S, Hebberecht L, Vancoillie L, Verhofstede C. Quantification of total HIV-1 DNA in buffy coat cells, feasibility and potential added value for clinical follow-up of HIV-1 infected patients on ART. J Clin Virol 2018; 106:58-63. [PMID: 30077957 DOI: 10.1016/j.jcv.2018.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Successfully treated HIV-1 infected patients have a sustained undetectable viral RNA load. In these cases the total HIV-1 DNA load may constitute a valuable tool to further follow the overall viral burden. The value of this marker outside of cure research has been rarely studied. OBJECTIVES To develop a quantitative (q)PCR for total HIV-1 DNA quantification in buffy coat cells and to evaluate the value of this parameter in clinical follow-up. STUDY DESIGN A qPCR using primers and a probe in the conserved HIV-1 LTR region was adapted for use on DNA extracted from buffy coat cells. Sensitivity, accuracy and reproducibility were evaluated using 8E5 cells and samples from naive and treatment experienced patients. The clinical value of DNA load analysis was assessed by testing 119 longitudinal samples from 9 patients before and after ART initiation and 249 cross sectional samples from therapy-experienced patients. RESULTS Inter- and intra-assay coefficients of variability were 5.56 and 5.94 (%CV). HIV-1 DNA was detected in 249 of the 263 (94.7%) patients on ART for at least 5 months (median: 53 months; IQR: 28-84 months). The HIV-1 DNA load varied between 0.60 and 3.37 copies/106 blood cells and showed significant correlation with the pre-ART CD4+ T-cell count nadir and peak viral RNA load. ART initiation resulted in a slow and limited decline of the total HIV-1 DNA concentration. CONCLUSIONS Quantification of total HIV-1 DNA from buffy coat cells is feasible, sensitive and reliable. Although determination of the on-therapy HIV-1 DNA load may be informative, regular testing has limited clinical value because of the very slow evolution.
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Affiliation(s)
- Virginie Mortier
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Els Demecheleer
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Delfien Staelens
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Marlies Schauvliege
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Kenny Dauwe
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Sylvie Dinakis
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Laura Hebberecht
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Leen Vancoillie
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1).
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Sculier D, Doco‐Lecompte T, Yerly S, Metzner KJ, Decosterd LA, Calmy A. Stable HIV-1 reservoirs on dolutegravir maintenance monotherapy: the MONODO study. HIV Med 2018; 19:572-577. [PMID: 29932298 PMCID: PMC6120531 DOI: 10.1111/hiv.12626] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Dolutegravir (DTG) is a highly effective integrase inhibitor with a strong genetic resistance barrier and a potential role in simplified HIV maintenance treatment. We assessed the feasibility of DTG maintenance monotherapy and measured HIV reservoirs on DTG monotherapy. METHODS An interventional, open-label, single-arm study including eight virologically suppressed HIV-1-infected patients switched to DTG 50 mg once daily for 24 weeks was performed. HIV-1 RNA levels in plasma and cerebrospinal and seminal fluids were measured at baseline and week 24, as well as HIV-1 DNA in peripheral cells and DTG concentrations in these compartments. RESULTS HIV-1 RNA remained undetectable in all samples of blood, cerebrospinal fluid and sperm throughout the 24 weeks, except for one cerebrospinal fluid sample with a value of 28 HIV-1 RNA copies/mL at week 24. One patient discontinued the study because of a neurological side effect. There was no change in the mean HIV-1 DNA level between baseline and week 24. Plasma and cerebrospinal fluid DTG concentrations reached therapeutic levels in all patients in these two compartments. CONCLUSIONS In this small sample of carefully selected patients, HIV-1 reservoirs were well controlled on DTG monotherapy over a period of 24 weeks. Viral suppression was also maintained throughout follow-up.
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Affiliation(s)
- D Sculier
- Division of Infectious DiseasesGeneva University HospitalsGenevaSwitzerland
| | - T Doco‐Lecompte
- Division of Infectious DiseasesGeneva University HospitalsGenevaSwitzerland
| | - S Yerly
- Laboratory of VirologyGeneva University HospitalsGenevaSwitzerland
| | - KJ Metzner
- Division of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichZurichSwitzerland
- Institute of Medical VirologyUniversity of ZurichZurichSwitzerland
| | - LA Decosterd
- Division of Clinical PharmacologyUniversity Hospital and University of LausanneLausanneSwitzerland
| | - A Calmy
- Division of Infectious DiseasesGeneva University HospitalsGenevaSwitzerland
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Duwal S, Dickinson L, Khoo S, von Kleist M. Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes. PLoS Comput Biol 2018; 14:e1006155. [PMID: 29902179 PMCID: PMC6001963 DOI: 10.1371/journal.pcbi.1006155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/21/2018] [Indexed: 01/02/2023] Open
Abstract
To achieve the 90-90-90 goals set by UNAIDS, the number of new HIV infections needs to decrease to approximately 500,000 by 2020. One of the 'five pillars' to achieve this goal is pre-exposure prophylaxis (PrEP). Truvada (emtricitabine-tenofovir) is currently the only medication approved for PrEP. Despite its advantages, Truvada is costly and requires individuals to adhere to the once-daily regimen. To improve PrEP, many next-generation regimen, including long-acting formulations, are currently investigated. However, pre-clinical testing may not guide candidate selection, since it often fails to translate into clinical efficacy. On the other hand, quantifying prophylactic efficacy in the clinic is ethically problematic and requires to conduct long (years) and large (N>1000 individuals) trials, precluding systematic evaluation of candidates and deployment strategies. To prioritize- and help design PrEP regimen, tools are urgently needed that integrate pharmacological-, viral- and host factors determining prophylactic efficacy. Integrating the aforementioned factors, we developed an efficient and exact stochastic simulation approach to predict prophylactic efficacy, as an example for dolutegravir (DTG). Combining the population pharmacokinetics of DTG with the stochastic framework, we predicted that plasma concentrations of 145.18 and 722.23nM prevent 50- and 90% sexual transmissions respectively. We then predicted the reduction in HIV infection when DTG was used in PrEP, PrEP 'on demand' and post-exposure prophylaxis (PEP) before/after virus exposure. Once daily PrEP with 50mg oral DTG prevented 99-100% infections, and 85% of infections when 50% of dosing events were missed. PrEP 'on demand' prevented 79-84% infections and PEP >80% when initiated within 6 hours after virus exposure and continued for as long as possible. While the simulation framework can easily be adapted to other PrEP candidates, our simulations indicated that oral 50mg DTG is non-inferior to Truvada. Moreover, the predicted 90% preventive concentrations can guide release kinetics of currently developed DTG nano-formulations.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics & Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Laura Dickinson
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Saye Khoo
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Max von Kleist
- Department of Mathematics & Computer Science, Freie Universität Berlin, Berlin, Germany
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Effect of Short-Term Antiretroviral Therapy Interruption on Levels of Integrated HIV DNA. J Virol 2018; 92:JVI.00285-18. [PMID: 29593048 DOI: 10.1128/jvi.00285-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/23/2018] [Indexed: 12/28/2022] Open
Abstract
Analytic treatment interruption (ATI) studies are required to evaluate strategies aimed at achieving ART-free HIV remission, but the impact of ATI on the viral reservoir remains unclear. We validated a DNA size selection-based assay for measuring levels of integrated HIV DNA and applied it to assess the effects of short-term ATI on the HIV reservoir. Samples from participants from four AIDS Clinical Trials Group ATI studies were assayed for integrated HIV DNA levels. Cryopreserved peripheral blood mononuclear cells (PBMCs) were obtained for 12 participants with available samples pre-ATI and approximately 6 months after ART resumption. Four participants also had samples available during the ATI. The median duration of ATI was 12 weeks. Validation of the HIV integrated DNA size-exclusion (HIDE) assay was performed using samples spiked with unintegrated HIV DNA, HIV-infected cell lines, and participant PBMCs. The HIDE assay eliminated 99% of unintegrated HIV DNA species and strongly correlated with the established Alu-gag assay. For the majority of individuals, integrated DNA levels increased during ATI and subsequently declined upon ART resumption. There was no significant difference in the levels of integrated HIV DNA between the pre- and post-ATI time points, with a median ratio of post- to pre-ATI HIV DNA levels of 0.95. Using a new integrated HIV DNA assay, we found minimal change in the levels of integrated HIV DNA in participants who underwent an ATI, followed by 6 months of ART. This suggests that short-term ATI can be conducted without a significant impact on the levels of integrated proviral DNA in the peripheral blood.IMPORTANCE Interventions aimed at achieving sustained antiretroviral therapy (ART)-free HIV remission require treatment interruption trials to assess their efficacy. However, these trials are accompanied by safety concerns related to the expansion of the viral reservoir. We validated an assay that uses an automated DNA size-selection platform for quantifying levels of integrated HIV DNA and is less sample- and labor-intensive than current assays. Using stored samples from AIDS Clinical Trials Group studies, we found that short-term ART discontinuation had minimal impact on integrated HIV DNA levels after ART resumption, providing reassurance about the reservoir effects of short-term treatment interruption trials.
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Abstract
OBJECTIVE To define the relationships between molecular measures of viral persistence in blood (i.e., plasma viremia, cellular HIV-1 DNA, and mRNA) and expressed or inducible virus from resting CD4 T cells of individuals on suppressive antiretroviral therapy. DESIGN We compared molecular measurements of HIV-1 in plasma and in uncultured peripheral blood mononuclear cells (PBMCs) to the levels of virions produced by either unstimulated or phorbol myristate acetate and ionomycin (PMA/iono)-stimulated PBMC or resting CD4 T cells from 21 donors on suppressive antiretroviral therapy. RESULTS We found that unstimulated virion release from cultured resting CD4 T cells was positively correlated with the levels of plasma viremia in vivo (Spearman rho = 0.67, P = 0.0017). We also found that levels of both cellular HIV-1 DNA and unspliced HIV-1 mRNA per million uncultured PBMC were positively correlated with the levels of inducible virion release from both PMA/iono-stimulated PBMC (total HIV-1 DNA: rho = 0.64, P = 0.0017; unspliced HIV-1 RNA: rho = 0.77, P < 0.001) and PMA/iono-stimulated resting CD4 T cells (total HIV-1 DNA: rho = 0.75, P < 0.001; unspliced HIV-1 RNA: rho = 0.75, P < 0.001). CONCLUSION These results show for the first time that there are strong associations between in-vivo measures of HIV-1 persistence and ex-vivo measures of spontaneous and inducible virus production from cultured PBMC and resting CD4 T cells. Findings from this study provide insight into the biology of HIV-1 persistence and suggest methods to guide the evaluation of clinical strategies to reduce the size of the viral reservoir.
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HIV reservoir dynamics in HAART-treated poor immunological responder patients under IL-7 therapy. AIDS 2018; 32:715-720. [PMID: 29369157 DOI: 10.1097/qad.0000000000001752] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Recombinant Human IL-7 (rhIL-7) therapy allows reconstituting systemic and tissue-associated CD4 T-cell populations in HIV-infected poor immunological responder (PIR) patients. However, in-vitro studies suggest that the impact of rhIL-7 treatment on HIV-DNA loads in vivo remains questionable. DESIGN We assessed the dynamics of circulating HIV-DNA loads in IL-7-treated HIV-infected PIR individuals. METHODS Forty-one rhIL-7-treated and 16 control participants from the INSPIRE-3 clinical trial were included. Participants received three weekly subcutaneous injections of rhIL-7. HIV-DNA was quantified by nested quantitative PCR in white blood cells sampled at D0, D28 and M3 and expressed as per milliliters and per CD4 T-cell. Changes in HIV-DNA loads in the CD4 compartment at M3 were confirmed on sorted CD4 cells. RESULTS Together with rhIL-7-induced T-cell expansion, we observed a significant raise in both infected cell frequencies and counts during the first 28 days of follow-up. During this period, HIV-DNA load per CD4 T-cell also increased, to a lower extent. Three months post-therapy, both the frequencies and counts of infected cells diminished in blood as compared with D28 but remained significantly higher than before IL-7 therapy. In contrast, infection frequencies strongly diminished within CD4 cells, reaching slightly but significantly lower levels than at baseline. CONCLUSION rhIL-7 treatment initially drives an expansion of HIV reservoir in PIR patients by D28. This expansion is probably not only because of infected cell proliferation, but also to possible enhanced neoinfection, despite highly active antiretroviral therapy. In contrast, subsequent reduction in HIV-DNA load per CD4 T-cell argues for partial elimination of infected cells between D28 and M3.
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Lu Z, Jiao Y, Li J, Lan G, Lu C, Li X, Tang Z, Wang N. After 18 months of antiretroviral therapy, total HIV DNA decreases more pronouncedly in patients infected by CRF01_AE than in those infected by subtype B and CRF07_BC. Microbiol Immunol 2018; 62:248-254. [PMID: 29377267 DOI: 10.1111/1348-0421.12578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/19/2022]
Abstract
Whether the amount of HIV DNA is associated with the subtype of HIV-1 after antiretroviral therapy (ART) has not been reported. In the present study, the amount of HIV DNA and RNA and CD4+T counts in blood and semen prior to and after 18 months of ART were compared in 48 patients infected by CRF01_AE, subtype B or CRF07_BC of HIV-1. Viral RNA was suppressed and CD4 cell count recovery achieved in all patients. The level of HIV DNA were similar before ART; however, patients with CRF01_AE had less HIV DNA after ART than those with subtype B and CRF07_BC infection. According to prediction of co-receptor usage by Geno2Pheno and PSSM in combination, more than 35.6% of clones for CRF01_AE were predicted as CXCR4-using before ART, whereas less than 6% of those for subtype B and CRF07_BC were predicted as CXCR4-using. After 18 months of ART, no CXCR4-using clones were predicted in any of the subtypes. Despite more HIV RNA and fewer CD4 + T cells in patients with CRF01_AE before therapy, no significant differences (P > 0.05) in viral RNA or CD4 cell counts were observed between the subtypes after 18 months of ART. Thus, 18 months of antiretroviral therapy was more efficient in patients with CRF01_AE. Considering that successful ART dramatically reduces the viral load in both blood and semen, risks of sexual transmission of HIV were reduced, contributing to prevention of rapid spread of HIV among men who have sex with men in the region.
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Affiliation(s)
- Zhenzhen Lu
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China.,Department of Infectious Diseases, Beijing 302 Hospital, Beijing 100069, China
| | - Yanmei Jiao
- AIDS Antiviral Treatment Clinic, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Jianjun Li
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Guanghua Lan
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Chunyan Lu
- AIDS Research Center, Ruikang Hospital affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, China
| | - Xuan Li
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhenzhu Tang
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Ning Wang
- Department of Infectious Diseases, Beijing 302 Hospital, Beijing 100069, China
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Ruhanya V, Jacobs GB, Glashoff RH, Engelbrecht S. Clinical Relevance of Total HIV DNA in Peripheral Blood Mononuclear Cell Compartments as a Biomarker of HIV-Associated Neurocognitive Disorders (HAND). Viruses 2017; 9:E324. [PMID: 29088095 PMCID: PMC5707531 DOI: 10.3390/v9110324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 12/19/2022] Open
Abstract
The pathogenesis of HIV-associated neurocognitive disorders is complex and multifactorial. It is hypothesized that the critical events initiating this condition occur outside the brain, particularly in the peripheral blood. Diagnoses of HIV-induced neurocognitive disorders largely rely on neuropsychometric assessments, which are not precise. Total HIV DNA in the peripheral blood mononuclear cells (PBMCs), quantified by PCR, correlate with disease progression, which is a promising biomarker to predict HAND. Numerous PCR assays for HIV DNA in cell compartments are prone to variation due to the lack of standardization and, therefore, their utility in predicting HAND produced different outcomes. This review evaluates the clinical relevance of total HIV DNA in circulating mononuclear cells using different published quantitative PCR (qPCR) protocols. The rationale is to shed light on the most appropriate assays and sample types used to accurately quantify HIV DNA load, which predicts severity of neurocognitive impairment. The role of monocytes as a vehicle for trafficking HIV into the CNS makes it the most suitable sample for determining a HAND associated reservoir. Studies have also shown significant associations between monocyte HIV DNA levels with markers of neurodamage. However, qPCR assays using PBMCs are cheaper and available commercially, thus could be beneficial in clinical settings. There is need, however, to standardise DNA extraction, normalisation and limit of detection.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, P.O. Box A178, Avondale Harare 00263, Zimbabwe.
| | - Graeme B Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
| | - Richard H Glashoff
- Division of Medical Microbiology and Immunology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
- Division of Medical Microbiology and Immunology, National Health Laboratory Service (NHLS), Tygerberg Business Unit, P.O. Box 241, Cape Town 8000, South Africa.
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
- Division of Medical Virology, National Health Laboratory Service (NHLS), Tygerberg Business Unit, P.O. Box 241, Cape Town 8000, South Africa.
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Murray JM, Zaunders J, Emery S, Cooper DA, Hey-Nguyen WJ, Koelsch KK, Kelleher AD. HIV dynamics linked to memory CD4+ T cell homeostasis. PLoS One 2017; 12:e0186101. [PMID: 29049331 PMCID: PMC5648138 DOI: 10.1371/journal.pone.0186101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/25/2017] [Indexed: 11/18/2022] Open
Abstract
The dynamics of latent HIV is linked to infection and clearance of resting memory CD4+ T cells. Infection also resides within activated, non-dividing memory cells and can be impacted by antigen-driven and homeostatic proliferation despite suppressive antiretroviral therapy (ART). We investigated whether plasma viral level (pVL) and HIV DNA dynamics could be explained by HIV’s impact on memory CD4+ T cell homeostasis. Median total, 2-LTR and integrated HIV DNA levels per μL of peripheral blood, for 8 primary (PHI) and 8 chronic HIV infected (CHI) individuals enrolled on a raltegravir (RAL) based regimen, exhibited greatest changes over the 1st year of ART. Dynamics slowed over the following 2 years so that total HIV DNA levels were equivalent to reported values for individuals after 10 years of ART. The mathematical model reproduced the multiphasic dynamics of pVL, and levels of total, 2-LTR and integrated HIV DNA in both PHI and CHI over 3 years of ART. Under these simulations, residual viremia originated from reactivated latently infected cells where most of these cells arose from clonal expansion within the resting phenotype. Since virion production from clonally expanded cells will not be affected by antiretroviral drugs, simulations of ART intensification had little impact on pVL. HIV DNA decay over the first year of ART followed the loss of activated memory cells (120 day half-life) while the 5.9 year half-life of total HIV DNA after this point mirrored the slower decay of resting memory cells. Simulations had difficulty reproducing the fast early HIV DNA dynamics, including 2-LTR levels peaking at week 12, and the later slow loss of total and 2-LTR HIV DNA, suggesting some ongoing infection. In summary, our modelling indicates that much of the dynamical behavior of HIV can be explained by its impact on memory CD4+ T cell homeostasis.
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Affiliation(s)
- John M. Murray
- School of Mathematics and Statistics, UNSW Australia, Sydney, NSW, Australia
- * E-mail:
| | - John Zaunders
- St Vincent's Hospital, Sydney, Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Sean Emery
- The Kirby Institute, University of New South Wales, Sydney, NSW Australia
| | - David A. Cooper
- The Kirby Institute, University of New South Wales, Sydney, NSW Australia
| | | | - Kersten K. Koelsch
- The Kirby Institute, University of New South Wales, Sydney, NSW Australia
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Abstract
PURPOSE OF REVIEW Despite the success of antiretroviral therapy in suppressing HIV, life-long therapy is required to avoid HIV reactivation from long-lived viral reservoirs. Currently, there is intense interest in searching for therapeutic interventions that can purge the viral reservoir to achieve complete remission in HIV patients off antiretroviral therapy. The evaluation of such interventions relies on our ability to accurately and precisely measure the true size of the viral reservoir. In this review, we assess the most commonly used HIV reservoir assays, as a clear understanding of the strengths and weaknesses of each is vital for the accurate interpretation of results and for the development of improved assays. RECENT FINDINGS The quantification of intracellular or plasma HIV RNA or DNA levels remains the most commonly used tests for the characterization of the viral reservoir. While cost-effective and high-throughput, these assays are not able to differentiate between replication-competent or defective fractions or quantify the number of infected cells. Viral outgrowth assays provide a lower bound for the fraction of cells that can produce infectious virus, but these assays are laborious, expensive and substantially underestimate the potential reservoir of replication-competent provirus. Newer assays are now available that seek to overcome some of these problems, including full-length proviral sequencing, inducible HIV RNA assays, ultrasensitive p24 assays and murine adoptive transfer techniques. The development and evaluation of strategies for HIV remission rely upon our ability to accurately and precisely quantify the size of the remaining viral reservoir. At this time, all current HIV reservoir assays have drawbacks such that combinations of assays are generally needed to gain a more comprehensive view of the viral reservoir. The development of novel, rapid, high-throughput assays that can sensitively quantify the levels of the replication-competent HIV reservoir is still needed.
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Affiliation(s)
- Radwa R Sharaf
- Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne St, Rm 421, Cambridge, Boston, MA, 02139, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne St, Rm 421, Cambridge, Boston, MA, 02139, USA.
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On the Death Rate of Abortively Infected Cells: Estimation from Simian-Human Immunodeficiency Virus Infection. J Virol 2017; 91:JVI.00352-17. [PMID: 28679753 DOI: 10.1128/jvi.00352-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/26/2017] [Indexed: 02/07/2023] Open
Abstract
Progressive T cell depletion during chronic human immunodeficiency virus type 1 (HIV) infection is a key mechanism that leads to the development of AIDS. Recent studies have suggested that most T cells in the tissue die through pyroptosis triggered by abortive infection, i.e., infection of resting T cells in which HIV failed to complete reverse transcription. However, the contribution of abortive infection to T cell loss and how quickly abortively infected cells die in vivo, key parameters for a quantitative understanding of T cell population dynamics, are not clear. Here, we infected rhesus macaques with simian-human immunodeficiency viruses (SHIV) and followed the dynamics of both plasma SHIV RNA and total cell-associated SHIV DNA. Fitting mathematical models to the data, we estimate that upon infection a majority of CD4+ T cells (approximately 65%, on average) become abortively infected and die at a relatively high rate of 0.27 day-1 (half-life, 2.6 days). This confirms the importance of abortive infection in driving T cell depletion. Further, we find evidence suggesting that an immune response may be restricting viral infection 1 to 3 weeks after infection. Our study serves as a step forward toward a quantitative understanding of the mechanisms driving T cell depletion during HIV infection.IMPORTANCE In HIV-infected patients, progressive CD4+ T cell loss ultimately leads to the development of AIDS. The mechanisms underlying this T cell loss are not clear. Recent experimental data suggest that the majority of CD4+ T cells in tissue die through abortive infection, where the accumulation of incomplete HIV transcripts triggers cell death. To investigate the role of abortive infection in driving CD4+ T cell loss in vivo, we infected macaques with simian-human immunodeficiency viruses (SHIV) and followed the viral kinetics of both plasma RNA and cell-associated DNA during infection. Fitting mathematical models, we estimated that a large fraction of infected cells dies through abortive infection and has a half-life of approximately 2.6 days. Our results provide the first in vivo quantitative estimates of parameters characterizing abortive infection and support the notion that abortive infection represents an important mechanism underlying progressive CD4+ T cell depletion in vivo.
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46
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Cardozo EF, Andrade A, Mellors JW, Kuritzkes DR, Perelson AS, Ribeiro RM. Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration. PLoS Pathog 2017; 13:e1006478. [PMID: 28678879 PMCID: PMC5513547 DOI: 10.1371/journal.ppat.1006478] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/17/2017] [Accepted: 06/18/2017] [Indexed: 02/07/2023] Open
Abstract
The kinetics of HIV-1 decay under treatment depends on the class of antiretrovirals used. Mathematical models are useful to interpret the different profiles, providing quantitative information about the kinetics of virus replication and the cell populations contributing to viral decay. We modeled proviral integration in short- and long-lived infected cells to compare viral kinetics under treatment with and without the integrase inhibitor raltegravir (RAL). We fitted the model to data obtained from participants treated with RAL-containing regimes or with a four-drug regimen of protease and reverse transcriptase inhibitors. Our model explains the existence and quantifies the three phases of HIV-1 RNA decay in RAL-based regimens vs. the two phases observed in therapies without RAL. Our findings indicate that HIV-1 infection is mostly sustained by short-lived infected cells with fast integration and a short viral production period, and by long-lived infected cells with slow integration but an equally short viral production period. We propose that these cells represent activated and resting infected CD4+ T-cells, respectively, and estimate that infection of resting cells represent ~4% of productive reverse transcription events in chronic infection. RAL reveals the kinetics of proviral integration, showing that in short-lived cells the pre-integration population has a half-life of ~7 hours, whereas in long-lived cells this half-life is ~6 weeks. We also show that the efficacy of RAL can be estimated by the difference in viral load at the start of the second phase in protocols with and without RAL. Overall, we provide a mechanistic model of viral infection that parsimoniously explains the kinetics of viral load decline under multiple classes of antiretrovirals.
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Affiliation(s)
- E Fabian Cardozo
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Adriana Andrade
- The Johns Hopkins University, Baltimore, MD, United States of America
| | - John W Mellors
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Daniel R Kuritzkes
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America.,Laboratório de Biomatemática, Faculdade de Medicina, Universidade de Lisboa. Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
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47
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Khoury G, Fromentin R, Solomon A, Hartogensis W, Killian M, Hoh R, Somsouk M, Hunt PW, Girling V, Sinclair E, Bacchetti P, Anderson JL, Hecht FM, Deeks SG, Cameron PU, Chomont N, Lewin SR. Human Immunodeficiency Virus Persistence and T-Cell Activation in Blood, Rectal, and Lymph Node Tissue in Human Immunodeficiency Virus-Infected Individuals Receiving Suppressive Antiretroviral Therapy. J Infect Dis 2017; 215:911-919. [PMID: 28453847 PMCID: PMC5407052 DOI: 10.1093/infdis/jix039] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 01/31/2017] [Indexed: 11/13/2022] Open
Abstract
Background Immune activation and inflammation remain elevated in human immunodeficiency virus (HIV)-infected individuals receiving antiretroviral therapy (ART) and may contribute to HIV persistence. Methods Using flow cytometry expression of CD38, HLA-DR and PD-1 were measured in blood (n = 48), lymph node (LN; n = 9), and rectal tissue (n = 17) from virally suppressed individuals. Total and integrated HIV DNA, 2-LTR circles, and cell-associated unspliced HIV RNA were quantified. Results CD4+ T cells from rectal tissue had a higher frequency of integrated HIV DNA compared with blood (4.26 fold-change in DNA; 95% confidence interval [CI] = 2.61-7.00; P < .001) and LN (2.32 fold-change in DNA; 95% CI = 1.22-4.41; P = .01). In rectal tissue, there were positive associations between integrated HIV DNA with PD-1+ CD4+ T-cells (1.44 fold-change in integrated HIV DNA per 10-unit increase in PD-1+ CD4+ T cells; 95% CI = 1.01-2.05; P = .045) and CD38+HLA-DR+ CD8+ T cells (1.40 fold-change in integrated HIV DNA per 1-unit increase in CD38+HLA-DR+ CD8+ T cells; 95% CI = 1.05-1.86; P = .02). Both associations were independent of current and nadir CD4+ T-cell counts. Conclusions During ART, rectal tissue is an important reservoir for HIV persistence with a high frequency of activated CD4+ and CD8+ T cells. PD-1 may represent a marker of HIV persistence in rectal tissue.
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Affiliation(s)
- Gabriela Khoury
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Australia
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Canada
| | - Ajantha Solomon
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Australia
| | - Wendy Hartogensis
- Department of Medicine, University of California, San Francisco, USA
| | - Marisela Killian
- Department of Medicine, University of California, San Francisco, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, USA
| | - Ma Somsouk
- Department of Medicine, University of California, San Francisco, USA
| | - Peter W Hunt
- Department of Medicine, University of California, San Francisco, USA
| | - Valerie Girling
- Department of Medicine, University of California, San Francisco, USA
| | | | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jenny L Anderson
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Australia
| | - Frederick M Hecht
- Department of Medicine, University of California, San Francisco, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, USA
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Australia
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Canada.,Department of Microbiology, Infectiology, and Immunology, Faculty of Medicine, Université de Montréal, Canada
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Australia
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Levels of HIV-1 persistence on antiretroviral therapy are not associated with markers of inflammation or activation. PLoS Pathog 2017; 13:e1006285. [PMID: 28426825 PMCID: PMC5398724 DOI: 10.1371/journal.ppat.1006285] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/09/2017] [Indexed: 11/19/2022] Open
Abstract
Antiretroviral therapy (ART) reduces levels of HIV-1 and immune activation but both can persist despite clinically effective ART. The relationships among pre-ART and on-ART levels of HIV-1 and activation are incompletely understood, in part because prior studies have been small or cross-sectional. To address these limitations, we evaluated measures of HIV-1 persistence, inflammation, T cell activation and T cell cycling in a longitudinal cohort of 101 participants who initiated ART and had well-documented sustained suppression of plasma viremia for a median of 7 years. During the first 4 years following ART initiation, HIV-1 DNA declined by 15-fold (93%) whereas cell-associated HIV-1 RNA (CA-RNA) fell 525-fold (>99%). Thereafter, HIV-1 DNA levels continued to decline slowly (5% per year) with a half-life of 13 years. Participants who had higher HIV-1 DNA and CA-RNA before starting treatment had higher levels while on ART, despite suppression of plasma viremia for many years. Markers of inflammation and T cell activation were associated with plasma HIV-1 RNA levels before ART was initiated but there were no consistent associations between these markers and HIV-1 DNA or CA-RNA during long-term ART, suggesting that HIV-1 persistence is not driving or driven by inflammation or activation. Higher levels of inflammation, T cell activation and cycling before ART were associated with higher levels during ART, indicating that immunologic events that occurred well before ART initiation had long-lasting effects despite sustained virologic suppression. These findings should stimulate studies of viral and host factors that affect virologic, inflammatory and immunologic set points prior to ART initiation and should inform the design of strategies to reduce HIV-1 reservoirs and dampen immune activation that persists despite ART.
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Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications. Clin Microbiol Rev 2017; 29:859-80. [PMID: 27559075 DOI: 10.1128/cmr.00015-16] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis.
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50
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Ruggiero A, Malatinkova E, Rutsaert S, Paxton WA, Vandekerckhove L, De Spiegelaere W. Utility of integrated HIV-1 DNA quantification in cure studies. Future Virol 2017. [DOI: 10.2217/fvl-2016-0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Numerous HIV-1 curative strategies have been proposed to eradicate the virus reservoir pool that remains integrated within target cells, despite successful antiretroviral therapy. To test the impact of such interventions on this reservoir, a universal marker of persistence is needed. Quantifying integrated HIV-1 DNA load has been proposed as a strong virological marker. In this paper, we provide a detailed description of the most commonly used assays to quantify integrated HIV-1 DNA and applications in relevant clinical studies produced over the last 20 years with a major focus on the recent literature. We discuss the potential for using this marker of virological persistence and the technical limitations that need to be addressed.
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Affiliation(s)
- Alessandra Ruggiero
- Department of Clinical Infection, Microbiology & Immunology (CIMI), Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - William A Paxton
- Department of Clinical Infection, Microbiology & Immunology (CIMI), Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Sciences, Ghent University, Belgium
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