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Semenova L, Wang Y, Falcinelli S, Archin N, Cooper-Volkheimer AD, Margolis DM, Goonetilleke N, Murdoch DM, Rudin CD, Browne EP. Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy. eLife 2024; 13:RP94899. [PMID: 39250423 DOI: 10.7554/elife.94899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024] Open
Abstract
Understanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning (ML) approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host-reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A leave-one-covariate-out inference approach identified specific HIV reservoir and clinical-demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical-demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, ML algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA . The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.
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Affiliation(s)
- Lesia Semenova
- Microsoft Research, Duke University, Durham, United States
| | - Yingfan Wang
- Department of Computer Science, Duke University, Durham, United States
| | - Shane Falcinelli
- UNC HIV Cure Center UNC Chapel Hill, Chapel Hill, United States
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, United States
| | - Nancie Archin
- UNC HIV Cure Center UNC Chapel Hill, Chapel Hill, United States
- Department of Medicine, UNC Chapel Hill, Chapel Hill, United States
| | | | - David M Margolis
- UNC HIV Cure Center UNC Chapel Hill, Chapel Hill, United States
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, United States
- Department of Medicine, UNC Chapel Hill, Chapel Hill, United States
| | - Nilu Goonetilleke
- UNC HIV Cure Center UNC Chapel Hill, Chapel Hill, United States
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, United States
| | - David M Murdoch
- Department of Medicine, Duke University, Durham, United States
| | - Cynthia D Rudin
- Department of Computer Science, Duke University, Durham, United States
| | - Edward P Browne
- UNC HIV Cure Center UNC Chapel Hill, Chapel Hill, United States
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, United States
- Department of Medicine, UNC Chapel Hill, Chapel Hill, United States
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De Nicolò A, Palermiti A, Dispinseri S, Marchetti G, Trunfio M, De Vivo E, D'Avolio A, Muscatello A, Gori A, Rusconi S, Bruzzesi E, Gabrieli A, Bernasconi DP, Bandera A, Nozza S, Calcagno A. Plasma, intracellular and lymph node antiretroviral concentrations and HIV DNA change during primary HIV infection: Results from the INACTION P25 study. Int J Antimicrob Agents 2024; 64:107200. [PMID: 38768738 DOI: 10.1016/j.ijantimicag.2024.107200] [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: 10/13/2023] [Revised: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Despite its effectiveness, combination antiretroviral treatment (cART) has a limited effect on HIV DNA reservoir, which establishes early during primary HIV infection (PHI) and is maintained by latency, homeostatic T-cells proliferation, and residual replication. This limited effect can be associated with low drug exposure in lymphoid tissues and/or suboptimal adherence to antiretroviral drugs (ARVs). The aim of this study was to assess ARV concentrations in plasma, peripheral blood mononuclear cells (PBMCs) and lymph nodes (LNs), and their association to HIV RNA and HIV DNA decay during PHI. Participants were randomised to receive standard doses of darunavir/cobicistat (Arm I), dolutegravir (Arm II) or both (Arm III), with a backbone of tenofovir alafenamide and emtricitabine. Total HIV DNA was measured using digital-droplet PCR in PBMCs at baseline, 12 and 48 weeks. Drug concentrations in plasma and PBMCs were determined at 2, 12 and 48 weeks (LNs at 12 weeks) by UHPLC-MS/MS. Seventy-two participants were enrolled, mostly male (n=68), with a median age of 34 years and variable Fiebig stages (V-VI 57.7%, I-II 23.9%, and III-IV 18.3%). Twenty-six patients were assigned to Arm I, 27 to Arm II and 19 to Arm III. After 48 weeks, most patients had undetectable viremia, with minor differences in HIV RNA decay between arms. Patients with Fiebig I-II showed faster HIV RNA and HIV DNA decay. Intracellular tissue penetration was high for nucleoside analogues and low-moderate for darunavir and dolutegravir. Only tenofovir diphosphate concentrations in PBMCs showed correlation with HIV DNA decay. Overall, these results indicate that the timing of treatment initiation and intracellular tenofovir penetration are primary and secondary factors, respectively, affecting HIV reservoir.
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Affiliation(s)
- Amedeo De Nicolò
- Laboratory of Clinical Pharmacology and Pharmacogenetics, Department of Medical Sciences, University of Turin, Turin.
| | - Alice Palermiti
- Laboratory of Clinical Pharmacology and Pharmacogenetics, Department of Medical Sciences, University of Turin, Turin
| | | | - Giulia Marchetti
- Clinic of Infectious Diseases, Department of Health Sciences, ASST Santi Paolo e Carlo, University of Milan, Milan
| | - Mattia Trunfio
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin
| | - Elisa De Vivo
- Laboratory of Clinical Pharmacology and Pharmacogenetics, Department of Medical Sciences, University of Turin, Turin
| | - Antonio D'Avolio
- Laboratory of Clinical Pharmacology and Pharmacogenetics, Department of Medical Sciences, University of Turin, Turin
| | - Antonio Muscatello
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan
| | - Andrea Gori
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan
| | - Stefano Rusconi
- UOC Malattie Infettive, Ospedale Civile di Legnano, ASST Ovest Milanese, Legnano; University of Milan, Milan
| | | | - Arianna Gabrieli
- Dipartimento di Scienze Biomediche e Cliniche, Ospedale L Sacco, Milan
| | - Davide Paolo Bernasconi
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4 School of Medicine and Surgery, University of Milano-Bicocca, Monza
| | | | - Silvia Nozza
- Department of Infectious Diseases, IRCCS Ospedale san Raffaele, Milan, Italy
| | - Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin
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Jimenez-Leon MR, Gasca-Capote C, Roca-Oporto C, Espinosa N, Sobrino S, Fontillon-Alberdi M, Gao C, Roseto I, Gladkov G, Rivas-Jeremias I, Neukam K, Sanchez-Hernandez JG, Rigo-Bonnin R, Cervera-Barajas AJ, Mesones R, García F, Alvarez-Rios AI, Bachiller S, Vitalle J, Perez-Gomez A, Camacho-Sojo MI, Gallego I, Brander C, McGowan I, Mothe B, Viciana P, Yu X, Lichterfeld M, Lopez-Cortes LF, Ruiz-Mateos E. Vedolizumab and ART in recent HIV-1 infection unveil the role of α4β7 in reservoir size. JCI Insight 2024; 9:e182312. [PMID: 38980725 PMCID: PMC11343594 DOI: 10.1172/jci.insight.182312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUNDWe evaluated the safety and viral rebound, after analytical treatment interruption (ATI), of vedolizumab and ART in recent HIV-1 infection. We used this model to analyze the effect of α4β7 on the HIV-1 reservoir size.METHODSParticipants started ART with monthly vedolizumab infusions, and ATI was performed at week 24. Biopsies were obtained from ileum and cecum at baseline and week 24. Vedolizumab levels, HIV-1 reservoir, flow cytometry, and cell-sorting and antibody competition experiments were assayed.RESULTSVedolizumab was safe and well tolerated. No participant achieved undetectable viremia off ART 24 weeks after ATI. Only a modest effect on the time to achieve more than 1,000 HIV-1 RNA copies/mL and the proportion of participants off ART was observed, being higher in the vedolizumab group compared with historical controls. Just before ATI, α4β7 expression was associated with HIV-1 DNA and RNA in peripheral blood and with PD1 and TIGIT levels. Importantly, a complete blocking of α4β7 was observed on peripheral CD4+ T cells but not in gut (ileum and cecum), where α4β7 blockade and vedolizumab levels were inversely associated with HIV-1 DNA.CONCLUSIONOur findings support α4β7 as an important determinant in HIV-1 reservoir size, suggesting the complete α4β7 blockade in tissue as a promising tool for HIV-cure combination strategies.TRIAL REGISTRATIONClinicalTrials.gov NCT03577782.FUNDINGThis work was supported by the Instituto de Salud Carlos III (Fondo Europeo de Desarrollo Regional, "a way to make Europe," research contracts FI17/00186 and FI19/00083 and research projects PI18/01532, PI19/01127, PI22/01796), Conserjería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía (research projects P20/00906), the Red Temática de Investigación Cooperativa en SIDA (RD16/0025/0020), and the Spanish National Research Council.
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Affiliation(s)
- Maria Reyes Jimenez-Leon
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Carmen Gasca-Capote
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Cristina Roca-Oporto
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Nuria Espinosa
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Isabelle Roseto
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Gregory Gladkov
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Inmaculada Rivas-Jeremias
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Karin Neukam
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | | | - Raul Rigo-Bonnin
- Department of Clinical Laboratory, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge, Universitat de Barcelona, Barcelona, Spain
| | | | - Rosario Mesones
- Clinical Trials Units, Virgen del Rocío University Hospital, Seville, Spain
| | - Federico García
- Departament of Microbiology, San Cecilio University Hospital, Instituto de Investigación Ibs, Granada, Ciber de Enfermedades Infecciosas, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Granada, Spain
| | | | - Sara Bachiller
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Joana Vitalle
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Alberto Perez-Gomez
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - María Inés Camacho-Sojo
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Isabel Gallego
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | | | | | - Beatriz Mothe
- Infectious Diseases Department and IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Badalona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain
| | - Pompeyo Viciana
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Luis F. Lopez-Cortes
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville, Virgen del Rocío University Hospital, Consejo Superior de Investigaciones Científicas, University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
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4
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Semenova L, Wang Y, Falcinelli S, Archin N, Cooper-Volkheimer AD, Margolis DM, Goonetilleke N, Murdoch DM, Rudin CD, Browne EP. Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567386. [PMID: 38014340 PMCID: PMC10680759 DOI: 10.1101/2023.11.16.567386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Understanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host-reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A Leave-One-Covariate-Out (LOCO) inference approach identified specific HIV reservoir and clinical-demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical-demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, machine learning algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA. The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.
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5
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Immonen TT, Fennessey CM, Lipkey L, Newman L, Macairan A, Bosche M, Waltz N, Del Prete GQ, Lifson JD, Keele BF. No evidence for ongoing replication on ART in SIV-infected macaques. Nat Commun 2024; 15:5093. [PMID: 38877003 PMCID: PMC11178840 DOI: 10.1038/s41467-024-49369-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
The capacity of HIV-1 to replicate during optimal antiretroviral therapy (ART) is challenging to assess directly. To gain greater sensitivity to detect evolution on ART, we used a nonhuman primate (NHP) model providing precise control over the level of pre-ART evolution and more comprehensive analyses than are possible with clinical samples. We infected 21 rhesus macaques (RMs) with the barcoded virus SIVmac239M and initiated ART early to minimize baseline genetic diversity. RMs were treated for 285-1200 days. We used several tests of molecular evolution to compare 1352 near-full-length (nFL) SIV DNA single genome sequences from PBMCs, lymph nodes, and spleen obtained near the time of ART initiation and those present after long-term ART, none of which showed significant changes to the SIV DNA population during ART in any animal. To investigate the possibility of ongoing replication in unsampled putative tissue sanctuaries during ART, we discontinued treatment in four animals and confirmed that none of the 336 nFL SIV RNA sequences obtained from rebound plasma viremia showed evidence of evolution. The rigorous nature of our analyses reinforced the emerging consensus of a lack of appreciable ongoing replication on effective ART and validates the relevance of this NHP model for cure studies.
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Affiliation(s)
- Taina T Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Laura Newman
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Agatha Macairan
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Marjorie Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Nora Waltz
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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6
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Salgado M, Gálvez C, Nijhuis M, Kwon M, Cardozo-Ojeda EF, Badiola J, Gorman MJ, Huyveneers LEP, Urrea V, Bandera A, Jensen BEO, Vandekerckhove L, Jurado M, Raj K, Schulze Zur Wiesch J, Bailén R, Eberhard JM, Nabergoj M, Hütter G, Saldaña-Moreno R, Oldford S, Barrett L, Ramirez MLM, Garba S, Gupta RK, Revollo B, Ferra-Coll C, Kuball J, Alter G, Sáez-Cirión A, Diez-Martin JL, Duke ER, Schiffer JT, Wensing A, Martinez-Picado J. Dynamics of virological and immunological markers of HIV persistence after allogeneic haematopoietic stem-cell transplantation in the IciStem cohort: a prospective observational cohort study. Lancet HIV 2024; 11:e389-e405. [PMID: 38816141 DOI: 10.1016/s2352-3018(24)00090-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Allogeneic haematopoietic stem-cell transplantation (allo-HSCT) markedly reduces HIV reservoirs, but the mechanisms by which this occurs are only partly understood. In this study, we aimed to describe the dynamics of virological and immunological markers of HIV persistence after allo-HSCT. METHODS In this prospective observational cohort study, we analysed the viral reservoir and serological dynamics in IciStem cohort participants with HIV who had undergone allo-HSCT and were receiving antiretroviral therapy, ten of whom had received cells from donors with the CCR5Δ32 mutation. Participants from Belgium, Canada, Germany, Italy, the Netherlands, Spain, Switzerland, and the UK were included in the cohort both prospectively and retrospectively between June 1, 2014 and April 30, 2019. In the first 6 months after allo-HSCT, participants had monthly assessments, with annual assessments thereafter, with the protocol tailored to accommodate for the individual health status of each participant. HIV reservoirs were measured in blood and tissues and HIV-specific antibodies were measured in plasma. We used the Wilcoxon signed-rank test to compare data collected before and after allo-HSCT in participants for whom longitudinal data were available. When the paired test was not possible, we used the Mann-Whitney U test. We developed a mathematical model to study the factors influencing HIV reservoir reduction in people with HIV after allo-HSCT. FINDINGS We included 30 people with HIV with haematological malignancies who received a transplant between Sept 1, 2009 and April 30, 2019 and were enrolled within the IciStem cohort and included in this analysis. HIV reservoirs in peripheral blood were reduced immediately after full donor chimerism was achieved, generally accompanied by undetectable HIV-DNA in bone marrow, ileum, lymph nodes, and cerebrospinal fluid, regardless of donor CCR5 genotype. HIV-specific antibody levels and functionality values declined more slowly than direct HIV reservoir values, decaying significantly only months after full donor chimerism. Mathematical modelling suggests that allogeneic immunity mediated by donor cells is the main viral reservoir depletion mechanism after massive reservoir reduction during conditioning chemotherapy before allo-HSCT (half-life of latently infected replication-competent cells decreased from 44 months to 1·5 months). INTERPRETATION Our work provides, for the first time, data on the effects of allo-HSCT in the context of HIV infection. Additionally, we raise the question of which marker can serve as the last reporter of the residual viraemia, postulating that the absence of T-cell immune responses might be a more reliable marker than antibody decline after allo-HSCT. FUNDING amfAR (American Foundation for AIDS Research; ARCHE Program), National Institutes of Health, National Institute of Allergy and Infectious Diseases, and Dutch Aidsfonds.
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Affiliation(s)
- Maria Salgado
- IrsiCaixa, Badalona, Spain; Germans Trias i Pujol Research Institute, Badalona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
| | | | - Monique Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands; HIV Pathogenesis Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Mi Kwon
- Department of Hematology, Hospital Universitario Gregorio Marañón, Institute of Health Research Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - E Fabian Cardozo-Ojeda
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Xencor, Pasadena, CA, USA
| | - Jon Badiola
- University Hospital Virgen de las Nieves, Granada, Spain
| | - Matthew J Gorman
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA; Moderna Therapeutics, Cambridge, MA, USA
| | - Laura E P Huyveneers
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Björn-Erik Ole Jensen
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Manuel Jurado
- University Hospital Virgen de las Nieves, Granada, Spain
| | | | - Julian Schulze Zur Wiesch
- Infectious Diseases Unit, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Rebeca Bailén
- Department of Hematology, Hospital Universitario Gregorio Marañón, Institute of Health Research Gregorio Marañón, Madrid, Spain
| | - Johanna M Eberhard
- Infectious Diseases Unit, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany; Helmholtz Institute for One Health, Greifswald, Germany
| | - Mitja Nabergoj
- Division of Hematology, Hôpitaux Universitaires de Genève, Geneva, Switzerland; Hematology Service, Institut Central des Hôpitaux, Sion, Switzerland
| | | | | | - Sharon Oldford
- Nova Scotia Health, Dalhousie University, Halifax, NS, Canada
| | - Lisa Barrett
- Nova Scotia Health, Dalhousie University, Halifax, NS, Canada
| | - Maria Luisa Montes Ramirez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; University Hospital La Paz, IdiPAZ, Madrid, Spain
| | - Salisu Garba
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Merck, Rahway, NJ, USA
| | | | - Boris Revollo
- Department of Infectious Diseases, University Hospital Germans Trias i Pujol, Institut Català d'Oncologia, Badalona, Spain
| | - Christelle Ferra-Coll
- Department of Hematology, University Hospital Germans Trias i Pujol, Institut Català d'Oncologia, Badalona, Spain; University of Vic-Central University of Catalonia, Vic, Spain
| | - Jurgen Kuball
- Department of Hematology and Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Galit Alter
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA; Moderna Therapeutics, Cambridge, MA, USA
| | - Asier Sáez-Cirión
- Viral Reservoirs and Immune Control Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Jose Luis Diez-Martin
- Department of Hematology, Hospital Universitario Gregorio Marañón, Institute of Health Research Gregorio Marañón, Madrid, Spain
| | - Elizabeth R Duke
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Medicine, Allergy and Infectious Diseases Division, University of Washington, WA, Seattle, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Medicine, Allergy and Infectious Diseases Division, University of Washington, WA, Seattle, USA
| | - Annemarie Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands; Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Javier Martinez-Picado
- IrsiCaixa, Badalona, Spain; Germans Trias i Pujol Research Institute, Badalona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; University of Vic-Central University of Catalonia, Vic, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Spain.
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7
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Zhang Z, Reece MD, Roa S, Tyor W, Franklin DR, Letendre SL, Marconi VC, Anderson AM, Gavegnano C. The identification of intact HIV proviral DNA from human cerebrospinal fluid. Neurotherapeutics 2024; 21:e00373. [PMID: 38749843 DOI: 10.1016/j.neurot.2024.e00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 07/15/2024] Open
Abstract
We evaluated the HIV-1 DNA reservoir in peripheral blood mononuclear cells (PBMC) and cerebrospinal fluid (CSF) in people with HIV (PWH) and associations to cognitive dysfunction. Using the intact proviral DNA assay (IPDA), an emerging technique to identify provirus that may be the source of viral rebound, we assessed HIV DNA in CSF and PBMC in PWH regardless of antiretroviral therapy (ART). CSF was used as a sampling surrogate for the central nervous system (CNS) as opposed to tissue. IDPA results (3' defective, 5' defective, and intact HIV DNA) were analyzed by compartment (Wilcoxon signed rank; matched and unmatched pairs). Cognitive performance, measured via a battery of nine neuropsychological (NP) tests, were analyzed for correlation to HIV DNA (Spearman's rho). 11 CSF and 8 PBMC samples from PWH were evaluated both unmatched and matched. Total CSF HIV DNA was detectable in all participants and was significantly higher than in matched PBMCs (p = 0.0039). Intact CSF HIV DNA was detected in 7/11 participants and correlated closely with those in PBMCs but tended to be higher in CSF than in PBMC. CSF HIV DNA did not correlate with global NP performance, but higher values did correlate with worse executive function (p = 0.0440). Intact HIV DNA is frequently present in the CSF of PWH regardless of ART. This further supports the presence of an HIV CNS reservoir and provides a method to study CNS reservoirs during HIV cure studies. Larger studies are needed to evaluate relationships with CNS clinical outcomes.
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Affiliation(s)
- Zhan Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Atlanta VA Medical Center, Atlanta, GA, USA
| | - Monica D Reece
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sebastian Roa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - William Tyor
- Atlanta VA Medical Center, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Donald R Franklin
- Department of Psychiatry, University of California at San Diego School of Medicine, La Jolla, CA, USA
| | - Scott L Letendre
- Department of Medicine, Division of Infectious Diseases, University of California at San Diego School of Medicine, La Jolla, CA, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA; Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Albert M Anderson
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Christina Gavegnano
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA; Center for the Study of Human Health, Emory College, Atlanta, GA, USA; Harvard Medical School, Center for Bioethics, Boston, MA, USA.
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8
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Hasler MF, Speck RF, Kadzioch NP. Humanized mice for studying HIV latency and potentially its eradication. Curr Opin HIV AIDS 2024; 19:157-167. [PMID: 38547338 DOI: 10.1097/coh.0000000000000855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PURPOSE OF THE REVIEW The quest for an HIV cure faces a formidable challenge: the persistent presence of latent viral infections within the cells and tissues of infected individuals. This review provides a thorough examination of discussions surrounding HIV latency, the use of humanized mouse models, and strategies aimed at eliminating the latent HIV reservoir. It explores the hurdles and advancements in understanding HIV pathogenesis, mainly focusing on establishing latent reservoirs in CD4 + T cells and macrophages. Introducing the concepts of functional and sterile cures, the review underscores the indispensable role of humanized mouse models in HIV research, offering crucial insights into the efficacy of cART and the ongoing pursuit of an HIV cure. RECENT FINDINGS Here, we highlight studies investigating molecular mechanisms and pathogenesis related to HIV latency in humanized mice and discuss novel strategies for eradicating latent HIV. Emphasizing the importance of analytical cART interruption in humanized mouse studies to gauge its impact on the latent reservoir accurately, the review underlines the ongoing progress and challenges in harnessing humanized mouse models for HIV research. SUMMARY This review suggests that humanized mice models provide valuable insights into HIV latency and potential eradication strategies, contributing significantly to the quest for an HIV cure.
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Affiliation(s)
- Moa F Hasler
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
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9
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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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10
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Cannon L, Fehrman S, Pinzone M, Weissman S, O'Doherty U. Machine Learning Bolsters Evidence That D1, Nef, and Tat Influence HIV Reservoir Dynamics. Pathog Immun 2024; 8:37-58. [PMID: 38292079 PMCID: PMC10827039 DOI: 10.20411/pai.v8i2.621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024] Open
Abstract
Background The primary hurdle to curing HIV is due to the establishment of a reservoir early in infection. In an effort to find new treatment strategies, we and others have focused on understanding the selection pressures exerted on the reservoir by studying how proviral sequences change over time. Methods To gain insights into the dynamics of the HIV reservoir we analyzed longitudinal near full-length sequences from 7 people living with HIV between 1 and 20 years following the initiation of antiretroviral treatment. We used this data to employ Bayesian mixed effects models to characterize the decay of the reservoir using single-phase and multiphasic decay models based on near full-length sequencing. In addition, we developed a machine-learning approach utilizing logistic regression to identify elements within the HIV genome most associated with proviral decay and persistence. By systematically analyzing proviruses that are deleted for a specific element, we gain insights into their role in reservoir contraction and expansion. Results Our analyses indicate that biphasic decay models of intact reservoir dynamics were better than single-phase models with a stronger statistical fit. Based on the biphasic decay pattern of the intact reservoir, we estimated the half-lives of the first and second phases of decay to be 18.2 (17.3 to 19.2, 95%CI) and 433 (227 to 6400, 95%CI) months, respectively.In contrast, the dynamics of defective proviruses differed favoring neither model definitively, with an estimated half-life of 87.3 (78.1 to 98.8, 95% CI) months during the first phase of the biphasic model. Machine-learning analysis of HIV genomes at the nucleotide level revealed that the presence of the splice donor site D1 was the principal genomic element associated with contraction. This role of D1 was then validated in an in vitro system. Using the same approach, we additionally found supporting evidence that HIV nef may confer a protective advantage for latently infected T cells while tat was associated with clonal expansion. Conclusions The nature of intact reservoir decay suggests that the long-lived HIV reservoir contains at least 2 distinct compartments. The first compartment decays faster than the second compartment. Our machine-learning analysis of HIV proviral sequences reveals specific genomic elements are associated with contraction while others are associated with persistence and expansion. Together, these opposing forces shape the reservoir over time.
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Affiliation(s)
- LaMont Cannon
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia
| | - Sophia Fehrman
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia
| | - Marilia Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sam Weissman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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11
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De Clercq J, De Scheerder MA, Mortier V, Verhofstede C, Vandecasteele SJ, Allard SD, Necsoi C, De Wit S, Gerlo S, Vandekerckhove L. Longitudinal patterns of inflammatory mediators after acute HIV infection correlate to intact and total reservoir. Front Immunol 2024; 14:1337316. [PMID: 38250083 PMCID: PMC10796502 DOI: 10.3389/fimmu.2023.1337316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Background Despite the beneficial effects of antiretroviral therapy (ART) initiation during acute HIV infection (AHI), residual immune activation remains a hallmark of treated HIV infection. Methods Plasma concentrations of 40 mediators were measured longitudinally in 39 early treated participants of a Belgian AHI cohort (HIV+) and in 21 HIV-negative controls (HIV-). We investigated the association of the inflammatory profile with clinical presentation, plasma viral load, immunological parameters, and in-depth characterization of the HIV reservoir. Results While levels of most soluble mediators normalized with suppressive ART, we demonstrated the persistence of a pro-inflammatory signature in early treated HIV+ participants in comparison to HIV- controls. Examination of these mediators demonstrated a correlation with their levels during AHI, which seemed to be viremia-driven, and suggested involvement of an activated myeloid compartment, IFN-γ-signaling, and inflammasome-related pathways. Interestingly, some of these pro-inflammatory mediators correlated with a larger reservoir size and slower reservoir decay. In contrast, we also identified soluble mediators which were associated with favorable effects on immunovirological outcomes and reservoir, both during and after AHI. Conclusion These data highlight how the persistent pro-inflammatory profile observed in early ART treated individuals is shaped during AHI and is intertwined with viral dynamics.
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Affiliation(s)
- Jozefien De Clercq
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Virginie Mortier
- Department of Diagnostic Sciences, Aids Reference Laboratory, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Department of Diagnostic Sciences, Aids Reference Laboratory, Ghent University, Ghent, Belgium
| | | | - Sabine D Allard
- Department of Internal Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Coca Necsoi
- Department of Infectious Diseases, Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Stéphane De Wit
- Department of Infectious Diseases, Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
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12
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Kuse N, Gatanaga H, Zhang Y, Chikata T, Oka S, Takiguchi M. Epitope-dependent effect of long-term cART on maintenance and recovery of HIV-1-specific CD8 + T cells. J Virol 2023; 97:e0102423. [PMID: 37877716 PMCID: PMC10688310 DOI: 10.1128/jvi.01024-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE HIV-1-specific CD8+ T cells are anticipated to become effector cells for curative treatment using the "shock and kill" approach in people living with HIV-1 (PLWH) under combined antiretroviral therapy (cART). Previous studies demonstrated that the frequency of HIV-1-specific CD8+ T cells is reduced under cART and their functional ability remains impaired. These studies analyzed T-cell responses to a small number of HIV-1 epitopes or overlapping HIV-1 peptides. Therefore, the features of CD8+ T cells specific for HIV-1 epitopes under cART remain only partially clarified. Here, we analyzed CD8+ T cells specific for 63 well-characterized epitopes in 90 PLWH. We demonstrated that CD8+ T cells specific for large numbers of HIV-1 epitopes were maintained in an epitope-dependent fashion under long-term cART and that long-term cART enhanced or restored the ability of HIV-1-specific T cells to proliferate in vitro. This study implies that some HIV-1-specific T cells would be useful as effector cells for curative treatment.
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Affiliation(s)
- Nozomi Kuse
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yu Zhang
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takayuki Chikata
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masafumi Takiguchi
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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13
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Kumar MR, Fray EJ, Bender AM, Zitzmann C, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir. Proc Natl Acad Sci U S A 2023; 120:e2313209120. [PMID: 37844236 PMCID: PMC10614214 DOI: 10.1073/pnas.2313209120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4+ T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t1/2 = 30.1 d) and a slower second phase (t1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.
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Affiliation(s)
- Mithra R. Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Emily J. Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Alexandra M. Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA02215
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Baltimore, MD21205
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14
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Reeves DB, Bacchus-Souffan C, Fitch M, Abdel-Mohsen M, Hoh R, Ahn H, Stone M, Hecht F, Martin J, Deeks SG, Hellerstein MK, McCune JM, Schiffer JT, Hunt PW. Estimating the contribution of CD4 T cell subset proliferation and differentiation to HIV persistence. Nat Commun 2023; 14:6145. [PMID: 37783718 PMCID: PMC10545742 DOI: 10.1038/s41467-023-41521-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
Persistence of HIV in people living with HIV (PWH) on suppressive antiretroviral therapy (ART) has been linked to physiological mechanisms of CD4+ T cells. Here, in the same 37 male PWH on ART we measure longitudinal kinetics of HIV DNA and cell turnover rates in five CD4 cell subsets: naïve (TN), stem-cell- (TSCM), central- (TCM), transitional- (TTM), and effector-memory (TEM). HIV decreases in TTM and TEM but not in less-differentiated subsets. Cell turnover is ~10 times faster than HIV clearance in memory subsets, implying that cellular proliferation consistently creates HIV DNA. The optimal mathematical model for these integrated data sets posits HIV DNA also passages between CD4 cell subsets via cellular differentiation. Estimates are heterogeneous, but in an average participant's year ~10 (in TN and TSCM) and ~104 (in TCM, TTM, TEM) proviruses are generated by proliferation while ~103 proviruses passage via cell differentiation (per million CD4). In simulations, therapies blocking proliferation and/or enhancing differentiation could reduce HIV DNA by 1-2 logs over 3 years. In summary, HIV exploits cellular proliferation and differentiation to persist during ART but clears faster in more proliferative/differentiated CD4 cell subsets and the same physiological mechanisms sustaining HIV might be temporarily modified to reduce it.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
- Department of Global Health, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA.
| | | | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | | | - Rebecca Hoh
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Mars Stone
- Vitalant Research Institute, 360 Spear St Suite 200, San Francisco, CA, 94105, USA
| | - Frederick Hecht
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Jeffrey Martin
- Epidemiology & Biostatistics, University of California San Francisco School of Medicine, 550 16th Street, San Francisco, CA, 94158, USA
| | - Steven G Deeks
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Marc K Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | - Joseph M McCune
- HIV Frontiers, Global Health Accelerator, Bill & Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98109, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
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15
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Takata H, Mitchell JL, Pacheco J, Pagliuzza A, Pinyakorn S, Buranapraditkun S, Sacdalan C, Leyre L, Nathanson S, Kakazu JC, Intasan J, Prueksakaew P, Chomchey N, Phanuphak N, de Souza M, Haddad EK, Rolland M, Tovanabutra S, Vasan S, Hsu DC, Chomont N, Trautmann L. An active HIV reservoir during ART is associated with maintenance of HIV-specific CD8 + T cell magnitude and short-lived differentiation status. Cell Host Microbe 2023; 31:1494-1506.e4. [PMID: 37708852 PMCID: PMC10564289 DOI: 10.1016/j.chom.2023.08.012] [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: 01/20/2023] [Revised: 06/02/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Before initiation of antiretroviral therapy (ART), HIV-specific CD8+ T cells are dysfunctional and short lived. To better understand the relationship between the HIV reservoir in CD4+ T cells and the magnitude and differentiation status of HIV-specific CD8+ T cells, we investigated these cells from acute and chronic HIV-infected individuals after 2 years of ART. Although both the HIV reservoir and the CD8+ T cell responses declined significantly after 2 years of ART, sustained HIV-specific CD8+ T cell responses correlated with a greater reduction of integrated HIV provirus. However, the magnitude of CD8+ T cells specific for HIV Gag, Pol, Nef, and Vif proteins positively associated with the active reservoir size during ART, measured as cell-associated RNA. Importantly, high HIV DNA levels strongly associate with maintenance of short-lived HIV-specific CD8+ T cells, regardless of ART initiation time. Our data suggest that the active reservoir maintains HIV-specific CD8+ T cell magnitude but prevents their differentiation into functional cells.
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Affiliation(s)
- Hiroshi Takata
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Julie L Mitchell
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Julian Pacheco
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC, Canada
| | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | | | - Carlo Sacdalan
- SEARCH Research Foundation, Bangkok, Thailand; Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Louise Leyre
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC, Canada
| | - Sam Nathanson
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Juyeon C Kakazu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | | | | | | | | | | | - Elias K Haddad
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University, Philadelphia, PA 19102, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC, Canada
| | - Lydie Trautmann
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA.
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16
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Bruzzesi E, Gabrieli A, Bernasconi D, Marchetti G, Calcagno A, Ripamonti D, Antinori A, Squillace N, Cingolani A, Muscatello A, Bandera A, Gori A, Rusconi S, Nozza S. HIV-DNA decrease during treatment in primary HIV-1 infection with three different drug regimens: Italian Network of Acute HIV Infection (INACTION) clinical trial. J Med Virol 2023; 95:e29114. [PMID: 37752816 DOI: 10.1002/jmv.29114] [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: 04/17/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 09/28/2023]
Abstract
As the introduction of antiretroviral therapy (ART) during primary HIV-1 infection (PHI) could restrict the establishment of HIV reservoirs, we aimed to assess the effect of three different ART regimens on HIV-DNA load in people living with HIV (PLWH), who started ART in PHI. Randomized, open-label, multicentric study, including subjects in PHI (defined as an incomplete HIV-1 Western blot and detectable plasma HIV-RNA) in the Italian Network of Acute HIV Infection cohort. Participants were randomly assigned (10:10:8) to a fixed-dose combination of tenofovir alafenamide fumarate (TAF) 10 mg plus emtricitabine (FTC) 200 mg, darunavir 800 mg, and cobicistat 150 mg once daily (group A), or TAF 25 mg plus FTC 200 mg, dolutegravir 50 mg once daily (group B), or an intensified four-drug regimen (TAF 10 mg plus FTC 200 mg, dolutegravir 50 mg, darunavir 800 mg, and cobicistat 150 mg once daily) (group C). The primary endpoint was the decrease of HIV-DNA copies/106 peripheral blood mononuclear cells (PBMCs) at weeks (W) 12 and 48. Secondary endpoints were increased in CD4+ cells and in CD4+/CD8+ ratio and percentage of PLWH reaching undetectable HIV-RNA. HIV-DNA was quantified by Droplet Digital PCR (Biorad QX100) and normalized to RPP30 reference gene. This study was registered in ClinicalTrials.gov (number NCT04225325). Among 78 participants enrolled, 30 were randomized to group 1, 28 to group 2, and 20 to group 3. At baseline, median CD4+ count was 658/µL (476-790), HIV-RNA 5.37 (4.38, 6.12) log10 copies/mL, without statistical difference in their change among groups at weeks 12 and 48 (p = 0.432 and 0.234, respectively). The trial was prematurely discontinued for slow accrual and for COVID-19 pandemic-associated restrictions. In the per-protocol analysis, PLWH (n = 72) with undetectable viral load was 54.3% at W12 and 86.4% at W48. Interestingly, the CD4/CD8 ratio progressively increased over time, up to normalization in almost half of the cohort by week 48, despite a deflection in group 3; no difference was observed by the Fiebig stage (I-III vs. IV-VI). HIV-DNA decreased from 4.46 (4.08, 4.81) log10 copies/106 PBMCs to 4.22 (3.79, 4.49) at week 12, and 3.87 (3.46, 4.34) at week 48, without difference among groups. At multivariable analysis, HIV-DNA delta at W48 was associated only with the increase of CD4+ count by 100 cells/mm3 but not with the Fiebig stage, the CD4+/CD8+ ratio, and treatment arm, despite a higher decrease in group 3. Six adverse events were recorded during our study, which did not cause any withdrawal from the study. We observed a decrease in HIV-DNA from baseline to W48 in PLWH treated during PHI, associated with an increase in CD4+ count, unrelated to the treatment arm.
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Affiliation(s)
| | - Arianna Gabrieli
- Dipartimento di Scienze Biomediche e Cliniche (DIBIC), Milan, Italy
| | - Davide Bernasconi
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4 School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases, Department of Health Sciences, ASST Santi Paolo e Carlo, University of Milan, Milan, Italy
- School of Medicine and Surgery, University of Milan, Milan, Italy
| | - Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Diego Ripamonti
- Infectious Disease Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Andrea Antinori
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Nicola Squillace
- Infectious Disease Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Antonella Cingolani
- Istituto Clinica di Malattie Infettive, Università Cattolica del Sacro Cuore, Rome, Italy
- UOC Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan
| | - Alessandra Bandera
- School of Medicine and Surgery, University of Milan, Milan, Italy
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan
| | - Andrea Gori
- School of Medicine and Surgery, University of Milan, Milan, Italy
| | - Stefano Rusconi
- School of Medicine and Surgery, University of Milan, Milan, Italy
- SC Malattie Infettive, Ospedale di Legnano, ASST Ovest Milanese, Legnano, Italy
| | - Silvia Nozza
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS Ospedale San Raffaele, Milan, Italy
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Botha JC, Demirov D, Gordijn C, Katusiime MG, Bale MJ, Wu X, Wells D, Hughes SH, Cotton MF, Mellors JW, Kearney MF, van Zyl GU. The largest HIV-1-infected T cell clones in children on long-term combination antiretroviral therapy contain solo LTRs. mBio 2023; 14:e0111623. [PMID: 37530525 PMCID: PMC10470503 DOI: 10.1128/mbio.01116-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Combination antiretroviral therapy (cART) suppresses viral replication but does not cure HIV infection because a reservoir of infectious (intact) HIV proviruses persists in long-lived CD4+T cells. However, a large majority (>95%) of HIV-infected cells that persist on effective cART carry defective (non-infectious) proviruses. Defective proviruses consisting of only a single LTR (solo long terminal repeat) are commonly found as endogenous retroviruses in many animal species, but the frequency of solo-LTR HIV proviruses has not been well defined. Here we show that, in five pediatric donors whose viremia was suppressed on cART for at least 5 years, the proviruses in the nine largest clones of HIV-infected cells were solo LTRs. The sizes of five of these clones were assayed longitudinally by integration site-specific quantitative PCR. Minor waxing and waning of the clones was observed, suggesting that these clones are generally stable over time. Our findings show that solo LTRs comprise a large fraction of the proviruses in infected cell clones that persist in children on long-term cART. IMPORTANCE This work highlights that severely deleted HIV-1 proviruses comprise a significant proportion of the proviral landscape and are often overlooked.
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Affiliation(s)
| | - Dimiter Demirov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Mary Grace Katusiime
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Michael J. Bale
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Xiaolin Wu
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Daria Wells
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | | | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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18
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Moretti S, Schietroma I, Sberna G, Maggiorella MT, Sernicola L, Farcomeni S, Giovanetti M, Ciccozzi M, Borsetti A. HIV-1-Host Interaction in Gut-Associated Lymphoid Tissue (GALT): Effects on Local Environment and Comorbidities. Int J Mol Sci 2023; 24:12193. [PMID: 37569570 PMCID: PMC10418605 DOI: 10.3390/ijms241512193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
HIV-1 replication in the gastrointestinal (GI) tract causes severe CD4+ T-cell depletion and disruption of the protective epithelial barrier in the intestinal mucosa, causing microbial translocation, the main driver of inflammation and immune activation, even in people living with HIV (PLWH) taking antiretroviral drug therapy. The higher levels of HIV DNA in the gut compared to the blood highlight the importance of the gut as a viral reservoir. CD4+ T-cell subsets in the gut differ in phenotypic characteristics and differentiation status from the ones in other tissues or in peripheral blood, and little is still known about the mechanisms by which the persistence of HIV is maintained at this anatomical site. This review aims to describe the interaction with key subsets of CD4+ T cells in the intestinal mucosa targeted by HIV-1 and the role of gut microbiome and its metabolites in HIV-associated systemic inflammation and immune activation that are crucial in the pathogenesis of HIV infection and related comorbidities.
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Affiliation(s)
- Sonia Moretti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Ivan Schietroma
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Giuseppe Sberna
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Maria Teresa Maggiorella
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Leonardo Sernicola
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
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19
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Kankaka EN, Redd AD, Khan A, Reynolds SJ, Saraf S, Kirby C, Lynch B, Hackman J, Tomusange S, Kityamuweesi T, Jamiru S, Anok A, Buule P, Bruno D, Martens C, Chang LW, Quinn TC, Prodger JL, Poon A. Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda. Virus Evol 2023; 9:vead046. [PMID: 37547379 PMCID: PMC10399970 DOI: 10.1093/ve/vead046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/15/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
The timing of the establishment of the HIV latent viral reservoir (LVR) is of particular interest, as there is evidence that proviruses are preferentially archived at the time of antiretroviral therapy (ART) initiation. Quantitative viral outgrowth assays (QVOAs) were performed using Peripheral Blood Mononuclear Cells (PBMC) collected from Ugandans living with HIV who were virally suppressed on ART for >1 year, had known seroconversion windows, and at least two archived ART-naïve plasma samples. QVOA outgrowth populations and pre-ART plasma samples were deep sequenced for the pol and gp41 genes. The bayroot program was used to estimate the date that each outgrowth virus was incorporated into the reservoir. Bayroot was also applied to previously published data from a South African cohort. In the Ugandan cohort (n = 11), 87.9 per cent pre-ART and 56.3 per cent viral outgrowth sequences were unique. Integration dates were estimated to be relatively evenly distributed throughout viremia in 9/11 participants. In contrast, sequences from the South African cohort (n = 9) were more commonly estimated to have entered the LVR close to ART initiation, as previously reported. Timing of LVR establishment is variable between populations and potentially viral subtypes, which could limit the effectiveness of interventions that target the LVR only at ART initiation.
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Affiliation(s)
- Edward Nelson Kankaka
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
| | - Andrew D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Faculty of Health Sciences, Anzio Rd, Observatory, Cape Town 7925, South Africa
| | - Amjad Khan
- Department of Pathology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, Ontario N6A 5K8, Canada
| | - Steven J Reynolds
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Sharada Saraf
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Charles Kirby
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
| | - Briana Lynch
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Jada Hackman
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Stephen Tomusange
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Taddeo Kityamuweesi
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Samiri Jamiru
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Aggrey Anok
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Paul Buule
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Daniel Bruno
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, 904 South Fourth Street, Hamilton, MT 59840, USA
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, 904 South Fourth Street, Hamilton, MT 59840, USA
| | - Larry W Chang
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, Ontario N6A 5K8, Canada
| | - Art Poon
- Department of Pathology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, Ontario N6A 5K8, Canada
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20
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Reeves DB, Gaebler C, Oliveira TY, Peluso MJ, Schiffer JT, Cohn LB, Deeks SG, Nussenzweig MC. Impact of misclassified defective proviruses on HIV reservoir measurements. Nat Commun 2023; 14:4186. [PMID: 37443365 PMCID: PMC10345136 DOI: 10.1038/s41467-023-39837-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Most proviruses persisting in people living with HIV (PWH) on antiretroviral therapy (ART) are defective. However, rarer intact proviruses almost always reinitiate viral rebound if ART stops. Therefore, assessing therapies to prevent viral rebound hinges on specifically quantifying intact proviruses. We evaluated the same samples from 10 male PWH on ART using the two-probe intact proviral DNA assay (IPDA) and near full length (nfl) Q4PCR. Both assays admitted similar ratios of intact to total HIV DNA, but IPDA found ~40-fold more intact proviruses. Neither assay suggested defective proviruses decay over 10 years. However, the mean intact half-lives were different: 108 months for IPDA and 65 months for Q4PCR. To reconcile this difference, we modeled additional longitudinal IPDA data and showed that decelerating intact decay could arise from very long-lived intact proviruses and/or misclassified defective proviruses: slowly decaying defective proviruses that are intact in IPDA probe locations (estimated up to 5%, in agreement with sequence library based predictions). The model also demonstrates how misclassification can lead to underestimated efficacy of therapies that exclusively reduce intact proviruses. We conclude that sensitive multi-probe assays combined with specific nfl-verified assays would be optimal to document absolute and changing levels of intact HIV proviruses.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Laboratory of Translational Immunology of Viral Infections, Department of Infectious Diseases, Charité -Universitätsmedizin, Berlin, Germany
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lillian B Cohn
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
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21
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Zhu T, Cao W, Li T. HIV DNA positively correlates with HLA-DR+CD8+ T lymphocytes over 8-year suppressive antiretroviral therapy. AIDS 2023; 37:1335-1337. [PMID: 37115824 PMCID: PMC10242515 DOI: 10.1097/qad.0000000000003587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
We studied the relationship between HIV DNA and CD8 + T-cell activation in a retrospective cohort. We observed that the expression level of HLA-DR remained high in CD8 + T-cells and was positively correlated with total HIV DNA [odds ratio (OR) = 1.86, P = 0.028) during 8 years of suppressive antiretroviral therapy (ART). This study illustrated the long-term interplay between HIV DNA reservoir and host inflammatory state despite viral suppression.
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Affiliation(s)
| | - Wei Cao
- Department of Infectious Diseases
| | - Taisheng Li
- Department of Infectious Diseases
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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22
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Scutari R, Galli L, Alteri C, Poli A, Piermatteo L, Bigoloni A, Perno CF, Lazzarin A, Ceccherini-Silberstein F, Castagna A, Santoro MM, Gianotti N. Evaluation of HIV-DNA and residual viremia levels through week 96 in HIV-infected individuals who continue a two-drug or switch to a three-drug integrase strand transfer inhibitor based regimen. Int J Antimicrob Agents 2023; 61:106771. [PMID: 36870403 DOI: 10.1016/j.ijantimicag.2023.106771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/09/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
OBJECTIVES To investigate HIV-DNA and residual viremia (RV) levels over 96 weeks (W96) in virologically suppressed HIV-1 infected individuals enrolled in the Be-OnE Study. Individuals were randomized to continue a two-drug regimen with dolutegravir (DTG) plus one RTI or to switch to elvitegravir/cobicistat/emtricitabine/tenofovir-alafenamide (E/C/F/TAF). STUDY DESIGN Total HIV-DNA and RV were evaluated at baseline, W48 and W96 with ddPCR technique. Potential relationships between viro-immunological parameters and between/within arms were also assessed. RESULTS Median (IQR) HIV-DNA was 2247 (767;4268), 1587 (556;3543) and 1076 (512;2345) copies/106 CD4+T-cells at baseline, W48 and at W96, respectively, while RV was 3 (1;5), 4 (1;9) and 2 (2;4) copies/mL, without significant differences between arms. A significant reduction in HIV-DNA and in RV from baseline to W96 was observed in the E/C/F/TAF-arm (HIV-DNA: -285 [-2257;-45], p=0.010; RV: (-1 [-3;0], p=0.007). In the DTG+1RTI-arm, HIV-DNA and RV levels remained stable (HIV-DNA: -549 [-2269;+307], p=0.182; RV: (-1 [-3;+1], p=0.280). For both HIV-DNA and RV, no significant changes were found overtime between the arms. A positive correlation was found between baseline HIV-DNA and HIV-DNA at W96 (E/C/F/TAF: rs=0.726, p=0.0004; DTG+1RTI: rs=0.589, p=0.010). In general, no significant correlations were found between HIV-DNA, RV and immunological parameters overtime. CONCLUSIONS In virologically suppressed individuals, a small reduction in the HIV-DNA and HIV-RNA levels was found from baseline to W96 in individuals who switched to the E/C/F/TAF arm compared to those who remained under DTG+1RTI. However, no significant differences were found in the changes of HIV-DNA and HIV-RNA between the two arms over time.
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Affiliation(s)
- Rossana Scutari
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Laura Galli
- Infectious Diseases, IRCCS San Raffaele, Milan, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Andrea Poli
- Infectious Diseases, IRCCS San Raffaele, Milan, Italy
| | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Alba Bigoloni
- Infectious Diseases, IRCCS San Raffaele, Milan, Italy
| | - Carlo Federico Perno
- Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | | | | | - Antonella Castagna
- Infectious Diseases, IRCCS San Raffaele, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
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23
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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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24
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Gunst JD, Pahus MH, Rosás-Umbert M, Lu IN, Benfield T, Nielsen H, Johansen IS, Mohey R, Østergaard L, Klastrup V, Khan M, Schleimann MH, Olesen R, Støvring H, Denton PW, Kinloch NN, Copertino DC, Ward AR, Alberto WDC, Nielsen SD, Puertas MC, Ramos V, Reeves JD, Petropoulos CJ, Martinez-Picado J, Brumme ZL, Jones RB, Fox J, Tolstrup M, Nussenzweig MC, Caskey M, Fidler S, Søgaard OS. Early intervention with 3BNC117 and romidepsin at antiretroviral treatment initiation in people with HIV-1: a phase 1b/2a, randomized trial. Nat Med 2022; 28:2424-2435. [PMID: 36253609 PMCID: PMC10189540 DOI: 10.1038/s41591-022-02023-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 01/26/2023]
Abstract
Attempts to reduce the human immunodeficiency virus type 1 (HIV-1) reservoir and induce antiretroviral therapy (ART)-free virologic control have largely been unsuccessful. In this phase 1b/2a, open-label, randomized controlled trial using a four-group factorial design, we investigated whether early intervention in newly diagnosed people with HIV-1 with a monoclonal anti-HIV-1 antibody with a CD4-binding site, 3BNC117, followed by a histone deacetylase inhibitor, romidepsin, shortly after ART initiation altered the course of HIV-1 infection ( NCT03041012 ). The trial was undertaken in five hospitals in Denmark and two hospitals in the United Kingdom. The coprimary endpoints were analysis of initial virus decay kinetics and changes in the frequency of CD4+ T cells containing intact HIV-1 provirus from baseline to day 365. Secondary endpoints included changes in the frequency of infected CD4+ T cells and virus-specific CD8+ T cell immunity from baseline to day 365, pre-ART plasma HIV-1 3BNC117 sensitivity, safety and tolerability, and time to loss of virologic control during a 12-week analytical ART interruption that started at day 400. In 55 newly diagnosed people (5 females and 50 males) with HIV-1 who received random allocation treatment, we found that early 3BNC117 treatment with or without romidepsin enhanced plasma HIV-1 RNA decay rates compared to ART only. Furthermore, 3BNC117 treatment accelerated clearance of infected cells compared to ART only. All groups had significant reductions in the frequency of CD4+ T cells containing intact HIV-1 provirus. At day 365, early 3BNC117 + romidepsin was associated with enhanced HIV-1 Gag-specific CD8+ T cell immunity compared to ART only. The observed virological and immunological effects of 3BNC117 were most pronounced in individuals whose pre-ART plasma HIV-1 envelope sequences were antibody sensitive. The results were not disaggregated by sex. Adverse events were mild to moderate and similar between the groups. During a 12-week analytical ART interruption among 20 participants, 3BNC117-treated individuals harboring sensitive viruses were significantly more likely to maintain ART-free virologic control than other participants. We conclude that 3BNC117 at ART initiation enhanced elimination of plasma viruses and infected cells, enhanced HIV-1-specific CD8+ immunity and was associated with sustained ART-free virologic control among persons with 3BNC117-sensitive virus. These findings strongly support interventions administered at the time of ART initiation as a strategy to limit long-term HIV-1 persistence.
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Affiliation(s)
- Jesper D Gunst
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Marie H Pahus
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Miriam Rosás-Umbert
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - I-Na Lu
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital-Amager and Hvidovre, Hvidovre, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Isik S Johansen
- Department of Infectious Diseases, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Rajesh Mohey
- Department of Internal Medicine, Regional Hospital Herning, Herning, Denmark
| | - Lars Østergaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Vibeke Klastrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Maryam Khan
- Department of Infectious Diseases, Imperial College Hospital, London, UK
- The National Institute for Health Research, Imperial Biomedical Research Centre, London, UK
| | - Mariane H Schleimann
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Olesen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Støvring
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Paul W Denton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Dennis C Copertino
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Adam R Ward
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Winiffer D Conce Alberto
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Silke D Nielsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Maria C Puertas
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBERINFEC, Madrid, Spain
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | | | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Julie Fox
- Department of Genitourinary Medicine and Infectious Disease, Guy's and St Thomas' National Health Service Trust, London, UK
- Department of Genitourinary Medicine and Infectious Disease, The National Institute for Health Research Biomedical Research Centre, King's College London, London, UK
| | - Martin Tolstrup
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Sarah Fidler
- Department of Infectious Diseases, Imperial College Hospital, London, UK
- The National Institute for Health Research, Imperial Biomedical Research Centre, London, UK
| | - Ole S Søgaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
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25
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Liu Z, Julius P, Kang G, West JT, Wood C. Subtype C HIV-1 reservoirs throughout the body in ART-suppressed individuals. JCI Insight 2022; 7:162604. [PMID: 36278485 PMCID: PMC9714794 DOI: 10.1172/jci.insight.162604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
Subtype B HIV-1 reservoirs have been intensively investigated, but reservoirs in other subtypes and how they respond to antiretroviral therapy (ART) is substantially less established. To characterize subtype C HIV-1 reservoirs, we implemented postmortem frozen, as well as formalin fixed paraffin embedded (FFPE) tissue sampling of central nervous system (CNS) and peripheral tissues. HIV-1 LTR, gag, envelope (env) DNA and RNA was quantified using genomic DNA and RNA extracted from frozen tissues. RNAscope was used to localize subtype C HIV-1 DNA and RNA in FFPE tissue. Despite uniform viral load suppression in our cohort, PCR results showed that subtype C HIV-1 proviral copies vary both in magnitude and tissue distribution, with detection primarily in secondary lymphoid tissues. Interestingly, the appendix harbored proviruses in all subjects. Unlike subtype B, subtype C provirus was rarely detectable in the CNS, and there was no detectable HIV-1 RNA. HIV-1 RNA was detected in peripheral lymphoid tissues of 6 out of 8 ART-suppressed cases. In addition to active HIV-1 expression in lymphoid tissues, RNAscope revealed HIV RNA detection in CD4-expressing cells in the appendix, suggesting that this tissue was a previously unreported potential treatment-resistant reservoir for subtype C HIV-1.
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Affiliation(s)
- Zhou Liu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
| | - Peter Julius
- Department of Pathology and Microbiology, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Guobin Kang
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
| | - John T. West
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
| | - Charles Wood
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, Louisiana, USA
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26
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Li J, Chen D, Wen Z, Du Y, Huang Z, Zhong H, Wang Y, Yin S. Real-world efficacy and safety of dolutegravir plus lamivudine versus tenofovir plus lamivudine and efavirenz in ART-naïve HIV-1-infected adults. Medicine (Baltimore) 2022; 101:e31100. [PMID: 36281149 PMCID: PMC9592519 DOI: 10.1097/md.0000000000031100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Limited real-world data on dolutegravir (DTG) plus lamivudine (3TC) for HIV-1-infected individuals have been reported. This study aimed to evaluated the real-world efficacy and safety of DTG + 3TC in ART-naïve HIV-1-infected adults in China. This real-world prospective observational cohort study enrolled HIV-1-infected adults receiving ART initiation with DTG + 3TC (D3 group) or tenofovir plus lamivudine and efavirenz (TDF + 3TC + EFV, TLE group) with subgroups of low viral load (LVL, ≤500,000 copies/mL) and high viral load (HVL, >500,000 copies/mL) according to baseline HIV-1 RNA. Efficacy were assessed by proportion of virologic suppression, changes of CD4+ cell count and CD4/CD8 ratio, HIV-1 DNA decay, and safety by symptoms and changes of laboratory indicators at week 4, 12, 24, 36, and 48. Totally 45 participants in D3 group and 95 in TLE group were enrolled. The proportion of HIV RNA < 50 copies/mL were 48.7% (19/39), 84.6% (33/39), 100% (39/39), 100% (39/39) in D3-LVL subgroup at week 4, 12, 24, 48, compared with 1.3% (1/75), 14.7% (11/75), 86.7% (65/75), 96.0% (72/75) in TLE-LVL subgroup, with P < .05 at week 4, 12, and 36. The proportion were 0.0% (0/6), 66.7% (4/6), 83.3% (5/6), 100% (6/6) in D3-HVL subgroup compared with 0.0% (0/20), 5.0% (1/20), 85.0% (17/20), 100% (20/20) in TLE-HVL subgroup, with P < .05 at week 12. No virologic rebound was observed in D3 group. Mean change of CD4/CD8 ratio were higher in D3-LVL versus TLE-LVL subgroup at each scheduled visit (P < .05), while CD4+ cell counts increased significantly in D3-HVL versus TLE-HVL subgroup at week 4 and 12 (P < .05). Less complaint of dizziness, insomnia, dreaminess and amnesia, lower elevated level of triglyceride and higher elevated level of creatinine from baseline to week 48 were documented in D3 group (P < .05). Total HIV-1 DNA decayed along with HIV-1 RNA after DTG + 3TC initiation in both D3-LVL and D3-HVL subgroups. DTG + 3TC achieved virological suppression more rapidly and stably versus TDF + 3TC + EFV in ART-naïve HIV-1-infected adults, with better immunological response and less adverse drug effect, and reduced total HIV-1 DNA effectively. DTG + 3TC is a potent regimen for ART-naïve individuals with HIV-1 infection.
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Affiliation(s)
- Jin Li
- Department of Infectious Diseases, The Ninth People’s Hospital of Dongguan, Dongguan, China
- *Correspondence: Jin Li, No. 88 Shaditang, Guancheng District, Dongguan, Guangdong 523000, China (e-mail: )
| | - Dabiao Chen
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiwei Wen
- Department of Infectious Diseases, The Ninth People’s Hospital of Dongguan, Dongguan, China
| | - Yanzhang Du
- Department of Infectious Diseases, The Ninth People’s Hospital of Dongguan, Dongguan, China
| | - Zhanlian Huang
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huijun Zhong
- Department of Infectious Diseases, The Ninth People’s Hospital of Dongguan, Dongguan, China
| | - Yanhao Wang
- Department of Infectious Diseases, The Ninth People’s Hospital of Dongguan, Dongguan, China
| | - Sichun Yin
- Department of Infectious Diseases, The Ninth People’s Hospital of Dongguan, Dongguan, China
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27
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Renault C, Bolloré K, Pisoni A, Motto-Ros C, Van de Perre P, Reynes J, Tuaillon E. Accuracy of real-time PCR and digital PCR for the monitoring of total HIV DNA under prolonged antiretroviral therapy. Sci Rep 2022; 12:9323. [PMID: 35665775 PMCID: PMC9167282 DOI: 10.1038/s41598-022-13581-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/21/2022] [Indexed: 12/16/2022] Open
Abstract
Total HIV DNA is a standard marker to monitor the HIV reservoir in people living with HIV. We investigated HIV DNA quantification accuracy by a real-time PCR kit (qPCR) and digital PCR (dPCR) method within the same set of primers and probes. Among 48 aviremic patients followed for up to 7 years with qPCR, the mean coefficient of variation of total HIV DNA between two successive measurements was 77% (± 0.42log10 HIVDNA copies/106 PBMC). The total HIV DNA quantified by the two PCR methods has a high correlation (0.99 and 0.83, for 8E5 and PLHIV samples, respectively), but we observed better repeatability and reproducibility of the dPCR compared to the qPCR (CV of 11.9% vs. 24.7% for qPCR, p-value = 0.024). Furthermore, we highlighted a decay of the number of HIV copies in the 8E5 cell line qPCR standard over time (from 0.73 to 0.43 copies per cell), contributing to variations of HIV DNA results in patients whose HIV reservoir should be theoretically stabilized. Our study highlighted that absolute quantification of total HIV DNA by dPCR allows more accurate monitoring of the HIV reservoir than qPCR in patients under prolonged antiretroviral therapy.
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Affiliation(s)
- Constance Renault
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France
| | - Karine Bolloré
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France
| | - Amandine Pisoni
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France.,CHU de Montpellier, Montpellier, France
| | - Camille Motto-Ros
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France.,CHU de Montpellier, Montpellier, France
| | - Jacques Reynes
- IRD UMI 233, INSERM U1175, Montpellier University, Montpellier, France.,Infectious Diseases Department, CHU de Montpellier, Montpellier, France
| | - Edouard Tuaillon
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France. .,CHU de Montpellier, Montpellier, France.
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28
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Magnasco L, Pincino R, Pasculli G, Bouba Y, Saladini F, Bavaro DF, De Vito A, Lattanzio R, Corsini R, Zazzi M, Incardona F, Rossetti B, Bezenchek A, Borghi V, Di Biagio A. Predictors of Virological Failure Among People Living with HIV Switching from an Effective First-Line Antiretroviral Regimen. AIDS Res Hum Retroviruses 2022; 38:463-471. [PMID: 34969260 DOI: 10.1089/aid.2021.0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aim of this study was to assess the predictors of virological failure (VF) among patients living with HIV (PLWHIV) switching from an effective first-line antiretroviral therapy (ART) regimen, and to evaluate the emergence of resistance-associated mutations. All adult patients enrolled in the Antiviral Response Cohort Analysis cohort who started ART after 2010, with at least 6 months of virological suppression (VS) before ART switch and with an available genotypic resistance test (GRT) at baseline were included. Thirty-two patients out of the 607 PLWHIV included (5.3%) experienced VF after a median of 11 months from ART switch. Younger age (adjusted Hazard Ratio [aHR] 0.96, 95% confidence interval [CI] 0.92-0.99, p = .023), being male who have sex with male (aHR 0.15, 95% CI 0.03-0.69, p = .014), and longer time from VS to ART switch (aHR 0.97, 95% CI 0.95-1.00, p = .021) resulted protective toward VF, while receiving a first-line regimen containing a backbone other than ABC/3TC or TXF/FTC (aHR 3.61, 95% CI 1.00-13.1, p = .050) and a boosted protease inhibitor as anchor drug (aHR 3.34, 95% CI 1.20-9.28, p = .021) were associated with higher risk of VF. GRT at the moment of VF was available only for 13 patients (40.6%). ART switch in patients with stable control of HIV infection is a safe practice, even if particular attention should be paid in certain cases of patients switching from regimens containing low-performance backbones or protease inhibitors.
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Affiliation(s)
- Laura Magnasco
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS per l'Oncologia, Genoa, Italy
| | - Rachele Pincino
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS per l'Oncologia, Genoa, Italy
- Department of Health's Sciences, University of Genoa, Genoa, Italy
| | - Giuseppe Pasculli
- Department of Computer, Control, and Management Engineering Antonio Ruberti (DIAG), La Sapienza University, Rome, Italy
| | - Yagai Bouba
- Department of Experimental Medicine, University of Rome "Tor Vergata," Rome, Italy
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Davide Fiore Bavaro
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari "Aldo Moro," Bari, Italy
| | - Andrea De Vito
- Unit of Infectious Diseases, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Rossana Lattanzio
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari "Aldo Moro," Bari, Italy
| | - Romina Corsini
- Infectious Diseases Unit, AUSL - IRCCS Reggio Emilia, Reggio Emilia, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Barbara Rossetti
- Infectious Diseases Unit, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | | | - Vanni Borghi
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy
| | - Antonio Di Biagio
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS per l'Oncologia, Genoa, Italy
- Department of Health's Sciences, University of Genoa, Genoa, Italy
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29
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Taramasso L, Bozzano F, Casabianca A, Orlandi C, Bovis F, Mora S, Giacomini M, Moretta L, Magnani M, Di Biagio A, De Maria A. Persistence of Unintegrated HIV DNA Associates With Ongoing NK Cell Activation and CD34+DNAM-1brightCXCR4+ Precursor Turnover in Vertically Infected Patients Despite Successful Antiretroviral Treatment. Front Immunol 2022; 13:847816. [PMID: 35558085 PMCID: PMC9088003 DOI: 10.3389/fimmu.2022.847816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The quantification of proviral DNA is raising interest in view of clinical management and functional HIV eradication. Measures of all unintegrated HIV DNA (uDNA) forms in infected reservoir cells provides information on recent replication events that is not found from other proviral DNA assays. To evaluate its actual relevance in a cohort of perinatally-infected adult HIV patients (PHIV), we studied how peripheral blood mononuclear cell uDNA levels correlated with total HIV DNA (tDNA) and with overall replication or innate immune control parameters including NK cell activation/exhaustion and lymphoid turnover. Twenty-two PHIV were included, with successfully controlled HIV (HIV RNA <50 copies/mL) on combined antiretroviral therapy for mean of 8.7 ± 3.9 years. uDNA accounted for 16 [5.2-83.5] copies/µg and was strongly correlated with tDNA (ρ=0.700, p=0.001). Flow cytometric analysis of peripheral NK cells showed that CD69 expression was directly correlated uDNA (p=0.0412), but not with tDNA. Interestingly, CD56-CD16+NK cells which include newly described inflammatory precursors and terminally differentiated cells were directly correlated with uDNA levels (p<0.001), but not with tDNA, and an inverse association was observed between the proportion of NKG2D+ NK cells and uDNA (ρ=-0.548, p=0.015). In addition, CD34+DNAM-1brightCXCR4+ inflammatory precursor frequency correlated directly with uDNA levels (ρ=0.579, p=0.0075). The frequencies of CD56-CD16+ and CD34+DNAM-1brightCXCR4+ cells maintained association with uDNA levels in a multivariable analysis (p=0.045 and p=0.168, respectively). Thus, control of HIV-1 reservoir in aviremic patients on ART is an active process associated with continuous NK cell intervention and turnover, even after many years of treatment. Quantification of linear and circular uDNA provides relevant information on the requirement for ongoing innate immune control in addition to ART, on recent replication history and may help stratify patients for functional HIV eradication protocols with targeted options.
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Affiliation(s)
- Lucia Taramasso
- Infectious Diseases Clinic, IRCCS Policlinico San Martino Hospital, Genoa, Italy
| | - Federica Bozzano
- Infectious Diseases Clinic, IRCCS Policlinico San Martino Hospital, Genoa, Italy
| | - Anna Casabianca
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Chiara Orlandi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Francesca Bovis
- Biostatistics Unit, Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Sara Mora
- Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Genoa, Italy
| | - Mauro Giacomini
- Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Genoa, Italy
| | - Lorenzo Moretta
- Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Antonio Di Biagio
- Infectious Diseases Clinic, IRCCS Policlinico San Martino Hospital, Genoa, Italy.,Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Andrea De Maria
- Infectious Diseases Clinic, IRCCS Policlinico San Martino Hospital, Genoa, Italy.,Department of Health Sciences, University of Genoa, Genoa, Italy
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30
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Duette G, Hiener B, Morgan H, Mazur FG, Mathivanan V, Horsburgh BA, Fisher K, Tong O, Lee E, Ahn H, Shaik A, Fromentin R, Hoh R, Bacchus-Souffan C, Nasr N, Cunningham AL, Hunt PW, Chomont N, Turville SG, Deeks SG, Kelleher AD, Schlub TE, Palmer S. The HIV-1 proviral landscape reveals that Nef contributes to HIV-1 persistence in effector memory CD4+ T cells. J Clin Invest 2022; 132:154422. [PMID: 35133986 PMCID: PMC8970682 DOI: 10.1172/jci154422] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/02/2022] [Indexed: 11/17/2022] Open
Abstract
Despite long-term antiretroviral therapy (ART), HIV-1 persists within a reservoir of CD4+ T cells that contribute to viral rebound if treatment is interrupted. Identifying the cellular populations that contribute to the HIV-1 reservoir and understanding the mechanisms of viral persistence are necessary to achieve an effective cure. In this regard, through Full-Length Individual Proviral Sequencing, we observed that the HIV-1 proviral landscape was different and changed with time on ART across naive and memory CD4+ T cell subsets isolated from 24 participants. We found that the proportion of genetically intact HIV-1 proviruses was higher and persisted over time in effector memory CD4+ T cells when compared with naive, central, and transitional memory CD4+ T cells. Interestingly, we found that escape mutations remained stable over time within effector memory T cells during therapy. Finally, we provided evidence that Nef plays a role in the persistence of genetically intact HIV-1. These findings posit effector memory T cells as a key component of the HIV-1 reservoir and suggest Nef as an attractive therapeutic target.
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Affiliation(s)
- Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Bonnie Hiener
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Hannah Morgan
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Fernando G. Mazur
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Vennila Mathivanan
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Bethany A. Horsburgh
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Katie Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Orion Tong
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Haelee Ahn
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Ansari Shaik
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Charline Bacchus-Souffan
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Stuart G. Turville
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Anthony D. Kelleher
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Timothy E. Schlub
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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31
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White JA, Simonetti FR, Beg S, McMyn NF, Dai W, Bachmann N, Lai J, Ford WC, Bunch C, Jones JL, Ribeiro RM, Perelson AS, Siliciano JD, Siliciano RF. Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proc Natl Acad Sci U S A 2022; 119:e2120326119. [PMID: 35110411 PMCID: PMC8833145 DOI: 10.1073/pnas.2120326119] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4+ T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ∼3 mo, the decay slope changes, and CD4+ T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie F McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas Bachmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - William C Ford
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christina Bunch
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joyce L Jones
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ruy M Ribeiro
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- HHMI, Baltimore, MD 21205
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32
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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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33
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Lau CY, Adan MA, Maldarelli F. Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. Viruses 2021; 13:2512. [PMID: 34960781 PMCID: PMC8708047 DOI: 10.3390/v13122512] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antiretroviral therapy (ART) effectively reduces cycles of viral replication but does not target proviral populations in cells that persist for prolonged periods and that can undergo clonal expansion. Consequently, chronic human immunodeficiency virus (HIV) infection is sustained during ART by a reservoir of long-lived latently infected cells and their progeny. This proviral landscape undergoes change over time on ART. One of the forces driving change in the landscape is the clonal expansion of infected CD4 T cells, which presents a key obstacle to HIV eradication. Potential mechanisms of clonal expansion include general immune activation, antigenic stimulation, homeostatic proliferation, and provirus-driven clonal expansion, each of which likely contributes in varying, and largely unmeasured, amounts to maintaining the reservoir. The role of clinical events, such as infections or neoplasms, in driving these mechanisms remains uncertain, but characterizing these forces may shed light on approaches to effectively eradicate HIV. A limited number of individuals have been cured of HIV infection in the setting of bone marrow transplant; information from these and other studies may identify the means to eradicate or control the virus without ART. In this review, we describe the mechanisms of HIV-1 persistence and clonal expansion, along with the attempts to modify these factors as part of reservoir reduction and cure strategies.
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Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
- Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
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34
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Anderson AM, Ma Q, Letendre SL, Iudicello J. Soluble Biomarkers of Cognition and Depression in Adults with HIV Infection in the Combination Therapy Era. Curr HIV/AIDS Rep 2021; 18:558-568. [PMID: 34780037 PMCID: PMC8860504 DOI: 10.1007/s11904-021-00581-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Cognitive impairment and depression continue to be common among people with HIV (PWH) in the combination antiretroviral therapy (ART) era. A better understanding of the biological mechanisms that may underpin these disorders is needed. The purpose of this review is to describe published findings on soluble biomarkers from blood and cerebrospinal fluid (CSF) that have been associated with either cognition or depression among PWH in the setting of ART. RECENT FINDINGS Several biomarkers, including those that reflect viral persistence, monocyte/macrophage activation, and other processes, are associated with cognition and depressive symptoms. Some but not all results have been consistent across multiple studies. More research has been published on biomarkers of cognition relative to biomarkers of depression (particularly from CSF). More studies are needed that investigate multiple biomarkers to understand the role of distinct but additive pathways in these disorders and to guide the development of new therapies.
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Affiliation(s)
- Albert M Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, 341 Ponce de Leon Avenue, Atlanta, GA, 30308, USA.
| | - Qing Ma
- University at Buffalo, Buffalo, NY, USA
| | - Scott L Letendre
- Departments of Medicine and Psychiatry, University of California at San Diego, San Diego, CA, USA
| | - Jennifer Iudicello
- Departments of Medicine and Psychiatry, University of California at San Diego, San Diego, CA, USA
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35
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Li Y, Mohammadi A, Li JZ. Challenges and Promise of Human Immunodeficiency Virus Remission. J Infect Dis 2021; 223:4-12. [PMID: 33586773 DOI: 10.1093/infdis/jiaa568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Antiretroviral therapy effectively controls human immunodeficiency virus (HIV) replication but it is unable to fully eradicate the HIV reservoir and treatment must be life-long. Progress toward a strategy for HIV remission will require overcoming key hurdles to fill gaps in our understanding of HIV persistence, but the identification of individuals who have attained sterilizing or functional HIV cure show that such a goal is achievable. In this review, we first outline challenges in targeting the HIV reservoir, including difficulties identifying HIV-infected cells, ongoing work elucidating the complex intracellular environment that contribute to HIV latency, and barriers to reactivating and clearing the HIV reservoir. We then review reported cases of HIV sterilizing cure and explore natural models of HIV remission and the promise that such HIV spontaneous and posttreatment controllers may hold in our search for a broadly-applicable strategy for the millions of patients living with HIV.
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Affiliation(s)
- Yijia Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Abbas Mohammadi
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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36
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Peng X, Xu Y, Huang Y, Zhu B. Intrapatient Development of Multi-Class Drug Resistance in an Individual Infected with HIV-1 CRF01_AE. Infect Drug Resist 2021; 14:3441-3448. [PMID: 34471364 PMCID: PMC8403562 DOI: 10.2147/idr.s323762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid expansion of access to antiretroviral therapy (ART) has led to the emergence of multi-class drug resistance (MDR) in people living with HIV (PLWH). However, the viral evolutionary dynamics of the development of MDR has not been well documented. For this study, plasma and peripheral blood mononuclear cells (PBMC) were longitudinally collected at different time points from a PLWH who suffered several periods of ART failure. Next generation sequencing (NGS) was used to analyze the distribution and percent of drug resistance mutations in PBMC and plasma. The results showed the gradual replacement of the wild type protease and integrase genotype by protease inhibitors (PI) and integrase strand transfer inhibitor (INSTI) drug resistant mutations when patient’s ART regimen was changed – driving the increase of genetic variability in HIV DNA. Sampling for this study was initiated after the patient was first diagnosed with ART failure, five years after ART treatment was first initiated. By that time, mutants resistant to the reverse transcriptase inhibitor nevirapine (NVP) had already replaced almost 100% of wild type. After the introduction of the protease inhibitor lopinavir/ritonavir (LPV/r) to the patient’s ART, resistant protease inhibitor (PI) mutants developed slowly. After one month, none were found in PMBC DNA; after sixteen months, less than 20% were mutants; and after three years (two months prior to the patient’s death) PI mutants were still under 50%. However, integrase strand transfer inhibitor (INSTI) mutations evolved much more quickly, replacing approximately 75% of the wild genotype in HIV DNA one year after addition of the integrase inhibitor raltegravir to the patient’s ART, and almost 100% after two years. In summary, our dataset provides the first analysis of the distribution and percent of drug resistance mutations in PBMC and plasma during the development of a four-class drug resistant HIV-1 CRF01_AE virion. The study also showed that months before drug resistant mutants could be found in plasma, NGS identified them in HIV DNA, demonstrating that this can be a very effective tool for early detection of the development of drug resistance.
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Affiliation(s)
- Xiaorong Peng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yufan Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Ying Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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37
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Anderson AM, Tang B, Vaida F, Mcclernon D, Deutsch R, Cherner M, Cookson D, Crescini M, Grant I, Ellis RJ, Letendre SL. Low-Level HIV RNA in Cerebrospinal Fluid and Neurocognitive Performance: A Longitudinal Cohort Study. J Acquir Immune Defic Syndr 2021; 87:1196-1204. [PMID: 33901102 PMCID: PMC8596378 DOI: 10.1097/qai.0000000000002714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/29/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cognitive complications persist in persons with HIV during suppressive antiretroviral therapy (ART). Low levels of HIV during ART could contribute to these complications. In this study, we measured cerebrospinal fluid (CSF) HIV using a single-copy assay (SCA) to investigate a possible relationship between low-level HIV and cognition. DESIGN/METHODS SCA data were analyzed from 3 consecutively paired CSF-plasma specimens collected over a mean of 456 days from 96 participants on suppressive ART. Using mixed models, the presence of CSF HIV by SCA as a risk factor for worse neurocognitive performance was examined. RESULTS At baseline on the SCA, 45.8% of participants had detectable plasma HIV RNA (median 8 copies/mL and interquartile range = 3-17 among detectable values) and 17.7% had detectable CSF HIV RNA (median CSF concentration= 3 copies/mL and interquartile range= 2-13 among detectable values). The frequency of CSF HIV RNA detection declined over time in CSF (P = 0.018) with a trend toward decline in plasma (P = 0.064). Detectable CSF HIV RNA during the study was associated with worse performance in the domains of recall (P = 0.014) and motor (P = 0.040) and a trend with worse overall global performance (P = 0.078). Integrase inhibitor use, although very infrequent in this cohort, was associated with better performance in 2 domains. CONCLUSIONS Low-level CSF HIV RNA declines with time but is associated with worse cognitive performance in 2 domains. Additional research is needed to better understand the relationship between HIV RNA persistence during long-term ART and central nervous system complications in persons with HIV.
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Affiliation(s)
- Albert M. Anderson
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine
| | - Bin Tang
- Department of Psychiatry, University of California, San Diego
| | - Florin Vaida
- Department of Psychiatry, University of California, San Diego
| | | | - Reena Deutsch
- Department of Psychiatry, University of California, San Diego
| | - Mariana Cherner
- Department of Psychiatry, University of California, San Diego
| | - Debra Cookson
- Department of Psychiatry, University of California, San Diego
| | | | - Igor Grant
- Department of Psychiatry, University of California, San Diego
| | - Ronald J. Ellis
- Department of Psychiatry, University of California, San Diego
- Department of Neurosciences, University of California, San Diego
| | - Scott L. Letendre
- Department of Psychiatry, University of California, San Diego
- Department of Medicine, University of California, San Diego
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38
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Pasternak AO, Vroom J, Kootstra NA, Wit FW, de Bruin M, De Francesco D, Bakker M, Sabin CA, Winston A, Prins JM, Reiss P, Berkhout B. Non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy is associated with lower cell-associated HIV RNA and DNA levels as compared with therapy based on protease inhibitors. eLife 2021; 10:68174. [PMID: 34387543 PMCID: PMC8460250 DOI: 10.7554/elife.68174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/07/2021] [Indexed: 11/28/2022] Open
Abstract
Background: It remains unclear whether combination antiretroviral therapy (ART) regimens differ in their ability to fully suppress human immunodeficiency virus (HIV) replication. Here, we report the results of two cross-sectional studies that compared levels of cell-associated (CA) HIV markers between individuals receiving suppressive ART containing either a non-nucleoside reverse transcriptase inhibitor (NNRTI) or a protease inhibitor (PI). Methods: CA HIV unspliced RNA and total HIV DNA were quantified in two cohorts (n = 100, n = 124) of individuals treated with triple ART regimens consisting of two nucleoside reverse transcriptase inhibitors (NRTIs) plus either an NNRTI or a PI. To compare CA HIV RNA and DNA levels between the regimens, we built multivariable models adjusting for age, gender, current and nadir CD4+ count, plasma viral load zenith, duration of virological suppression, NRTI backbone composition, low-level plasma HIV RNA detectability, and electronically measured adherence to ART. Results: In both cohorts, levels of CA HIV RNA and DNA strongly correlated (rho = 0.70 and rho = 0.54) and both markers were lower in NNRTI-treated than in PI-treated individuals. In the multivariable analysis, CA RNA in both cohorts remained significantly reduced in NNRTI-treated individuals (padj = 0.02 in both cohorts), with a similar but weaker association between the ART regimen and total HIV DNA (padj = 0.048 and padj = 0.10). No differences in CA HIV RNA or DNA levels were observed between individual NNRTIs or individual PIs, but CA HIV RNA was lower in individuals treated with either nevirapine or efavirenz, compared to PI-treated individuals. Conclusions: All current classes of antiretroviral drugs only prevent infection of new cells but do not inhibit HIV RNA transcription in long-lived reservoir cells. Therefore, these differences in CA HIV RNA and DNA levels by treatment regimen suggest that NNRTIs are more potent in suppressing HIV residual replication than PIs, which may result in a smaller viral reservoir size. Funding: This work was supported by ZonMw (09120011910035) and FP7 Health (305522).
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Affiliation(s)
- Alexander O Pasternak
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jelmer Vroom
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ferdinand Wnm Wit
- Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marijn de Bruin
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Davide De Francesco
- Institute for Global Health, University College London, London, United Kingdom
| | - Margreet Bakker
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, United Kingdom
| | - Alan Winston
- Medicine, Imperial College London, London, United Kingdom
| | - Jan M Prins
- Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, New Caledonia
| | - Peter Reiss
- Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Berkhout
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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39
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Pino M, Pereira Ribeiro S, Pagliuzza A, Ghneim K, Khan A, Ryan E, Harper JL, King CT, Welbourn S, Micci L, Aldrete S, Delman KA, Stuart T, Lowe M, Brenchley JM, Derdeyn CA, Easley K, Sekaly RP, Chomont N, Paiardini M, Marconi VC. Increased homeostatic cytokines and stability of HIV-infected memory CD4 T-cells identify individuals with suboptimal CD4 T-cell recovery on-ART. PLoS Pathog 2021; 17:e1009825. [PMID: 34449812 PMCID: PMC8397407 DOI: 10.1371/journal.ppat.1009825] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/23/2021] [Indexed: 01/12/2023] Open
Abstract
Clinical outcomes are inferior for individuals with HIV having suboptimal CD4 T-cell recovery during antiretroviral therapy (ART). We investigated if the levels of infection and the response to homeostatic cytokines of CD4 T-cell subsets contributed to divergent CD4 T-cell recovery and HIV reservoir during ART by studying virologically-suppressed immunologic responders (IR, achieving a CD4 cell count >500 cells/μL on or before two years after ART initiation), and virologically-suppressed suboptimal responders (ISR, did not achieve a CD4 cell count >500 cells/μL in the first two years after ART initiation). Compared to IR, ISR demonstrated higher levels of HIV-DNA in naïve, central (CM), transitional (TM), and effector (EM) memory CD4 T-cells in blood, both pre- and on-ART, and specifically in CM CD4 T-cells in LN on-ART. Furthermore, ISR had higher pre-ART plasma levels of IL-7 and IL-15, cytokines regulating T-cell homeostasis. Notably, pre-ART PD-1 and TIGIT expression levels were higher in blood CM and TM CD4 T-cells for ISR; this was associated with a significantly lower fold-changes in HIV-DNA levels between pre- and on-ART time points exclusively on CM and TM T-cell subsets, but not naïve or EM T-cells. Finally, the frequency of CM CD4 T-cells expressing PD-1 or TIGIT pre-ART as well as plasma levels of IL-7 and IL-15 predicted HIV-DNA content on-ART. Our results establish the association between infection, T-cell homeostasis, and expression of PD-1 and TIGIT in long-lived CD4 T-cell subsets prior to ART with CD4 T-cell recovery and HIV persistence on-ART.
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Affiliation(s)
- Maria Pino
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Susan Pereira Ribeiro
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, QC, Canada
| | - Khader Ghneim
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Anum Khan
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Emily Ryan
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Justin L. Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Colin T. King
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Sarah Welbourn
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Luca Micci
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Sol Aldrete
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Keith A. Delman
- Division of Surgical Oncology, Department of Surgery, Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Theron Stuart
- Emory Vaccine Center, Emory University, Hope Clinic, Decatur, Georgia, United States of America
| | - Michael Lowe
- Division of Surgical Oncology, Department of Surgery, Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Cynthia A. Derdeyn
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Kirk Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Rafick P. Sekaly
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, QC, Canada
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Vincent C. Marconi
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
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40
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Scutari R, Costabile V, Galli L, Bellocchi MC, Carioti L, Barbaliscia S, Poli A, Galli A, Perno CF, Santoro MM, Castagna A, Ceccherini-Silberstein F, Alteri C, Spagnuolo V. Impact of Analytical Treatment Interruption on Burden and Diversification of HIV Peripheral Reservoir: A Pilot Study. Viruses 2021; 13:v13071403. [PMID: 34372609 PMCID: PMC8310290 DOI: 10.3390/v13071403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/03/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND If analytical antiretroviral-treatment (ART) interruption (ATI) might significantly impact quantitative or qualitative peripheral-total HIV-DNA is still debated. METHODS Six chronically HIV-1 infected patients enrolled in APACHE-study were analysed for peripheral-total HIV-DNA and residual viremia, major-resistance-mutations (MRMs) and C2-V3-C3 evolution at pre-ATI (T1), during ATI (T2) and at achievement of virological success after ART-resumption (post-ATI, T3). These data were obtained at three comparable time-points in five chronically HIV-1 infected patients on suppressive ART for ≥1 year, enrolled in MODAt-study. RESULTS At T1, APACHE and MODAt individuals had similar peripheral-total HIV-DNA and residual viremia (p = 0.792 and 0.662, respectively), and no significant changes for these parameters were observed between T1 and T3 in both groups. At T1, 4/6 APACHE and 2/5 MODAt carried HIV-DNA MRMs. MRMs disappeared at T3 in 3/4 APACHE. All disappearing MRMs were characterized by T1 intra-patient prevalence <80%, and mainly occurred in APOBEC3-related sites. All MRMs persisted over-time in the 2 MODAt. C2-V3-C3 genetic-distance significantly changed from T1 to T3 in APACHE individuals (+0.36[0.11-0.41], p = 0.04), while no significant changes were found in MODAt. Accordingly, maximum likelihood trees (bootstrap > 70%) and genealogical sorting indices (GSI > 0.50 with p-value < 0.05) showed that T1 C2-V3-C3 DNA sequences were distinct from T2 and T3 viruses in 4/6 APACHE. Virus populations at all three time-points were highly interspersed in MODAt. CONCLUSIONS This pilot study indicates that short ATI does not alter peripheral-total HIV-DNA burden and residual viremia, but in some cases could cause a genetic diversification of peripheral viral reservoir in term of both MRMs rearrangement and viral evolution.
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Affiliation(s)
- Rossana Scutari
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Valentino Costabile
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy;
| | - Laura Galli
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
| | - Maria Concetta Bellocchi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Silvia Barbaliscia
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Andrea Poli
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
| | - Andrea Galli
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
| | - Carlo Federico Perno
- Unit of Diagnostic Microbiology and Immunology, Department of Laboratories, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Maria Mercedes Santoro
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Antonella Castagna
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesca Ceccherini-Silberstein
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.); (S.B.); (M.M.S.); (F.C.-S.)
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy;
- Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Correspondence: ; Tel.: +39-(0)6-6859-7096
| | - Vincenzo Spagnuolo
- Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy; (L.G.); (A.P.); (A.G.); (A.C.); (V.S.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
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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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42
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Bayón-Gil Á, Puertas MC, Urrea V, Bailón L, Morón-López S, Cobarsí P, Brander C, Mothe B, Martinez-Picado J. HIV-1 DNA decay dynamics in early treated individuals: practical considerations for clinical trial design. J Antimicrob Chemother 2021; 75:2258-2263. [PMID: 32335675 PMCID: PMC7366202 DOI: 10.1093/jac/dkaa139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 01/28/2023] Open
Abstract
Background Initiation of combination antiretroviral therapy (cART) soon after HIV-1 infection limits the establishment of viral reservoirs. Thus, early treated individuals are preferred candidates to evaluate novel viral remission strategies. However, their cART-dependent HIV-1 DNA decay dynamics are still poorly defined. This can hamper the design and interpretation of results from clinical trials intended to further reduce viral reservoirs. Objectives To clarify the duration of cART needed for the HIV-1 reservoir to be stabilized in early treated individuals. Methods We characterized the longitudinal decline of total HIV-1 DNA levels by droplet digital PCR in 21 individuals initiating cART within 6 months after estimated HIV-1 acquisition. Measurements were taken at cART initiation, after 6 months and annually until Year 4. Correlations between virological and clinical parameters were statistically analysed. Statistical modelling was performed applying a mixed-effects model. Results Total HIV-1 DNA experienced a median overall decrease of 1.43 log10 units (IQR = 1.17–1.69) throughout the 4 years of follow-up. Baseline levels for total HIV-1 DNA, viral load, absolute CD4+ T cell count and CD4+/CD8+ ratio correlate with final HIV-1 DNA measurements (R2 = 0.68, P < 0.001; R2 = 0.54, P = 0.012; R2 = −0.47, P = 0.031; and R2 = −0.59, P = 0.0046, respectively). Statistical modelling shows that after 2 years on cART the viral reservoir had reached a set point. Conclusions A waiting period of 2 years on cART should be considered when designing interventions aiming to impact latent HIV-1 reservoir levels and viral rebound kinetics after cART discontinuation, in order to facilitate interpretation of results and enhance the chance of viral control.
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Affiliation(s)
| | | | - Víctor Urrea
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | - Lucía Bailón
- Fight AIDS Foundation (FLS), Infectious Disease Service, Germans Trias i Pujol University Hospital, Badalona, Spain
| | | | - Patricia Cobarsí
- Fight AIDS Foundation (FLS), Infectious Disease Service, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.,Aelix Therapeutics, Barcelona, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Fight AIDS Foundation (FLS), Infectious Disease Service, Germans Trias i Pujol University Hospital, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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Lombardi F, Belmonti S, Borghetti A, Fabbiani M, Marchetti S, Tamburrini E, Cauda R, di Giambenedetto S. Evolution of cellular HIV DNA levels in virologically suppressed patients switching to dolutegravir/lamivudine versus maintaining a triple regimen: a prospective, longitudinal, matched, controlled study. J Antimicrob Chemother 2021; 75:1599-1603. [PMID: 32101614 DOI: 10.1093/jac/dkaa058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/22/2020] [Accepted: 01/29/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To assess the impact of switching to dolutegravir plus lamivudine maintenance therapy on the HIV cellular reservoir size. PATIENTS AND METHODS This was a prospective, longitudinal, matched, controlled study. We enrolled virologically suppressed patients on stable three-drug ART who switched at baseline (BL) to dolutegravir/lamivudine (DT group) or maintained triple therapy (TT group); subjects in the TT group were matched 1:1 with those in the DT group according to age, gender, years since HIV diagnosis, years on ART and anchor drug. Total blood-associated HIV DNA levels were assessed by droplet digital PCR at BL and after 48 weeks (T48). Results were expressed as log10 HIV DNA copies/106 leucocytes. RESULTS We enrolled 40 patients in the DT group and 40 in the TT group; the two groups were homogeneous for all main characteristics except nadir CD4 cell count. At BL, HIV DNA levels were comparable between the DT and TT groups: 2.27 (IQR 1.97-2.47) and 2.26 (IQR 2.05-2.61) log10 HIV DNA copies/106 leucocytes, respectively. Change in HIV DNA load from BL to T48 was -0.105 (IQR -0.384 to 0.121, P = 0.041) in the DT group and -0.132 (IQR -0.362 to 0.046, P = 0.005) in the TT group, with a comparable decline observed between the two groups (P = 0.821). A higher HIV DNA decline was associated with higher BL CD4/CD8 ratio. CONCLUSIONS Maintenance therapy with dolutegravir/lamivudine had the same impact as the triple regimen on HIV DNA levels after 48 weeks of treatment. These data seem to support the effectiveness of a dolutegravir/lamivudine dual regimen in controlling the magnitude of the cellular reservoir (www.clinicaltrials.gov, number NCT02836782).
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Affiliation(s)
- Francesca Lombardi
- Università Cattolica del Sacro Cuore, Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Rome, Italy
| | - Simone Belmonti
- Università Cattolica del Sacro Cuore, Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Rome, Italy
| | - Alberto Borghetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Malattie Infettive, Rome, Italy
| | - Massimiliano Fabbiani
- Infectious and Tropical Diseases Unit, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Simona Marchetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Institute of Microbiology and Virology, Rome, Italy
| | - Enrica Tamburrini
- Università Cattolica del Sacro Cuore, Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Malattie Infettive, Rome, Italy
| | - Roberto Cauda
- Università Cattolica del Sacro Cuore, Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Malattie Infettive, Rome, Italy
| | - Simona di Giambenedetto
- Università Cattolica del Sacro Cuore, Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Malattie Infettive, Rome, Italy
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Yue Y, Li Y, Cui Y, Wang N, Huang Y, Cao W, Han Y, Zhu T, Lyu W, Xie J, Song X, Li Y, Wang T, Zhu T, Li T. Therapeutic prediction of HIV-1 DNA decay: a multicenter longitudinal cohort study. BMC Infect Dis 2021; 21:592. [PMID: 34157979 PMCID: PMC8218450 DOI: 10.1186/s12879-021-06267-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Factors predicting peripheral blood total HIV-1 DNA size in chronically infected patients with successfully suppressed viremia remain unclear. Prognostic power of such factors are of clinical significance for making clinical decisions. METHODS Two sets of study populations were included: 490 China AIDS Clinical Trial (CACT) participants (Training cohort, followed up for 144 to 288 weeks) and 117 outpatients from Peking Union Medical College Hospital (PUMCH) (Validation cohort, followed up for more than 96 weeks). All patients were chronically HIV-1-infected and achieved successful HIV-1 plasma RNA suppression within week 48. Total HIV-1 DNA in blood at baseline, 12, 24, 48, 96, 144 and 288 weeks after combined antiretroviral therapy (cART) initiation were quantified. Generalized estimating equations and logistic regression methods were used to derive and validate a predictive model of total HIV-1 DNA after 96 weeks of cART. RESULTS The total HIV-1 DNA rapidly decreased from baseline [median = 3.00 log10 copies/106 peripheral blood mononuclear cells (PBMCs)] to week 24 (median = 2.55 log10 copies/106 PBMCs), and leveled off afterwards. Of the 490 patients who had successful HIV-1 plasma RNA suppression by 96 w post-cART, 92 (18.8%) had a low total HIV-1 DNA count (< 100 copies/106 PBMCs) at week 96. In the predictive model, lower baseline total HIV-1 DNA [risk ratio (RR) = 0.08, per 1 log10 copies/106 PBMCs, P < 0.001] and higher baseline CD4+ T cell count (RR = 1.72, per 100 cells/μL, P < 0.001) were significantly associated with a low total HIV-1 DNA count at week 96. In an independent cohort of 117 patients, this model achieved a sensitivity of 75.00% and specificity of 69.52%. CONCLUSIONS Baseline total HIV-1 DNA and CD4+ T cell count are two independent predictors of total HIV-1 DNA after treatment. The derived model based on these two baseline factors provides a useful prognostic tool in predicting HIV-1 DNA reservoir control during cART.
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Affiliation(s)
- Yongsong Yue
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Yijia Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Division of Infectious Diseases, Massachusetts General Hospital and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yizhi Cui
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Nidan Wang
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - Wei Cao
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Zhu
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Lyu
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Xie
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaojing Song
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yanling Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Tuofu Zhu
- Department of Laboratory Medicine, School of Medicine, University of Washington, 325 Ninth Ave, Seattle, WA, 98104-2499, USA.
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China. .,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Katusiime MG, Van Zyl GU, Cotton MF, Kearney MF. HIV-1 Persistence in Children during Suppressive ART. Viruses 2021; 13:v13061134. [PMID: 34204740 PMCID: PMC8231535 DOI: 10.3390/v13061134] [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: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
There is a growing number of perinatally HIV-1-infected children worldwide who must maintain life-long ART. In early life, HIV-1 infection is established in an immunologically inexperienced environment in which maternal ART and immune dynamics during pregnancy play a role in reservoir establishment. Children that initiated early antiretroviral therapy (ART) and maintained long-term suppression of viremia have smaller and less diverse HIV reservoirs than adults, although their proviral landscape during ART is reported to be similar to that of adults. The ability of these early infected cells to persist long-term through clonal expansion poses a major barrier to finding a cure. Furthermore, the effects of life-long HIV persistence and ART are yet to be understood, but growing evidence suggests that these individuals are at an increased risk for developing non-AIDS-related comorbidities, which underscores the need for an HIV cure.
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Affiliation(s)
- Mary Grace Katusiime
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD 21702, USA;
- Correspondence:
| | - Gert U. Van Zyl
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service Tygerberg, Cape Town 8000, South Africa;
| | - Mark F. Cotton
- Department of Pediatrics and Child Health, Tygerberg Children’s Hospital and Family Center for Research with Ubuntu, Stellenbosch University, Cape Town 7505, South Africa;
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD 21702, USA;
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Zhang LX, Song JW, Zhang C, Fan X, Huang HH, Xu RN, Liu JY, Zhang JY, Wang LF, Zhou CB, Jin L, Shi M, Wang FS, Jiao YM. Dynamics of HIV reservoir decay and naïve CD4 T-cell recovery between immune non-responders and complete responders on long-term antiretroviral treatment. Clin Immunol 2021; 229:108773. [PMID: 34102315 DOI: 10.1016/j.clim.2021.108773] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/12/2021] [Accepted: 06/03/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The dynamics of viral reservoir decay and naïve CD4 T-cell recovery between immunological non-responders (INR) and complete responders (CR) during long-term antiretroviral treatment (ART) are not fully known. METHODS Twenty-eight chronic HIV-infected individuals on 5-year ART were divided into two groups: INR (CD4 counts ≤350 cells/μL, n = 13) and CR (CD4 counts ≥500 cells/μL, n = 15). The levels of HIV DNA and cell-associated HIV RNA (CA-RNA), CD4 counts, naïve CD4 counts and their correlations were analyzed at baseline, years 1, 3 and 5 of ART between the two groups. Expression of PD-1 on CD4 T-cells was quantified by flow cytometry. Linear mixed effect models were used to estimate the change procession in repeated measurements over 5 years. Slopes of the above-mentioned indicators were estimated using participant-specific linear regressions, respectively. RESULTS INR maintained higher levels of HIV DNA and CA-RNA with higher percentages of PD-1+CD4 T-cells compared with CR during 5-year ART, concurrent with lower naïve CD4 T-cells. However, the rates of HIV DNA and CA-RNA decay in INR were not different from that in CR over time, and INR had higher rates of naïve CD4 T-cell percentage recovery. The baseline levels of HIV DNA were positively associated with the 5-year levels of HIV DNA, but negatively associated with the 5-year naïve CD4 counts. CONCLUSIONS INR maintained significantly higher viral reservoir and lower naïve CD4 T-cells compared with CR during 5-year ART, however, the rates of reservoir decay and naïve CD4 T-cell percentage growth within INR were not lower than that in CR over time.
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Affiliation(s)
- Lu-Xue Zhang
- Infectious Disease Department, Xuanwu Hospital, Capital Medical University, Beijing, China; Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jin-Wen Song
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chao Zhang
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xing Fan
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hui-Huang Huang
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ruo-Nan Xu
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jia-Ye Liu
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ji-Yuan Zhang
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Li-Feng Wang
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chun-Bao Zhou
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lei Jin
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ming Shi
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fu-Sheng Wang
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Yan-Mei Jiao
- Treatment and Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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Di Carlo D, Falasca F, Palermo E, Mezzaroma I, Fimiani C, Siccardi G, Celani L, Di Campli FM, d'Ettorre G, Antonelli G, Turriziani O. Dolutegravir-Based Regimen for Maintenance of Viral Suppression in People Living with HIV: 48-Week Results in Real-Life Setting. AIDS Res Hum Retroviruses 2021; 37:478-485. [PMID: 33487130 DOI: 10.1089/aid.2020.0196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To evaluate the efficacy, safety, and tolerability of switching to a dolutegravir (DTG)-based regimen in a cohort of virological suppressed HIV-infected patients who have previously been treated with different antiretroviral combination. The dynamics of total HIV-DNA and levels of high-sensitivity c-reactive protein, interleukin-6, soluble-CD14, and D-Dimer were also analyzed. Ninety-six individuals who switched to a DTG-containing regimen were followed up for 48 weeks. HIV RNA, CD4+ T cell count, weight, and levels of laboratory parameters were recorded at baseline, after 24 and 48 weeks of treatment for all study participants. In a subgroup of patients, HIV DNA and inflammation/coagulation marker levels were also analyzed until week 24. Ninety-three out of 96 patients maintained virological suppression, including patients who switched to dual-therapy from triple-drug combination. Eighteen out of 96 patients had residual viremia at baseline, of which 13 reached the maximal viral suppression at W48. Serum creatinine levels showed a significant increase at weeks 24 and 48. A progressive reduction of total cholesterol was observed from week 24 and up to week 48. No variation in body mass index was detected. HIV DNA, inflammation, and coagulation marker levels did not significantly change during follow-up. Switching to a DTG-based regimen may be a key option for achieving and maintaining maximal virological suppression, even in patients showing residual viremia at baseline. Furthermore, the improvement in blood lipid profile and the overall tolerability observed in this study strongly support the use of these regimens in the aging HIV population.
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Affiliation(s)
- Daniele Di Carlo
- Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
| | - Francesca Falasca
- Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
| | - Enrico Palermo
- Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Ivano Mezzaroma
- Department of Translational and Precision Medicine, University of Rome Sapienza, Rome, Italy
| | - Caterina Fimiani
- Department of Infectious Diseases, Umberto I University Hospital, Rome, Italy
| | - Guido Siccardi
- Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | - Luigi Celani
- Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | | | - Gabriella d'Ettorre
- Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
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48
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Powell L, Dhummakupt A, Siems L, Singh D, Le Duff Y, Uprety P, Jennings C, Szewczyk J, Chen Y, Nastouli E, Persaud D. Clinical validation of a quantitative HIV-1 DNA droplet digital PCR assay: Applications for detecting occult HIV-1 infection and monitoring cell-associated HIV-1 dynamics across different subtypes in HIV-1 prevention and cure trials. J Clin Virol 2021; 139:104822. [PMID: 33930698 PMCID: PMC8212401 DOI: 10.1016/j.jcv.2021.104822] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/06/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND In HIV-1-exposed infants, nucleic acid testing (NAT) is required to diagnose infection since passively transferred maternal antibodies preclude antibody testing. The sensitivity of clinical NAT assays is lowered with infant antiretroviral prophylaxis and, with empiric very early antiretroviral treatment of high-risk infants, thereby impacting early infant diagnosis. Similarly, adult HIV-1 infections acquired under pre-exposure prophylaxis may occur at low levels, with undetectable plasma viremia and indeterminate antibody tests, for which HIV-1 DNA testing maybe a useful adjunct. Cell-associated HIV-1 DNA concentrations are also used to monitor HIV-1 persistence in viral reservoirs with relevance to HIV-1 cure therapeutics, particularly in perinatal infections. OBJECTIVES We clinically validated an HIV-1 DNA quantitative assay using droplet digital PCR (ddPCR), across different HIV-1 subtypes. STUDY DESIGN The analytical sensitivity and specificity of an HIV-1 DNA ddPCR assay was determined using serial dilutions of a plasmid containing HIV-1 LTR-gag spiked into peripheral blood mononuclear cells (PBMCs), with MOLT-4 cells or PBMCs infected with different HIV-1 subtypes (A, B and C), and U1 cells spiked into PBMCs. Inter- and intra-run variability were used to determine assay precision. RESULTS The HIV-1 LTR-gag ddPCR assay was reliable and reproducible, and exhibited high analytical specificity with sensitivity to near single copy level, across multiple HIV-1 subtypes, and a limit of detection of 4.09 copies/million PBMCs. CONCLUSIONS This assay has applications for detecting occult HIV-1-infection in the setting of combination and long-acting regimens used for HIV-1 prevention, across different HIV-1 subtypes, in infants and adults, and in HIV-1 cure interventions.
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Affiliation(s)
- Laura Powell
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Adit Dhummakupt
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Lilly Siems
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Dolly Singh
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Yann Le Duff
- Center for AIDS Reagents, National Institute for Biological Standards and Controls, England, UK
| | - Priyanka Uprety
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson University Hospital, Rutgers University, New Brunswick, NJ, United States
| | - Cheryl Jennings
- Rush University Medical Center, Department of Molecular Pathogens and Immunity, Chicago, IL, United States
| | - Joseph Szewczyk
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Ya Chen
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Eleni Nastouli
- Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health and Francis Crick Institute, London, UK
| | - Deborah Persaud
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States; Departments of Molecular Microbiology and Immunology and International Health, Johns Hopkins Bloomberg School of Public Health, United States.
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49
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Horsburgh BA, Hiener B, Fisher K, Lee E, Morgan H, Eden JS, von Stockenstrom S, Odevall L, Milush JM, Hoh R, Fromentin R, Chomont N, Hecht FM, Schlub TE, Deeks SG, Palmer S. Cellular activation, differentiation and proliferation influence the dynamics of genetically-intact proviruses over time. J Infect Dis 2021; 225:1168-1178. [PMID: 34037766 PMCID: PMC8974828 DOI: 10.1093/infdis/jiab291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/24/2021] [Indexed: 11/14/2022] Open
Abstract
Human immunodeficiency virus (HIV) persists in cells despite antiretroviral therapy; however, the influence of cellular mechanisms such as activation, differentiation, and proliferation upon the distribution of proviruses over time is unclear. To address this, we used full-length sequencing to examine proviruses within memory CD4+ T-cell subsets longitudinally in 8 participants. Over time, the odds of identifying a provirus increased in effector and decreased in transitional memory cells. In all subsets, more activated (HLA-DR–expressing) cells contained a higher frequency of intact provirus, as did more differentiated cells such as transitional and effector memory subsets. The proportion of genetically identical proviruses increased over time, indicating that cellular proliferation was maintaining the persistent reservoir; however, the number of genetically identical proviral clusters in each subset was stable. As such, key biological processes of activation, differentiation, and proliferation influence the dynamics of the HIV reservoir and must be considered during the development of any immune intervention.
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Affiliation(s)
- Bethany A Horsburgh
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Bonnie Hiener
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Katie Fisher
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Hannah Morgan
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Susanne von Stockenstrom
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Lina Odevall
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Jeffrey M Milush
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9 Canada
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9 Canada
| | - Frederick M Hecht
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Timothy E Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
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50
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Henrich TJ, Schreiner C, Cameron C, Hogan LE, Richardson B, Rutishauser RL, Deitchman AN, Chu S, Rogers R, Thanh C, Gibson EA, Zarinsefat A, Bakkour S, Aweeka F, Busch MP, Liegler T, Baker C, Milush J, Deeks SG, Stock PG. Everolimus, an mTORC1/2 inhibitor, in ART-suppressed individuals who received solid organ transplantation: A prospective study. Am J Transplant 2021; 21:1765-1779. [PMID: 32780519 PMCID: PMC9177122 DOI: 10.1111/ajt.16244] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/30/2020] [Accepted: 07/19/2020] [Indexed: 01/25/2023]
Abstract
Pharmacologic inhibition of the mammalian target of rapamycin (mTOR) in the setting of renal transplantation has previously been associated with lower human immunodeficiency virus 1 (HIV-1) DNA burden, and in vitro studies suggest that mTOR inhibition may lead to HIV transcriptional silencing. Because prospective clinical trials are lacking, we conducted an open-label, single-arm study to determine the impact of the broad mTOR inhibitor, everolimus, on residual HIV burden, transcriptional gene expression profiles, and immune responses in HIV-infected adult solid organ transplant (SOT) recipients on antiretroviral therapy. Whereas everolimus therapy did not have an overall effect on cell-associated HIV-1 DNA and RNA levels in the entire cohort, participants who maintained everolimus time-averaged trough levels >5 ng/mL during the first 2 months of therapy had significantly lower RNA levels up to 6 months after the cessation of study drug. Time-averaged everolimus trough levels significantly correlated with greater inhibition of mTOR gene pathway transcriptional activity. Everolimus treatment also led to decreased PD-1 expression on certain T cell subsets. These data support the rationale for further study of the effects of mTOR inhibition on HIV transcriptional silencing in non-SOT populations, either alone or in combination with other strategies. Trial Registration: ClinicalTrials.gov NCT02429869.
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Affiliation(s)
- Timothy J. Henrich
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Corinna Schreiner
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA,Institute of Biochemistry and Molecular Biology, Ulm University, Germany
| | - Cheryl Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Louise E. Hogan
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Brian Richardson
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Rachel L. Rutishauser
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Amelia N. Deitchman
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA
| | - Simon Chu
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Rodney Rogers
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Thanh
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Erica A. Gibson
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Arya Zarinsefat
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | | | - Francesca Aweeka
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA
| | | | - Teri Liegler
- Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA
| | - Christopher Baker
- Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA
| | - Jeffrey Milush
- Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA
| | - Peter G. Stock
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
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