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McCutcheon K, Nqebelele U, Murray L, Thomas TS, Mpanya D, Tsabedze N. Cardiac and Renal Comorbidities in Aging People Living With HIV. Circ Res 2024; 134:1636-1660. [PMID: 38781295 PMCID: PMC11122746 DOI: 10.1161/circresaha.124.323948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Contemporary World Health Organization data indicates that ≈39 million people are living with the human immunodeficiency virus. Of these, 24 million have been reported to have successfully accessed combination antiretroviral therapy. In 1996, the World Health Organization endorsed the widespread use of combination antiretroviral therapy, transforming human immunodeficiency virus infection from being a life-threatening disease to a chronic illness characterized by multiple comorbidities. The increased access to combination antiretroviral therapy has translated to people living with human immunodeficiency virus (PLWH) no longer having a reduced life expectancy. Although aging as a biological process increases exposure to oxidative stress and subsequent systemic inflammation, this effect is likely enhanced in PLWH as they age. This narrative review engages the intricate interplay between human immunodeficiency virus associated chronic inflammation, combination antiretroviral therapy, and cardiac and renal comorbidities development in aging PLWH. We examine the evolving demographic profile of PLWH, emphasizing the increasing prevalence of aging individuals within this population. A central focus of the review discusses the pathophysiological mechanisms that underpin the heightened susceptibility of PLWH to renal and cardiac diseases as they age.
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Affiliation(s)
| | - Unati Nqebelele
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, Western Cape, South Africa (U.N.)
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Western Cape, South Africa (U.N.)
| | - Lyle Murray
- Division of Infectious Diseases, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand and the Charlotte Maxeke Johannesburg Academic Hospital, South Africa (L.M.)
| | - Teressa Sumy Thomas
- Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand and the Chris Hani Baragwanath Academic Hospital, Johannesburg, Gauteng, South Africa (T.S.T.)
| | - Dineo Mpanya
- Division of Cardiology, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa (D.M., N.T.)
| | - Nqoba Tsabedze
- Division of Cardiology, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa (D.M., N.T.)
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2
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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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3
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Mazzuti L, Turriziani O, Mezzaroma I. The Many Faces of Immune Activation in HIV-1 Infection: A Multifactorial Interconnection. Biomedicines 2023; 11:biomedicines11010159. [PMID: 36672667 PMCID: PMC9856151 DOI: 10.3390/biomedicines11010159] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Chronic immune activation has a significant role in HIV-1 disease pathogenesis and CD4+ T-cell depletion. The causes of chronic inflammation and immune activation are incompletely understood, but they are likely multifactorial in nature, involving both direct and indirect stimuli. Possible explanations include microbial translocation, coinfection, and continued presence of competent replicating virus. In fact, long-term viral suppression treatments are unable to normalize elevated markers of systemic immune activation. Furthermore, high levels of pro-inflammatory cytokines increase susceptibility to premature aging of the immune system. The phenomenon of "inflammaging" has begun to be evident in the last decades, as a consequence of increased life expectancy due to the introduction of cART. Quality of life and survival have improved substantially; however, PLWH are predisposed to chronic inflammatory conditions leading to age-associated diseases, such as inflammatory bowel disease, neurocognitive disorders, cardiovascular diseases, metabolic syndrome, bone abnormalities, and non-HIV-associated cancers. Several approaches have been studied in numerous uncontrolled and/or randomized clinical trials with the aim of reducing immune activation/inflammatory status in PLWH, none of which have achieved consistent results.
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Affiliation(s)
- Laura Mazzuti
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Ombretta Turriziani
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Ivano Mezzaroma
- Department of Translational and Precision Medicine, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence:
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4
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Cardozo-Ojeda EF, Perelson AS. Modeling HIV-1 Within-Host Dynamics After Passive Infusion of the Broadly Neutralizing Antibody VRC01. Front Immunol 2021; 12:710012. [PMID: 34531859 PMCID: PMC8438300 DOI: 10.3389/fimmu.2021.710012] [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: 05/14/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
VRC01 is a broadly neutralizing antibody that targets the CD4 binding site of HIV-1 gp120. Passive administration of VRC01 in humans has assessed the safety and the effect on plasma viremia of this monoclonal antibody (mAb) in a phase 1 clinical trial. After VRC01 infusion, the plasma viral load in most of the participants was reduced but had particular dynamics not observed during antiretroviral therapy. In this paper, we introduce different mathematical models to explain the observed dynamics and fit them to the plasma viral load data. Based on the fitting results we argue that a model containing reversible Ab binding to virions and clearance of virus-VRC01 complexes by a two-step process that includes (1) saturable capture followed by (2) internalization/degradation by phagocytes, best explains the data. This model predicts that VRC01 may enhance the clearance of Ab-virus complexes, explaining the initial viral decay observed immediately after antibody infusion in some participants. Because Ab-virus complexes are assumed to be unable to infect cells, i.e., contain neutralized virus, the model predicts a longer-term viral decay consistent with that observed in the VRC01 treated participants. By assuming a homogeneous viral population sensitive to VRC01, the model provides good fits to all of the participant data. However, the fits are improved by assuming that there were two populations of virus, one more susceptible to antibody-mediated neutralization than the other.
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Affiliation(s)
- E Fabian Cardozo-Ojeda
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
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Morón-López S, Navarro J, Jimenez M, Rutsaert S, Urrea V, Puertas MC, Torrella A, De Clercq L, Ribas BP, Gálvez C, Salgado M, Vandekerckhove L, Blanco J, Crespo M, Martinez-Picado J. Switching From a Protease Inhibitor-based Regimen to a Dolutegravir-based Regimen: A Randomized Clinical Trial to Determine the Effect on Peripheral Blood and Ileum Biopsies From Antiretroviral Therapy-suppressed Human Immunodeficiency Virus-infected Individuals. Clin Infect Dis 2020; 69:1320-1328. [PMID: 30590412 PMCID: PMC6763634 DOI: 10.1093/cid/ciy1095] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 12/23/2022] Open
Abstract
Background Optimization of combination antiretroviral therapy (cART) can impact the human immunodeficiency virus (HIV) reservoir. We evaluated the effect on the HIV reservoir in peripheral blood and ileum biopsies in patients switching from boosted protease inhibitor (PI/r)–based therapy to dolutegravir (DTG)–based therapy. Methods Impact of Integrase-inhibitor DOlutegravir On the viral Reservoir (INDOOR) is a phase 4 open-label clinical trial that randomly included 42 HIV type 1–infected individuals on effective cART: 20 who switched from PI/r-based to DTG-based cART (switch group), and 22 who remained in PI/r-based regimens (control group). We analyzed blood and ileum biopsies to quantify episomal, total, and integrated HIV DNA, cell-associated HIV RNA, residual plasma viremia, T-cell subsets, cell activation, and inflammation markers. Results There were no related adverse events or treatment discontinuations due to drug intolerance. The HIV reservoir was consistently larger in ileal than in peripheral CD4+ T cells in both groups (P < .01). Residual viremia in plasma decreased in the switch group (P = .03). However, we did not observe significant longitudinal changes in low-level viral replication, total and integrated HIV reservoir, HIV transcription, T-cell maturation subsets, immunoactivation markers, inflammatory soluble proteins, or cellular markers of latently infected cells. Conclusions The INDOOR study is the first evaluation of changes in HIV reservoir size in ileum biopsies and in peripheral blood in individuals switched from PI/r- to DTG-based cART. Although this switch was safe and well tolerated, it had no impact on a large array of immunological and inflammatory markers or on HIV reservoir markers in peripheral or in ileal CD4+ T cells. Clinical Trials Registration EudraCT 2014-004331-39.
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Affiliation(s)
| | - Jordi Navarro
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron.,Departament de Medicina, Universitat Autònoma de Barcelona.,Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Sofie Rutsaert
- Human Immunodeficiency Virus Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Belgium
| | | | | | - Ariadna Torrella
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron
| | - Laura De Clercq
- Human Immunodeficiency Virus Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Belgium
| | | | | | | | - Linos Vandekerckhove
- Human Immunodeficiency Virus Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Belgium
| | - Julià Blanco
- AIDS Research Institute IrsiCaixa, Badalona.,University of Vic-Central University of Catalonia
| | - Manel Crespo
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron.,Infectious Diseases Unit, Internal Medicine Department, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Sanitaria Galicia Sur
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Badalona.,University of Vic-Central University of Catalonia.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
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6
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Jagarapu A, Piovoso MJ, Zurakowski R. An Integrated Spatial Dynamics-Pharmacokinetic Model Explaining Poor Penetration of Anti-retroviral Drugs in Lymph Nodes. Front Bioeng Biotechnol 2020; 8:667. [PMID: 32676500 PMCID: PMC7333380 DOI: 10.3389/fbioe.2020.00667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Although combined anti-retroviral therapy (cART) suppresses plasma HIV viremia below the limit of detection in a majority of HIV patients, evidence is emerging that the distribution of the anti-retroviral drugs is heterogeneous in tissue. Clinical studies measuring antiretroviral drug concentrations in lymph nodes (LNs) revealed lower concentrations compared to peripheral blood levels suggesting poor drug penetration properties. Our current study is an attempt to understand this poor anti-retroviral drug penetration inside lymph node lobules through integrating known pharmacokinetic and pharmacodynamic (PK/PD) parameters of the anti-retroviral drugs into a spatial model of reaction and transport dynamics within a solid lymph node lobule. Simulated drug penetration values were compared against experimental results whenever available or matched with data that is available for other drugs in a similar class. Our integrated spatial dynamics pharmacokinetic model reproduced the experimentally observed exclusion of antivirals from lymphoid sites. The strongest predictor of drug exclusion from the lymphoid lobule, independent of drug class, was lobule size; large lobules (high inflammation) exhibited high levels of drug exclusion. PK/PD characteristics associated with poor lymphoid penetration include high cellular uptake rates and low intracellular half-lives. To determine whether this exclusion might lead to ongoing replication, target CD4+ T cell, infected CD4+ T cell, free virus, and intracellular IC50 values of anti-retroviral drugs were incorporated into the model. Notably, for median estimates of PK/PD parameters and lobule diameters consistent with low to moderate inflammation, the model predicts no ongoing viral replication, despite substantial exclusion of the drugs from the lymphoid site. Monte-Carlo studies drawn from the prior distributions of the PK/PD parameters predicts increases in site-specific HIV replication in a small fraction of the patient population for lobule diameters greater than 0.2 mm; this fraction increases as the site diameter/ inflammation level increases. The model shows that cART consisting of two nRTIs and one PI is the most likely treatment combination to support formation of a sanctuary site, a finding that is consistent with clinical observations.
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Affiliation(s)
- Aditya Jagarapu
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States
| | - Michael J Piovoso
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States
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7
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Pinzone MR, Bertuccio MP, VanBelzen DJ, Zurakowski R, O'Doherty U. Next-Generation Sequencing in a Direct Model of HIV Infection Reveals Important Parallels to and Differences from In Vivo Reservoir Dynamics. J Virol 2020; 94:e01900-19. [PMID: 32051279 PMCID: PMC7163122 DOI: 10.1128/jvi.01900-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) represents a powerful tool to unravel the genetic make-up of the HIV reservoir, but limited data exist on its use in vitro Moreover, most NGS studies do not separate integrated from unintegrated DNA, even though selection pressures on these two forms should be distinct. We reasoned we could use NGS to compare the infection of resting and activated CD4 T cells in vitro to address how the metabolic state affects reservoir formation and dynamics. To address these questions, we obtained HIV sequences 2, 4, and 8 days after NL4-3 infection of metabolically activated and quiescent CD4 T cells (cultured with 2 ng/ml interleukin-7). We compared the composition of integrated and total HIV DNA by isolating integrated HIV DNA using pulsed-field electrophoresis before performing sequencing. After a single-round infection, the majority of integrated HIV DNA was intact in both resting and activated T cells. The decay of integrated intact proviruses was rapid and similar in both quiescent and activated T cells. Defective forms accumulated relative to intact ones analogously to what is observed in vivo Massively deleted viral sequences formed more frequently in resting cells, likely due to lower deoxynucleoside triphosphate (dNTP) levels and the presence of multiple restriction factors. To our surprise, the majority of these deleted sequences did not integrate into the human genome. The use of NGS to study reservoir dynamics in vitro provides a model that recapitulates important aspects of reservoir dynamics. Moreover, separating integrated from unintegrated HIV DNA is important in some clinical settings to properly study selection pressures.IMPORTANCE The major implication of our work is that the decay of intact proviruses in vitro is extremely rapid, perhaps as a result of enhanced expression. Gaining a better understanding of why intact proviruses decay faster in vitro might help the field identify strategies to purge the reservoir in vivo When used wisely, in vitro models are a powerful tool to study the selective pressures shaping the viral landscape. Our finding that massively deleted sequences rarely succeed in integrating has several ramifications. It demonstrates that the total HIV DNA can differ substantially in character from the integrated HIV DNA under certain circumstances. The presence of unintegrated HIV DNA has the potential to obscure selection pressures and confound the interpretation of clinical studies, especially in the case of trials involving treatment interruptions.
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Affiliation(s)
- Marilia Rita Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Paola Bertuccio
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - D Jake VanBelzen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Ryan Zurakowski
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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8
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Jacobs JL, Halvas EK, Tosiano MA, Mellors JW. Persistent HIV-1 Viremia on Antiretroviral Therapy: Measurement and Mechanisms. Front Microbiol 2019; 10:2383. [PMID: 31681237 PMCID: PMC6804636 DOI: 10.3389/fmicb.2019.02383] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 10/01/2019] [Indexed: 12/28/2022] Open
Abstract
HIV-1 viremia persists at low-levels despite clinically effective antiretroviral therapy (ART). Here we review new methods to quantify and characterize persistent viremia at the single genome level, and discuss the mechanisms of persistence including clonal expansion of infected cells and tissue origins of viremia. A deeper understanding of how viremia persists on ART is critically important to the design of therapies to eliminate viremia and achieve a functional cure for HIV-1.
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Affiliation(s)
- Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Elias K Halvas
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Melissa A Tosiano
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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9
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Cannon L, Vargas-Garcia CA, Jagarapu A, Piovoso MJ, Zurakowski R. HIV 2-LTR experiment design optimization. PLoS One 2018; 13:e0206700. [PMID: 30408070 PMCID: PMC6224063 DOI: 10.1371/journal.pone.0206700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/17/2018] [Indexed: 01/20/2023] Open
Abstract
Clinical trials are necessary in order to develop treatments for diseases; however, they can often be costly, time consuming, and demanding to the patients. This paper summarizes several common methods used for optimal design that can be used to address these issues. In addition, we introduce a novel method for optimizing experiment designs applied to HIV 2-LTR clinical trials. Our method employs Bayesian techniques to optimize the experiment outcome by maximizing the Expected Kullback-Leibler Divergence (EKLD) between the a priori knowledge of system parameters before the experiment and the a posteriori knowledge of the system parameters after the experiment. We show that our method is robust and performs equally well if not better than traditional optimal experiment design techniques.
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Affiliation(s)
- LaMont Cannon
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States of America
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Cesar A. Vargas-Garcia
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States of America
- Fundación Universitaria Konrad Lorenz, Bogota, Colombia
| | - Aditya Jagarapu
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States of America
| | - Michael J. Piovoso
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States of America
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States of America
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States of America
- * E-mail:
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10
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Cardozo EF, Piovoso MJ, Zurakowski R. Increased inflammation in sanctuary sites may explain viral blips in HIV infection. IET Syst Biol 2018; 10:153-66. [PMID: 27444025 DOI: 10.1049/iet-syb.2015.0066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Combined antiretroviral therapy (cART) suppress HIV-1 viral replication, such that viral load in plasma remains below the limit of detection in standard assays. However, intermittent episodes of transient viremia (blips) occur in a set of HIV-patients. Given that follicular hyperplasia occurs during lymphoid inflammation as a normal response to infection, it is hypothesised that when the diameter of the lymph node follicle (LNF) increases and crosses a critical size, a viral blip occurs due to cryptic viremia. To study this hypothesis, a theoretical analysis of a mathematical model is performed to find the conditions for virus suppression in all compartments and different scenarios of LNF size changes are simulated. According to the analysis, blips with duration of around 30 days arise when the diameter rise rate is between 0.02 and 0.03 days(-1). Moreover, the final diameter of the site is directly related to the steady states of the virus load after the occurrence of a blip. When the value of R0 is around 2.1, to have a steady-state below the limit of detection after the viral blip, the maximum final diameters should be greater than 0.7 mm so that there is a relative loss of connection between compartments.
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Affiliation(s)
- E Fabian Cardozo
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
| | - Michael J Piovoso
- Electrical Engineering Department, Pennsylvania State University, Malvern, Pennsylvania 19355, USA
| | - Ryan Zurakowski
- Electrical and Computer Engineering Department, University of Delaware, Newark, Delaware 19716, USA
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11
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Abstract
PURPOSE OF REVIEW To provide a summary of the contributions of mathematical modeling to understanding of HIV persistence during antiretroviral therapy. RECENT FINDINGS Although HIV persistence during therapy could be caused by continual viral replication or slow-decaying latent infection, most evidence points toward the latter mechanism. The latent reservoir is maintained by a balance of cell death, proliferation, and reactivation, and new methods to estimate the relative contributions of these rates use a wide range of experimental data. This has led to new quantitative predictions about the potential benefit of therapies such as latency-reversing agents or antiproliferative drugs. SUMMARY Results of these mathematical modeling studies can be used to design and interpret future trials of new therapies targeting HIV persistence.
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Affiliation(s)
- Alison L Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, USA
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12
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Dynamics of Simian Immunodeficiency Virus Two-Long-Terminal-Repeat Circles in the Presence and Absence of CD8 + Cells. J Virol 2018; 92:JVI.02100-17. [PMID: 29643246 DOI: 10.1128/jvi.02100-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 04/08/2018] [Indexed: 12/28/2022] Open
Abstract
CD8+ cells play a key role in human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection, but their specific mechanism(s) of action in controlling the virus is unclear. Two-long-terminal-repeat (2-LTR) circles are extrachromosomal products generated upon failed integration of HIV/SIV. To understand the specific effects of CD8+ cells on infected cells, we analyzed the dynamics of 2-LTR circles in SIVmac251-infected rhesus macaques (RMs) treated with an integrase inhibitor (INT). Twenty RMs underwent CD8+ cell depletion and received raltegravir (RAL) monotherapy or a combination of both. Blood, lymph nodes (LNs), and gut biopsy specimens were routinely sampled. Plasma viral loads (pVLs) and 2-LTR circles from peripheral blood mononuclear cells (PBMCs) and LN lymphocytes were measured with quantitative reverse transcription-PCR (qRT-PCR). In the CD8 depletion group, an ∼1-log increase in pVLs and a slow increase in PBMC 2-LTRs occurred following depletion. In the INT group, a strong decline in pVLs upon treatment initiation and no change in 2-LTR levels were observed. In the INT and CD8+ cell depletion group, an increase in pVLs following CD8 depletion similar to that in the CD8 depletion group was observed, with a modest decline following INT initiation, and 2-LTR circles significantly increased in PBMCs and LNs. Analyzing the 2-LTR data across all treatment groups with a mathematical model indicates that the data best support an effect of CD8+ cells in killing cells prior to viral integration. Sensitivity analyses of these results confirm that effect but also allow for additional effects, which the data do not discriminate well. Overall, we show that INT does not significantly increase the levels of 2-LTR circles. However, CD8+ cell depletion increases the 2-LTR levels, which are enhanced in the presence of an INT.IMPORTANCE CD8+ T cells play an essential role in controlling HIV and SIV infection, but the specific mechanisms involved remain poorly understood. Due to failed viral infection, HIV and SIV can form 2-LTR extrachromosomal circles that can be quantified. We present novel data on the dynamics of these 2-LTR forms in a SIV-infected macaque model under three different treatment conditions: depletion of CD8+ cells, administration of the integrase inhibitor in a monotherapy, which favors the formation of 2-LTR circles, and a combination of the two treatments. We used a new mathematical model to help interpret the data, and the results suggest that CD8+ cells exert a killing effect on infected cells prior to virus integration. These results provide new insights into the mechanisms of action of CD8+ cells in SIV infection. Confirmation of our results would be an important step in understanding immune control of HIV.
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Martinez-Picado J, Zurakowski R, Buzón MJ, Stevenson M. Episomal HIV-1 DNA and its relationship to other markers of HIV-1 persistence. Retrovirology 2018; 15:15. [PMID: 29378611 PMCID: PMC5789633 DOI: 10.1186/s12977-018-0398-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/19/2018] [Indexed: 11/30/2022] Open
Abstract
Reverse transcription of HIV-1 results in the generation of a linear cDNA that serves as the precursor to the integrated provirus. Other classes of extrachromosomal viral cDNA molecules can be found in acutely infected cells including the 1-LTR and 2-LTR circles of viral DNA, also referred as episomal HIV-1 DNA. Circulating CD4+ T-cells of treatment-naïve individuals contain significant levels of unintegrated forms of HIV-1 DNA. However, the importance of episomal HIV-1 DNA in the study of viral persistence during antiviral therapy (ART) is debatable. 2-LTR circles are preferentially observed in the effector memory CD4+ T cell subset of long-term treated subjects. Treatment intensification of standard regimens has been used to determine if more potent ART can impact viral reservoir activity. Adding a potent antiretroviral drug to a stable triple-drug regimen has no measurable impact on plasma HIV-1 RNA levels, suggesting that ongoing cycles of HIV-1 replication are not a major mechanism driving persistent plasma viremia during triple-drug ART. However, in randomized clinical trials of HIV-1-infected adults on apparently effective ART, the addition of an integrase inhibitor (raltegravir) to stable regimens resulted in a transient increase in 2-LTR circles in some patients, suggesting a pre-intensification steady-state in which the processes of virion generation and de novo infection were occurring. Mathematical modeling of 2-LTR production during integrase inhibitor intensification suggests the coexistence, at different levels, of ongoing de novo infection and de novo replication mechanisms, specifically in inflamed lymphoid drug sanctuaries. Most reports looking into potential changes in 2-LTR circles in interventional clinical studies have simultaneously assessed other potential surrogate markers of viral persistence. Transient increases in 2-LTR circles have been correlated to decreases in CD8+ T-cell activation, transient CD45RA−CD4+ T-cell redistribution, and decreases in the hypercoagulation biomarker D-dimer in ART-intensified individuals. It is difficult, however, to establish a systematic association because the level of correlation with different types of markers differs significantly among studies. In conclusion, despite suppressive ART, a steady-state of de novo infection may persist in some infected individuals and that this may drive immune activation and inflammation changes reflecting residual viral reservoir activity during otherwise apparently suppressive ART.
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Affiliation(s)
- Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, University Hospital Germans Trias i Pujol, Ctra. de Canyet s/n, Badalona, 08916, Barcelona, Spain. .,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - María José Buzón
- Infectious Diseases Department, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Mario Stevenson
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
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Experiment Design for Early Molecular Events in HIV Infection. PROCEEDINGS OF THE ... AMERICAN CONTROL CONFERENCE. AMERICAN CONTROL CONFERENCE 2018; 2017:122-127. [PMID: 29332992 DOI: 10.23919/acc.2017.7962941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The recent introduction of integrase inhibitors to the HIV antiviral repertoire permits us to create in vitro experiments that reliably terminate HIV infection at the point of chromosomal integration. This allows us to isolate the dynamics of a single round of infection, without needing to account for the influence of multiple overlapping rounds of infection. By measuring the various nucleic acid concentrations in a population of infected target cells at multiple time points, we can infer the rates of these molecular events with great accuracy, which allows us to compare the rates between target cells with different functional phenotypes. This information will help in understanding the behavior of the various populations of reservoir cells such as active and quiescent T-cells which maintain HIV infection in treated patients. In this paper, we introduce a family of models of the early molecular events in HIV infection, with either linear dynamics or age-structured delays at each step. We introduce an experimental design metric based on the delta AIC (Akaike Information Criteria) between a model fit for simulated data from a matching model vs a mismatched model, which allows us to determine a candidate experiment design's ability to discriminate between models. Using parameters values drawn from experimentally-derived priors corrupted with appropriate measurement noise, we confirm that a proposed sampling schedule at different time points allows us to consistently discriminate between candidate models.
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Abstract
The introduction of combination antiretroviral therapy (cART) in the 1990s has dramatically changed the course of HIV infection, decreasing the risk for both AIDS- and non-AIDS-related events. Cancers, cardiovascular disease (CVD), liver and kidney disease, neurological disorders and frailty have become of great importance lately in the clinical management as they represent the principal cause of death in people living with HIV who receive cART (Kirk et al. in Clin Infect Dis 45(1):103-10, 2007; Strategies for Management of Antiretroviral Therapy Study et al. N Engl J Med 355(22):2283-2296, 2006; Ances et al. J Infect Dis 201(3):336-340, 2010; Desquilbet et al. J Gerontol A Biol Sci Med Sci 62(11):1279-1286, 2007; Lifson et al. HIV Clin Trials 9(3):177-185, 2008). Despite the undeniable achievements of cART, we are now faced with its limitations: a considerable proportion of individuals, referred as to immunological non-responders, fails to reconstitute the immune system despite optimal treatment and viral suppression (Kelley et al. Clin Infect Dis 48(6):787-794, 2009; Robbins et al. Clin Infect Dis 48(3):350-361, 2009) and remains at high risk for opportunistic infections and non-AIDS-related events (Strategies for Management of Antiretroviral Therapy Study et al. N Engl J Med 355(22):2283-2296, 2006). Moreover, the generalized state of immune activation and inflammation, linked to serious non-AIDS events, persists despite successful HIV suppression with cART. Finally, the current strategies have so far failed to eradicate the virus, and inflammation appears a driving force in viral persistence. In the light of all this, it is of fundamental importance to investigate the pathophysiological processes that link incomplete immune recovery, immune activation and HIV persistence to design targeted therapies that could impact on the three.
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Affiliation(s)
- Elena Bruzzesi
- Laboratory of Immunoregulation, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. .,Department of Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, Italy.
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Cannon L, Jagarapu A, Vargas-Garcia CA, Piovoso MJ, Zurakowski R. Implications of Measurement Assay Type in Design of HIV Experiments. PROCEEDINGS OF THE ... IEEE CONFERENCE ON DECISION & CONTROL. IEEE CONFERENCE ON DECISION & CONTROL 2017; 2017:4106-4111. [PMID: 29445252 PMCID: PMC5809129 DOI: 10.1109/cdc.2017.8264262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Time series measurements of circular viral episome (2-LTR) concentrations enable indirect quantification of persistent low-level Human Immunodeficiency Virus (HIV) replication in patients on Integrase-Inhibitor intensified Combined Antiretroviral Therapy (cART). In order to determine the magnitude of these low level infection events, blood has to be drawn from a patients at a frequency and volume that is strictly regulated by the Institutional Review Board (IRB). Once the blood is drawn, the 2-LTR concentration is determined by quantifying the amount of HIV DNA present in the sample via a PCR (Polymerase Chain Reaction) assay. Real time quantitative Polymerase Chain Reaction (qPCR) is a widely used method of performing PCR; however, a newer droplet digital Polymerase Chain Reaction (ddPCR) method has been shown to provide more accurate quantification of DNA. Using a validated model of HIV viral replication, this paper demonstrates the importance of considering DNA quantification assay type when optimizing experiment design conditions. Experiments are optimized using a Genetic Algorithm (GA) to locate a family of suboptimal sample schedules which yield the highest fitness. Fitness is defined as the expected information gained in the experiment, measured by the Kullback-Leibler Divergence (KLD) between the prior and posterior distributions of the model parameters. We compare the information content of the optimized schedules to uniform schedules as well as two clinical schedules implemented by researchers at UCSF and the University of Melbourne. This work shows that there is a significantly greater gain information in experiments using a ddPCR assay vs. a qPCR assay and that certain experiment design considerations should be taken when using either assay.
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Affiliation(s)
- LaMont Cannon
- University of Delaware Biomedical Engineering Department, Newark, DE 19716, USA
| | - Aditya Jagarapu
- University of Delaware Biomedical Engineering Department, Newark, DE 19716, USA
| | - Cesar A Vargas-Garcia
- University of Delaware Electrical and Computer Engineering Department Newark, DE 19716, USA
| | - Michael J Piovoso
- University of Delaware Electrical and Computer Engineering Department Newark, DE 19716, USA
| | - Ryan Zurakowski
- University of Delaware Biomedical Engineering Department, Newark, DE 19716, USA
- University of Delaware Electrical and Computer Engineering Department Newark, DE 19716, USA
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17
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Abstract
Purpose of review The present review will highlight some of the recent findings regarding the capacity of HIV-1 to replicate during antiretroviral therapy (ART). Recent findings Although ART is highly effective at inhibiting HIV replication, it is not curative. Several mechanisms contribute to HIV persistence during ART, including HIV latency, immune dysfunction, and perhaps persistent low-level spread of the virus to uninfected cells (replication). The success in curing HIV will depend on efficiently targeting these three aspects. The degree to which HIV replicates during ART remains controversial. Most studies have failed to find any evidence of HIV evolution in blood, even with samples collected over many years, although a recent very intensive study of three individuals suggested that the virus population does shift, at least during the first few months of therapy. Stronger but still not definitive evidence for replication comes from a series of studies in which standard regimens were intensified with an integration inhibitor, resulting in changes in episomal DNA (blood) and cell-associated RNA (tissue). Limited drug penetration within tissues and the presence of immune sanctuaries have been argued as potential mechanisms allowing HIV to spread during ART. Mathematical models suggest that HIV replication and evolution is possible even without the selection of fully drug-resistant variants. As persistent HIV replication could have clinical consequences and might limit the efficacy of curative interventions, determining if HIV replicates during ART and why, should remain a key focus of the HIV research community. Summary Residual viral replication likely persists in lymphoid tissues, at least in a subset of individuals. Abnormal levels of immune activation might contribute to sustain virus replication.
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Abstract
Viral latency is a major barrier to curing HIV infection with antiretroviral therapy, and consequently, for eliminating the disease globally. The establishment, maintenance, and potential clearance of latent infection are complex dynamic processes and can be best understood and described with the help of mathematical models. Here we review the use of viral dynamics models for HIV, with a focus on applications to the latent reservoir. Such models have been used to explain the multiphasic decay of viral load during antiretroviral therapy, the early seeding of the latent reservoir during acute infection and the limited inflow during treatment, the dynamics of viral blips, and the phenomenon of posttreatment control. In addition, mathematical models have been used to predict the efficacy of potential HIV cure strategies, such as latency-reversing agents, early treatment initiation, or gene therapies, and to provide guidance for designing trials of these novel interventions.
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Wang X, Mink G, Lin D, Song X, Rong L. Influence of raltegravir intensification on viral load and 2-LTR dynamics in HIV patients on suppressive antiretroviral therapy. J Theor Biol 2016; 416:16-27. [PMID: 28025011 DOI: 10.1016/j.jtbi.2016.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 11/21/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022]
Abstract
Antiretroviral therapy can suppress HIV-1 plasma viral load to below the detection limit but cannot eradicate the virus. Whether residual ongoing viral replication persists during suppressive therapy remains unclear. A few clinical studies showed that treatment intensification with an additional drug led to a lower viral load or an increase in 2-LTR (long terminal repeat), a marker for ongoing viral replication. However, some other studies found no change in the viral load and 2-LTR. In this paper, we developed multi-stage models to evaluate the influence of treatment intensification with the integrase inhibitor raltegravir on viral load and 2-LTR dynamics in HIV patients under suppressive therapy. We analyzed one model and obtained the local and global stability of the steady states. The model and its variation predict that raltegravir intensification induces a very minor decrease in the viral load and a minor increase in 2-LTR. We also compared modeling prediction with the 2-LTR data in a raltegravir intensification study. To achieve the 2-LTR increase observed in some patients, the level of viral replication needs to be substantially high, which is inconsistent with the sustained viral suppression in patients during treatment intensification. These modeling results, together with the theoretical estimate of the upper bound of the 2-LTR increase, suggest that treatment intensification with raltegravir has a minor effect on the plasma viremia and 2-LTR in patients under suppressive therapy. Other treatment strategies have to be developed for the cure or functional control of the infection.
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Affiliation(s)
- Xia Wang
- College of Mathematics and Information Science, Xinyang Normal University, Xinyang 464000, China
| | - Gregory Mink
- Department of Mathematics and Statistics, Oakland University, Rochester, MI 48309, United States
| | - Daniel Lin
- Department of Mathematics and Statistics, Oakland University, Rochester, MI 48309, United States
| | - Xinyu Song
- College of Mathematics and Information Science, Xinyang Normal University, Xinyang 464000, China.
| | - Libin Rong
- Department of Mathematics and Statistics, Oakland University, Rochester, MI 48309, United States.
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20
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Abraham G, Jagarapu A, Cannon L, Zurakowski R. Order preservation of expected information content using Unscented Transform approximation of multivariate prior distributions in HIV 2-LTR experiment design. PROCEEDINGS OF THE ... IEEE CONFERENCE ON DECISION & CONTROL. IEEE CONFERENCE ON DECISION & CONTROL 2016; 2016:5597-5602. [PMID: 29332990 PMCID: PMC5761742 DOI: 10.1109/cdc.2016.7799129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Numerical computation of the expected information content of a prospective experimental design is computationally expensive, requiring calculating the Kullback-Leibler divergence of the posterior distribution from the prior for simulated data from a large sample of points from the prior distribution. In this work, we investigate whether the Unscented Transform (UT) of the prior distribution can provide an adequate estimate of the expected information content in the context of experiment design for a previously validated HIV-1 2-LTR model. Three different schedules with evenly distributed time points have been used to generate the experimental data along with the incorporation of qPCR noise for the study. The UT shows promise in estimating information content by preserving the optimal ordering of 2-LTR sample collection schedules, when compared to completely stochastic sampling from the underlying multivariate distributions.
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Affiliation(s)
- George Abraham
- Swarthmore College Engineering Department. Swarthmore, PA 19081, USA.
| | - Aditya Jagarapu
- University of Delaware Biomedical Engineering Department. Newark, DE 19716, USA.
| | - Lamont Cannon
- University of Delaware Biomedical Engineering Department. Newark, DE 19716, USA.
| | - Ryan Zurakowski
- University of Delaware Biomedical Engineering Department. Newark, DE 19716, USA.
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21
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Cannon L, Garcia CAV, Piovoso MJ, Zurakowski R. Prospective HIV Clinical Trial Comparison by Expected Kullback-Leibler Divergence. PROCEEDINGS OF THE ... AMERICAN CONTROL CONFERENCE. AMERICAN CONTROL CONFERENCE 2016; 2016:1295-1300. [PMID: 29332991 DOI: 10.1109/acc.2016.7525096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The sample frequency and volume of blood that can be drawn from a single patient is meticulously restricted under the human subject protection protocols established by an institutional review board (IRB). Consequently, the amount of samples that can be taken during a particular experiment is limited. In order to ensure an effective experiment design, considerations must be taken choosing when to take patient samples. A validated model of HIV-1 viral replication and 2-LTR production is exploited to find sub-optimal sampling schedules that maximize information content of the experiment outcome. This is done through a Forward Stepwise Regression (FSR) process with Kullback Liebler Divergence (KLD) as a selection criterion. Suboptimal schedules are found for an experiment taking four sample points over a possible span of 20 weeks. All schedules found with the FSR process contain significantly more information than both a uniform schedule and a schedule used in a previous experiment with 4 sample points. This work demonstrates the advantages of using KLD as a tool in the experiment design process to increase information content.
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Affiliation(s)
- LaMont Cannon
- University of Delaware Biomedical Engineering Department, Newark, DE 19716, USA
| | | | - Michael J Piovoso
- University of Delaware Electrical and Computer Engineering Department Newark, DE 19716, USA
| | - Ryan Zurakowski
- University of Delaware Biomedical Engineering Department, Newark, DE 19716, USA.,University of Delaware Electrical and Computer Engineering Department Newark, DE 19716, USA
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22
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Hill AL, Rosenbloom DIS, Goldstein E, Hanhauser E, Kuritzkes DR, Siliciano RF, Henrich TJ. Real-Time Predictions of Reservoir Size and Rebound Time during Antiretroviral Therapy Interruption Trials for HIV. PLoS Pathog 2016; 12:e1005535. [PMID: 27119536 PMCID: PMC4847932 DOI: 10.1371/journal.ppat.1005535] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 03/08/2016] [Indexed: 01/17/2023] Open
Abstract
Monitoring the efficacy of novel reservoir-reducing treatments for HIV is challenging. The limited ability to sample and quantify latent infection means that supervised antiretroviral therapy (ART) interruption studies are generally required. Here we introduce a set of mathematical and statistical modeling tools to aid in the design and interpretation of ART-interruption trials. We show how the likely size of the remaining reservoir can be updated in real-time as patients continue off treatment, by combining the output of laboratory assays with insights from models of reservoir dynamics and rebound. We design an optimal schedule for viral load sampling during interruption, whereby the frequency of follow-up can be decreased as patients continue off ART without rebound. While this scheme can minimize costs when the chance of rebound between visits is low, we find that the reservoir will be almost completely reseeded before rebound is detected unless sampling occurs at least every two weeks and the most sensitive viral load assays are used. We use simulated data to predict the clinical trial size needed to estimate treatment effects in the face of highly variable patient outcomes and imperfect reservoir assays. Our findings suggest that large numbers of patients-between 40 and 150-will be necessary to reliably estimate the reservoir-reducing potential of a new therapy and to compare this across interventions. As an example, we apply these methods to the two "Boston patients", recipients of allogeneic hematopoietic stem cell transplants who experienced large reductions in latent infection and underwent ART-interruption. We argue that the timing of viral rebound was not particularly surprising given the information available before treatment cessation. Additionally, we show how other clinical data can be used to estimate the relative contribution that remaining HIV+ cells in the recipient versus newly infected cells from the donor made to the residual reservoir that eventually caused rebound. Together, these tools will aid HIV researchers in the evaluating new potentially-curative strategies that target the latent reservoir.
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Affiliation(s)
- Alison L. Hill
- Program for Evolutionary Dynamics, Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Daniel I. S. Rosenbloom
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Edward Goldstein
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Emily Hanhauser
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine and Howard Hughes Medical Institute, Baltimore, Maryland, United States of America
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
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23
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Conway JM, Perelson AS. Residual Viremia in Treated HIV+ Individuals. PLoS Comput Biol 2016; 12:e1004677. [PMID: 26735135 PMCID: PMC4703306 DOI: 10.1371/journal.pcbi.1004677] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022] Open
Abstract
Antiretroviral therapy (ART) effectively controls HIV infection, suppressing HIV viral loads. However, some residual virus remains, below the level of detection, in HIV-infected patients on ART. The source of this viremia is an area of debate: does it derive primarily from activation of infected cells in the latent reservoir, or from ongoing viral replication? Observations seem to be contradictory: there is evidence of short term evolution, implying that there must be ongoing viral replication, and viral strains should thus evolve. However, phylogenetic analyses, and rare emergent drug resistance, suggest no long-term viral evolution, implying that virus derived from activated latent cells must dominate. We use simple deterministic and stochastic models to gain insight into residual viremia dynamics in HIV-infected patients. Our modeling relies on two underlying assumptions for patients on suppressive ART: that latent cell activation drives viral dynamics and that the reproductive ratio of treated infection is less than 1. Nonetheless, the contribution of viral replication to residual viremia in patients on ART may be non-negligible. However, even if the portion of viremia attributable to viral replication is significant, our model predicts (1) that latent reservoir re-seeding remains negligible, and (2) some short-term viral evolution is permitted, but long-term evolution can still be limited: stochastic analysis of our model shows that de novo emergence of drug resistance is rare. Thus, our simple models reconcile the seemingly contradictory observations on residual viremia and, with relatively few parameters, recapitulates HIV viral dynamics observed in patients on suppressive therapy. In HIV+ individuals, antiretroviral therapy (ART) effectively controls HIV viral loads to below levels detectable by routine tests. However, more sensitive tests can detect some residual viremia. The source of this virus is a matter of debate: does it derive from ongoing viral replication, or from viral production following activation of latently infected cells? Experimental observations support both sides of the argument: in patients on therapy, HIV shows no long-term evolution, and emergence of drug-resistant mutants is rare, implying no ongoing viral replication, but there remains short-term evolution, implying the opposite. To reconcile these observations, we propose a mathematical model of latently and productively infected cells and virus. Using our models we predict that, in patients on suppressive ART, the contribution of viral replication to residual virus, while small, yields short term-evolution. But even if the contribution is large, for example if adherence to therapy is poor, long-term evolution can still be limited, and de novo emergence of drug resistance is rare. Thus, our simple models reconcile the seemingly contradictory observations on residual viremia.
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Affiliation(s)
- Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics (CIDD), The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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Lau JW, Levy DN, Wodarz D. Contribution of HIV-1 genomes that do not integrate to the basic reproductive ratio of the virus. J Theor Biol 2014; 367:222-229. [PMID: 25496730 DOI: 10.1016/j.jtbi.2014.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/11/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
Recent experimental data indicate that HIV-1 DNA that fails to integrate (from now on called uDNA) can by itself successfully produce infectious offspring virions in resting T cells that become activated after infection. This scenario is likely important at the initial stages of the infection. We use mathematical models to calculate the relative contribution of unintegrated and integrated viral DNA to the basic reproductive ratio of the virus, R0, and the models are parameterized with preliminary data. This is done in the context of both free virus spread and transmission of the virus through virological synapses. For free virus transmission, we find that under preliminary parameter estimates, uDNA might contribute about 20% to the total R0. This requires that a single copy of uDNA can successfully replicate. If the presence of more than one uDNA copy is required for replication, uDNA does not contribute to R0. For synaptic transmission, uDNA can contribute to R0 regardless of the number of uDNA copies required for replication. The larger the number of viruses that are successfully transmitted per synapse, however, the lower the contribution of uDNA to R0 because this increases the chances that at least one virus integrates. Using available parameter values, uDNA can maximally contribute 20% to R0 in this case. We argue that the contribution of uDNA to virus reproduction might also be important for continued low level replication of HIV-1 in the presence of integrase inhibitor therapy. Assuming a 20% contribution of uDNA to the overall R0, our calculations suggest that R0=1.6 in the absence of virus integration. While these are rough estimates based on preliminary data that are currently available, this analysis provides a framework for future experimental work which should directly measure key parameters.
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Affiliation(s)
- John Wei Lau
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697, USA.
| | - David N Levy
- Department of Basic Science, New York University College of Dentistry, 921 Schwartz Building, 345 East 24th Street, New York, NY 10010-9403, USA
| | - Dominik Wodarz
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697, USA.
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25
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Lafeuillade A, Assi A, Poggi C, Bresson-Cuquemelle C, Jullian E, Tamalet C. Failure of combined antiretroviral therapy intensification with maraviroc and raltegravir in chronically HIV-1 infected patients to reduce the viral reservoir: the IntensHIV randomized trial. AIDS Res Ther 2014; 11:33. [PMID: 25320633 PMCID: PMC4197239 DOI: 10.1186/1742-6405-11-33] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/27/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Ongoing HIV-1 replication in lymphoid cells is one explanation of the persistence of HIV-1 reservoirs despite highly active antiretroviral therapy (cART). We tested the potential of cART intensification by Maraviroc plus Raltegravir to decrease proviral HIV-1 DNA levels in lymphoid cells during a randomized trial. PATIENTS AND METHODS We randomly assigned for 48 weeks 22 patients to continue their current first line regimen of Truvada® plus Kaletra® or intensify it with Maraviroc and Raltegravir. The primary objective was to obtain a 50% decrease in proviral HIV-1 DNA levels in lymphoid cells with intensification. Blood samples were drawn at W-2, W0, W2, W4, W12, W24 and W48. Plasma viremia, cellular proviral DNA and cellular RNA, 2-LTR circles and lymphocytes subsets were assayed using validated methods. Patients in the intensified group underwent a gut biopsy at baseline and W48 to measure proviral DNA levels. Statistical analysis used parametric and non-parametric tests. RESULTS Ten patients in each arm completed the trial. The 2 populations were comparable at baseline. No change in the reservoir size was observed in the intensified arm compared to the control arm measured in peripheral blood mononuclear cells (PBMCs). No change in the reservoir size was observed in gut proviral DNA in the intensified arm. In this group, no increase in 2-LTR circles was observed as early as 2 weeks after intensification and no change was found in residual plasma RNA levels measured by the single copy assay. However, a decrease in CD8(+) T cells activation was observed at 24 and 48 weeks, as well as in PBMCs HIV-1 RNA levels. CONCLUSION We conclude that the intensification of a Protease Inhibitor regimen with Maraviroc and Raltegravir does not impact the blood proviral DNA reservoir of HIV but can decrease the cell-associated HIV RNA, the CD8 activation and has a possible impact on rectal proviral HIV DNA in some patients. TRIAL REGISTRATION ClinicalTrials.gov identifier number NCT00935480.
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Predicting the outcomes of treatment to eradicate the latent reservoir for HIV-1. Proc Natl Acad Sci U S A 2014; 111:13475-80. [PMID: 25097264 DOI: 10.1073/pnas.1406663111] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Massive research efforts are now underway to develop a cure for HIV infection, allowing patients to discontinue lifelong combination antiretroviral therapy (ART). New latency-reversing agents (LRAs) may be able to purge the persistent reservoir of latent virus in resting memory CD4(+) T cells, but the degree of reservoir reduction needed for cure remains unknown. Here we use a stochastic model of infection dynamics to estimate the efficacy of LRA needed to prevent viral rebound after ART interruption. We incorporate clinical data to estimate population-level parameter distributions and outcomes. Our findings suggest that ∼2,000-fold reductions are required to permit a majority of patients to interrupt ART for 1 y without rebound and that rebound may occur suddenly after multiple years. Greater than 10,000-fold reductions may be required to prevent rebound altogether. Our results predict large variation in rebound times following LRA therapy, which will complicate clinical management. This model provides benchmarks for moving LRAs from the laboratory to the clinic and can aid in the design and interpretation of clinical trials. These results also apply to other interventions to reduce the latent reservoir and can explain the observed return of viremia after months of apparent cure in recent bone marrow transplant recipients and an immediately-treated neonate.
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Abstract
BACKGROUND Latent HIV-1-infected cells generated early in the infection are responsible for viral persistence, and we hypothesized that addition of maraviroc to triple therapy in patients recently infected with HIV-1 could accelerate decay of the viral reservoir. METHODS Patients recently infected (<24 weeks) by chemokine receptor 5 (CCR5)-using HIV-1 were randomized to a raltegravir + tenofovir/emtricitabine regimen (control arm, n = 15) or the same regimen intensified with maraviroc (+MVC arm, n = 15). Plasma viral load, cell-associated HIV-1 DNA (total, integrated, and episomal), and activation/inflammation markers were measured longitudinally. RESULTS Plasma viral load decayed in both groups, reaching similar residual levels at week 48. Total cell-associated HIV-1 DNA also decreased in both groups during the first month, although subsequently at a slightly faster rate in the +MVC arm. The transient increase in two long terminal repeat (2-LTR) circles observed in both groups early after initiation of treatment decreased earlier in MVC-treated individuals. Early (week 12) increase of CD4 T-cell counts was higher in the +MVC arm. Conversely, CD8 T-cell counts and CD4 T-cell activation decreased slower in the +MVC arm. Absolute CD4 T-cell and CD8 T-cell counts, immune activation, CD4/CD8 T-cell ratio, and soluble inflammation markers were similar in both arms at the end of the study. CONCLUSION Addition of maraviroc in early integrase inhibitor-based treatment of HIV-1 infection results in faster reduction of 2-LTR newly infected cells and recovery of CD4 T-cell counts, and a modest reduction in total reservoir size after 48 weeks of treatment. Paradoxically, CCR5 blockade also induced a slower decrease in plasma viremia and immune activation.
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Spatial modeling of HIV cryptic viremia and 2-LTR formation during raltegravir intensification. J Theor Biol 2013; 345:61-9. [PMID: 24378646 DOI: 10.1016/j.jtbi.2013.12.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/31/2013] [Accepted: 12/16/2013] [Indexed: 11/21/2022]
Abstract
Combination Antiretroviral Therapy (cART) can suppress plasma HIV below the limit of detection in normal assays. Recently reported results suggest that viral replication may continue in some patients, despite undetectable levels in the blood. It has been suggested that the appearance of the circularized episomal HIV DNA artifact 2-LTR following treatment intensification with the integrase inhibitor raltegravir is a marker of ongoing viral replication. Other work has suggested that lymphoid organs may be a site of reduced antiviral penetration and increased viral production. In this study we model the hypothesis that this ongoing replication occurs in lymphoid follicle sanctuary sites and investigate the patterns of 2-LTR formation expected after raltegravir application. Experimental data is used to estimate the reaction and diffusion parameters in the model, and Monte-Carlo simulations are used to explore model behavior subject to variation in these rates. The results suggest that conditions for the formation of an observed transient peak in 2-LTR formation following raltegravir intensification include a sanctuary site diameter larger than 0.2mm, a viral basic reproductive ratio within the site larger than 1, and a total volume of active sanctuary sites above 20mL. Significant levels of uncontrolled replication can occur in the sanctuary sites without measurable changes in the plasma viral load. By contrast, subcritical replication (where the basic reproductive ratio of the virus is less than 1 in all sites) always results in monotonic increases of measured 2-LTR following raltegravir intensification, occurring at levels below the limit of detection.
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