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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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Long-term antiretroviral therapy initiated in acute HIV infection prevents residual dysfunction of HIV-specific CD8+ T cells. EBioMedicine 2022; 84:104253. [PMID: 36088683 PMCID: PMC9471490 DOI: 10.1016/j.ebiom.2022.104253] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Background Harnessing CD8+ T cell responses is being explored to achieve HIV remission. Although HIV-specific CD8+ T cells become dysfunctional without treatment, antiretroviral therapy (ART) partially restores their function. However, the extent of this recovery under long-term ART is less understood. Methods We analyzed the differentiation status and function of HIV-specific CD8+ T cells after long-term ART initiated in acute or chronic HIV infection ex vivo and upon in vitro recall. Findings ART initiation in any stage of acute HIV infection promoted the persistence of long-lived HIV-specific CD8+ T cells with high expansion (P<0·0008) and cytotoxic capacity (P=0·02) after in vitro recall, albeit at low cell number (P=0·003). This superior expansion capacity correlated with stemness (r=0·90, P=0·006), measured by TCF-1 expression, similar to functional HIV-specific CD8+ T cells found in spontaneous controllers. Importanly, TCF-1 expression in these cells was associated with longer time to viral rebound ranging from 13 to 48 days after ART interruption (r =0·71, P=0·03). In contrast, ART initiation in chronic HIV infection led to more differentiated HIV-specific CD8+ T cells lacking stemness properties and exhibiting residual dysfunction upon recall, with reduced proliferation and cytolytic activity. Interpretation ART initiation in acute HIV infection preserves functional HIV-specific CD8+ T cells, albeit at numbers too low to control viral rebound post-ART. HIV remission strategies may need to boost HIV-specific CD8+ T cell numbers and induce stem cell-like properties to reverse the residual dysfunction persisting on ART in people treated after acute infection prior to ART release. Funding U.S. National Institutes of Health and U.S. Department of Defense.
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Adams P, Berkhout B, Pasternak AO. Towards a molecular profile of antiretroviral therapy-free HIV remission. Curr Opin HIV AIDS 2022; 17:301-307. [PMID: 35938464 DOI: 10.1097/coh.0000000000000749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW To summarize the current status and highlight recent findings on predictive biomarkers for posttreatment HIV control (PTC) and virological remission. While historically, many studies focused on virological markers, there is an increasing tendency to enter immune and metabolic factors into the equation. RECENT FINDINGS On the virological side, several groups reported that cell-associated HIV RNA could predict time to viral rebound. Recent data hints at the possible importance of the genic location and chromatin context of the integrated provirus, although these factors still need to be assessed in relation to PTC and virological remission. Evidence from immunological studies highlighted innate and humoral immunity as important factors for prolonged HIV remission. Interestingly, novel metabolic markers have emerged, which offer additional angles to our understanding of latency and viral rebound. SUMMARY Facilitating PTC and virological remission remain top priorities for the HIV cure research. We advocate for clear and precise definitions for both phenomena in order to avoid misconceptions and to strengthen the conclusions that can be drawn. As no one-size-fits-all marker has emerged yet, more biomarkers are on the horizon, and viral rebound is a complex and heterogeneous process, it is likely that a combination of various biomarkers in cohesion will be necessary for a more accurate prediction of antiretroviral therapy-free HIV remission.
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Affiliation(s)
- Philipp Adams
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Peters RJ, Stevenson M. Irreversible Loss of HIV-1 Proviral Competence in Myeloid Cells upon Suppression of NF-κB Activity. J Virol 2022; 96:e0048422. [PMID: 35604217 PMCID: PMC9215224 DOI: 10.1128/jvi.00484-22] [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: 03/23/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Although antiretroviral therapy (ART) sustains potent suppression of plasma viremia in people with HIV-1 infection (PWH), reservoirs of viral persistence rekindle viral replication and viremia if ART is halted. Understanding the nature of viral reservoirs and their persistence mechanisms remains fundamental to further research aiming to eliminate them and achieve ART-free viral remission or virological cure. CD4+ T-cell models have helped to define the mechanisms that regulate HIV-1 latency as well as to identify potential latency manipulators, and we similarly hoped to extend this understanding to macrophages given the increasing evidence of a role for myeloid cells in HIV-1 persistence under ART (T. Igarashi, C. R. Brown, Y. Endo, A. Buckler-White, et al., Proc Natl Acad Sci U S A 98:658-663, 2001, https://doi.org/10.1073/pnas.98.2.658; J. M. Orenstein, C. Fox, and S. M. Wahl, Science 276:1857-1861, 1997, https://doi.org/10.1126/science.276.5320.1857). In the pursuit of a primary cell model of macrophage latency using monocyte-derived macrophages (MDMs), we observed that NF-κB inhibition, originally intended to promote synchronous entry into a latent state, led to an irreversible loss of proviral competence. Proviruses were refractory to latency reversal agents (LRAs), yet host cell functions such as phagocytic capacity and cytokine production remained intact. Even after NF-κB inhibition was relieved and NF-κB action was restored, proviruses remained refractory to reactivation. Agents that interfere with the NF-κB-HIV-1 axis in myeloid cells may provide an approach with which to render myeloid cell reservoirs inert. IMPORTANCE Although HIV-1 infection can be suppressed using antiretroviral therapy, it cannot yet be cured. This is because HIV-1 integrates itself into host cells and may become dormant but also remains ready to emerge from such reservoirs when antiretroviral therapy stops. The CD4+ T cell has been the most actively investigated cell type in reservoir research due to its prominent role in hosting HIV-1; however, HIV-1 can infect and fall latent in myeloid cells, and therefore, their role must also be assessed in pursuit of a cure. Here, we show that caffeic acid and resveratrol, two nontoxic chemicals, both of which interfere with the same set of host mechanisms, can each prevent HIV-1 reactivation from latency in myeloid cells even after either chemical is removed and previous cell functionality is restored. Strategies to interfere with latency underlie the future of HIV-1 cure research, and our findings help to focus such strategies on an important but often neglected cell type.
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Affiliation(s)
- Rebecca J. Peters
- Department of Microbiology and Immunology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
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Mori L, Valente ST. Cure and Long-Term Remission Strategies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2407:391-428. [PMID: 34985678 DOI: 10.1007/978-1-0716-1871-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.
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Affiliation(s)
- Luisa Mori
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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Ivison GT, Vendrame E, Martínez-Colón GJ, Ranganath T, Vergara R, Zhao NQ, Martin MP, Bendall SC, Carrington M, Cyktor JC, McMahon DK, Eron J, Jones RB, Mellors JW, Bosch RJ, Gandhi RT, Holmes S, Blish CA. Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients. Front Cell Infect Microbiol 2022; 12:757846. [PMID: 35223535 PMCID: PMC8866573 DOI: 10.3389/fcimb.2022.757846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The latent HIV-1 reservoir represents a major barrier to achieving a long-term antiretroviral therapy (ART)-free remission or cure for HIV-1. Natural Killer (NK) cells are innate immune cells that play a critical role in controlling viral infections and have been shown to be involved in preventing HIV-1 infection and, in those who are infected, delaying time to progression to AIDS. However, their role in limiting HIV-1 persistence on long term ART is still uncharacterized. To identify associations between markers of HIV-1 persistence and the NK cell receptor-ligand repertoire, we used twin mass cytometry panels to characterize the peripheral blood NK receptor-ligand repertoire in individuals with long-term antiretroviral suppression enrolled in the AIDS Clinical Trial Group A5321 study. At the time of testing, participants had been on ART for a median of 7 years, with virological suppression <50 copies/mL since at most 48 weeks on ART. We found that the NK cell receptor and ligand repertoires did not change across three longitudinal samples over one year-a median of 25 weeks and 50 weeks after the initial sampling. To determine the features of the receptor-ligand repertoire that associate with markers of HIV-1 persistence, we performed a LASSO normalized regression. This analysis revealed that the NK cell ligands CD58, HLA-B, and CRACC, as well as the killer cell immunoglobulin-like receptors (KIRs) KIR2DL1, KIR2DL3, and KIR2DS4 were robustly predictive of markers of HIV-1 persistence, as measured by total HIV-1 cell-associated DNA, HIV-1 cell-associated RNA, and single copy HIV-RNA assays. To characterize the roles of cell populations defined by multiple markers, we augmented the LASSO analysis with FlowSOM clustering. This analysis found that a less mature NK cell phenotype (CD16+CD56dimCD57-LILRB1-NKG2C-) was associated with lower HIV-1 cell associated DNA. Finally, we found that surface expression of HLA-Bw6 measured by CyTOF was associated with lower HIV-1 persistence. Genetic analysis revealed that this was driven by lower HIV-1 persistence in HLA-Bw4/6 heterozygotes. These findings suggest that there may be a role for NK cells in controlling HIV-1 persistence in individuals on long-term ART, which must be corroborated by future studies.
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Affiliation(s)
- Geoffrey T Ivison
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Elena Vendrame
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Giovanny J Martínez-Colón
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Thanmayi Ranganath
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Rosemary Vergara
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Nancy Q Zhao
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Maureen P Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.,Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Boston, MA, United States
| | - Joshua C Cyktor
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Deborah K McMahon
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
| | - Joseph Eron
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Center for AIDS Research, Harvard University, Boston, MA, United States
| | - Susan Holmes
- Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, CA, United States
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
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Siliciano JD, Siliciano RF. In Vivo Dynamics of the Latent Reservoir for HIV-1: New Insights and Implications for Cure. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:271-294. [PMID: 34736342 DOI: 10.1146/annurev-pathol-050520-112001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although antiretroviral therapy (ART) can reduce viremia to below the limit of detection and allow persons living with HIV-1 (PLWH) to lead relatively normal lives, viremia rebounds when treatment is interrupted. Rebound reflects viral persistence in a stable latent reservoir in resting CD4+ T cells. This reservoir is now recognized as the major barrier to cure and is the focus of intense international research efforts. Strategies to cure HIV-1 infection include interventions to eliminate this reservoir, to prevent viral rebound from the reservoir, or to enhance immune responses such that viral replication is effectively controlled. Here we consider recent developments in understanding the composition of the reservoir and how it can be measured in clinical studies. We also discuss exciting new insights into the in vivo dynamics of the reservoir and the reasons for its remarkable stability. Finally we discuss recent discoveries on the complex processes that govern viral rebound. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; .,Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA
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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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Non-invasive plasma glycomic and metabolic biomarkers of post-treatment control of HIV. Nat Commun 2021; 12:3922. [PMID: 34188039 PMCID: PMC8241829 DOI: 10.1038/s41467-021-24077-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Non-invasive biomarkers that predict HIV remission after antiretroviral therapy (ART) interruption are urgently needed. Such biomarkers can improve the safety of analytic treatment interruption (ATI) and provide mechanistic insights into the host pathways involved in post-ART HIV control. Here we report plasma glycomic and metabolic signatures of time-to-viral-rebound and probability-of-viral-remission using samples from two independent cohorts. These samples include a large number of post-treatment controllers, a rare population demonstrating sustained virologic suppression after ART-cessation. These signatures remain significant after adjusting for key demographic and clinical confounders. We also report mechanistic links between some of these biomarkers and HIV latency reactivation and/or myeloid inflammation in vitro. Finally, machine learning algorithms, based on selected sets of these biomarkers, predict time-to-viral-rebound with 74% capacity and probability-of-viral-remission with 97.5% capacity. In summary, we report non-invasive plasma biomarkers, with potential functional significance, that predict both the duration and probability of HIV remission after treatment interruption.
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10
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Pasternak AO, Psomas CK, Berkhout B. Predicting Post-treatment HIV Remission: Does Size of the Viral Reservoir Matter? Front Microbiol 2021; 12:648434. [PMID: 33717047 PMCID: PMC7952863 DOI: 10.3389/fmicb.2021.648434] [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: 12/31/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
Combination antiretroviral therapy (ART) suppresses human immunodeficiency virus (HIV) replication and improves immune function. However, due to the persistence of long-lived HIV reservoirs, therapy interruption almost inevitably leads to a fast viral rebound. A small percentage of individuals who are able to control HIV replication for extended periods after therapy interruption are of particular interest because they may represent a model of long-term HIV remission without ART. These individuals are characterized by a limited viral reservoir and low reservoir measures can predict post-treatment HIV remission. However, most individuals with a low reservoir still experience fast viral rebound. In this Perspective, we discuss the possible reasons behind this and propose to develop an integral profile, composed of viral and host biomarkers, that could allow the accurate prediction of post-treatment HIV remission. We also propose to incorporate information on the chromatin context of the proviral integration sites into the characterization of the HIV reservoir, as this likely influences the reactivation capacity of latent proviruses and, together with the actual number of intact proviruses, contributes to the replication competence of the reservoir.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Christina K Psomas
- Department of Infectious Diseases and Internal Medicine, European Hospital, Marseille, France
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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11
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Moranguinho I, Valente ST. Block-And-Lock: New Horizons for a Cure for HIV-1. Viruses 2020; 12:v12121443. [PMID: 33334019 PMCID: PMC7765451 DOI: 10.3390/v12121443] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
HIV-1/AIDS remains a global public health problem. The world health organization (WHO) reported at the end of 2019 that 38 million people were living with HIV-1 worldwide, of which only 67% were accessing antiretroviral therapy (ART). Despite great success in the clinical management of HIV-1 infection, ART does not eliminate the virus from the host genome. Instead, HIV-1 remains latent as a viral reservoir in any tissue containing resting memory CD4+ T cells. The elimination of these residual proviruses that can reseed full-blown infection upon treatment interruption remains the major barrier towards curing HIV-1. Novel approaches have recently been developed to excise or disrupt the virus from the host cells (e.g., gene editing with the CRISPR-Cas system) to permanently shut off transcription of the virus (block-and-lock and RNA interference strategies), or to reactivate the virus from cell reservoirs so that it can be eliminated by the immune system or cytopathic effects (shock-and-kill strategy). Here, we will review each of these approaches, with the major focus placed on the block-and-lock strategy.
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12
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Saha A, Dixit NM. Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection. PLoS Comput Biol 2020; 16:e1008434. [PMID: 33253162 PMCID: PMC7728175 DOI: 10.1371/journal.pcbi.1008434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 12/10/2020] [Accepted: 10/11/2020] [Indexed: 01/26/2023] Open
Abstract
Passive immunization with broadly neutralizing antibodies (bNAbs) of HIV-1 appears a promising strategy for eliciting long-term HIV-1 remission. When administered concomitantly with the cessation of antiretroviral therapy (ART) to patients with established viremic control, bNAb therapy is expected to prolong remission. Surprisingly, in clinical trials on chronic HIV-1 patients, the bNAb VRC01 failed to prolong remission substantially. Identifying the cause of this failure is important for improving VRC01-based therapies and unraveling potential vulnerabilities of other bNAbs. In the trials, viremia resurged rapidly in most patients despite suppressive VRC01 concentrations in circulation, suggesting that VRC01 resistance was the likely cause of failure. ART swiftly halts viral replication, precluding the development of resistance during ART. If resistance were to emerge post ART, virological breakthrough would have taken longer than without VRC01 therapy. We hypothesized therefore that VRC01-resistant strains must have been formed before ART initiation, survived ART in latently infected cells, and been activated during VRC01 therapy, causing treatment failure. Current assays preclude testing this hypothesis experimentally. We developed a mathematical model based on the hypothesis and challenged it with available clinical data. The model integrated within-host HIV-1 evolution, stochastic latency reactivation, and viral dynamics with multiple-dose VRC01 pharmacokinetics. The model predicted that single but not higher VRC01-resistant mutants would pre-exist in the latent reservoir. We constructed a virtual patient population that parsimoniously recapitulated inter-patient variations. Model predictions with this population quantitatively captured data of VRC01 failure from clinical trials, presenting strong evidence supporting the hypothesis. We attributed VRC01 failure to single-mutant VRC01-resistant proviruses in the latent reservoir triggering viral recrudescence, particularly when VRC01 was at trough levels. Pre-existing resistant proviruses in the latent reservoir may similarly compromise other bNAbs. Our study provides a framework for designing bNAb-based therapeutic protocols that would avert such failure and maximize HIV-1 remission. Antiretroviral therapy (ART) can control but not eradicate HIV-1. Stopping ART leads to rapid viral resurgence and progressive disease. ART is therefore administered lifelong. Tremendous efforts are ongoing to devise strategies that will enable stopping ART and yet prevent viral resurgence. One such strategy involves the administration of broadly neutralizing antibodies (bNAbs) of HIV-1 at the time of stopping ART. This strategy is expected to delay if not prevent viral resurgence. Surprisingly, treatment with VRC01, a potent bNAb, resulted in hardly any improvement in viral remission. In this study, we elucidate the cause of this failure. We hypothesized that VRC01-resistant strains may pre-exist in latently infected cells, which are unaffected by ART. They can thus outlast ART and get reactivated, triggering VRC01 failure. We built a detailed mathematical model based on this hypothesis and showed that it quantitatively captured observations of VRC01 failure in clinical trials on chronic HIV-1 patients. Our study thus identifies a potential vulnerability of bNAbs, namely, bNAb-resistant strains pre-existing in latently infected cells. Our model offers a framework for predicting bNAb-based treatment protocols that would preclude failure due to pre-existing resistance and maximally prolong remission.
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Affiliation(s)
- Ananya Saha
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
- * E-mail:
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13
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Desikan R, Raja R, Dixit NM. Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection. PLoS Comput Biol 2020; 16:e1008064. [PMID: 32817614 PMCID: PMC7462315 DOI: 10.1371/journal.pcbi.1008064] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/01/2020] [Accepted: 06/17/2020] [Indexed: 01/01/2023] Open
Abstract
Antiretroviral therapy (ART) for HIV-1 infection is life-long. Stopping therapy typically leads to the reignition of infection and progressive disease. In a major breakthrough, recent studies have shown that early initiation of ART can lead to sustained post-treatment control of viremia, raising hopes of long-term HIV-1 remission. ART, however, elicits post-treatment control in a small fraction of individuals treated. Strikingly, passive immunization with broadly neutralizing antibodies (bNAbs) of HIV-1 early in infection was found recently to elicit long-term control in a majority of SHIV-infected macaques, suggesting that HIV-1 remission may be more widely achievable. The mechanisms underlying the control elicited by bNAb therapy, however, remain unclear. Untreated infection typically leads to progressive disease. We hypothesized that viremic control represents an alternative but rarely realized outcome of the infection and that early bNAb therapy triggers a dynamical switch to this outcome. To test this hypothesis, we constructed a model of viral dynamics with bNAb therapy and applied it to analyse clinical data. The model fit quantitatively the complex longitudinal viral load data from macaques that achieved lasting control. The model predicted, consistently with our hypothesis, that the underlying system exhibited bistability, indicating two potential outcomes of infection. The first had high viremia, weak cytotoxic effector responses, and high effector exhaustion, marking progressive disease. The second had low viremia, strong effector responses, and low effector exhaustion, indicating lasting viremic control. Further, model predictions suggest that early bNAb therapy elicited lasting control via pleiotropic effects. bNAb therapy lowers viremia, which would also limit immune exhaustion. Simultaneously, it can improve effector stimulation via cross-presentation. Consequently, viremia may resurge post-therapy, but would encounter a primed effector population and eventually get controlled. ART suppresses viremia but does not enhance effector stimulation, explaining its limited ability to elicit post-treatment control relative to bNAb therapy. In a remarkable advance in HIV cure research, a recent study showed that 3 weekly doses of HIV-1 broadly neutralizing antibodies (bNAbs) soon after infection kept viral levels controlled for years in most macaques treated. If translated to humans, this bNAb therapy may elicit a functional cure, or long-term remission, of HIV-1 infection, eliminating the need for life-long antiretroviral therapy (ART). How early bNAb therapy works remains unknown. Here, we elucidate the mechanism using mathematical modeling and analysis of in vivo data. We predict that early bNAb therapy suppresses viremia, which reduces exhaustion of cytotoxic effector cells, and enhances antigen uptake and effector stimulation. Collectively, these effects drive infection to lasting control. Model predictions based on these effects fit in vivo data quantitatively. ART controls viremia but does not improve effector stimulation, explaining its weaker ability to induce lasting control post-treatment. Our findings may help improve strategies for achieving functional cure of HIV-1 infection.
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Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
- * E-mail: (RD); (NMD)
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
- * E-mail: (RD); (NMD)
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14
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Abstract
DESIGN This was an exploratory, single-arm clinical trial that tested the immune enhancement effects of 24-weeks of Toll-like receptor 9 (TLR9) agonist (MGN1703; Lefitolimod; 60 mg × 2 weekly) therapy. METHODS We enrolled HIV-1-infected individuals on suppressive combination antiretroviral therapy. Safety was assessed throughout the study. The primary outcome was reduction in total CD4 T-cell viral DNA levels. Secondary outcomes included safety, detailed immunological and virological analyses, and time to viral rebound (viral load > 5000 copies/ml) after randomization into an analytical treatment interruption (ATI). RESULTS A total of 12 individuals completed the treatment phase and nine completed the ATI. Adverse events were limited and consistent with previous reports for MGN1703. Although the dosing regimen led to potent T-cell activation and increased HIV-1-specific T-cell responses, there were no cohort-wide changes in persistent virus (total CD4 T cells viral DNA; P = 0.34). No difference in time to rebound was observed between the ATI arms (log rank P = 0.25). One of nine ATI participants, despite harboring a large replication-competent reservoir, controlled viremia for 150 days via both HIV-1-specific cellular and antibody-mediated immune responses. CONCLUSION A period of 24 weeks of MGN1703 treatment was safe and improved innate as well as HIV-1-specific adaptive immunity in HIV-1+ individuals. These findings support the incorporation of TLR9 agonism into combination HIV-1 cure strategies. TRIAL NAME AND REGISTRATION TLR9 Enhancement of antiviral immunity in chronic HIV-1 infection: a phase 1B/2A trial; ClinicalTrials.gov NCT02443935.
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15
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Caskey M, Klein F, Nussenzweig MC. Broadly neutralizing anti-HIV-1 monoclonal antibodies in the clinic. Nat Med 2019; 25:547-553. [PMID: 30936546 PMCID: PMC7322694 DOI: 10.1038/s41591-019-0412-8] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/05/2019] [Indexed: 12/12/2022]
Abstract
Combination anti-retroviral therapy (ART) has revolutionized the treatment and prevention of HIV-1 infection. Taken daily, ART prevents and suppresses the infection. However, ART interruption almost invariably leads to rebound viremia in infected individuals due to a long-lived latent reservoir of integrated proviruses. Therefore, ART must be administered on a life-long basis. Here we review recent preclinical and clinical studies suggesting that immunotherapy may be an alternative or an adjuvant to ART because, in addition to preventing new infections, anti-HIV-1 antibodies clear the virus, directly kill infected cells and produce immune complexes that can enhance host immunity to the virus.
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Affiliation(s)
- Marina Caskey
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY, USA.
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine, Cologne, Germany.
- German Center for Infection Research, partner site Bonn-Cologne, Cologne, Germany.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA.
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16
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Baral S, Raja R, Sen P, Dixit NM. Towards multiscale modeling of the CD8 + T cell response to viral infections. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1446. [PMID: 30811096 PMCID: PMC6614031 DOI: 10.1002/wsbm.1446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/22/2022]
Abstract
The CD8+ T cell response is critical to the control of viral infections. Yet, defining the CD8+ T cell response to viral infections quantitatively has been a challenge. Following antigen recognition, which triggers an intracellular signaling cascade, CD8+ T cells can differentiate into effector cells, which proliferate rapidly and destroy infected cells. When the infection is cleared, they leave behind memory cells for quick recall following a second challenge. If the infection persists, the cells may become exhausted, retaining minimal control of the infection while preventing severe immunopathology. These activation, proliferation and differentiation processes as well as the mounting of the effector response are intrinsically multiscale and collective phenomena. Remarkable experimental advances in the recent years, especially at the single cell level, have enabled a quantitative characterization of several underlying processes. Simultaneously, sophisticated mathematical models have begun to be constructed that describe these multiscale phenomena, bringing us closer to a comprehensive description of the CD8+ T cell response to viral infections. Here, we review the advances made and summarize the challenges and opportunities ahead. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Cell Fates Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models.
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Affiliation(s)
- Subhasish Baral
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Pramita Sen
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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17
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Abuharfeil NM, Yaseen MM, Alsheyab FM. Harnessing Antibody-Dependent Cellular Cytotoxicity To Control HIV-1 Infection. ACS Infect Dis 2019; 5:158-176. [PMID: 30525453 DOI: 10.1021/acsinfecdis.8b00167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Passive administration of broadly neutralizing anti-human immunodeficiency virus type 1 (HIV-1) antibodies (bNAbs) has been recently suggested as a promising alternative therapeutic approach for HIV-1 infection. Although the success behind the studies that used this approach has been attributed to the potency and neutralization breadth of anti-HIV-1 antibodies, several lines of evidence support the idea that specific antibody-dependent effector functions, particularly antibody-dependent cellular cytotoxicity (ADCC), play a critical role in controlling HIV-1 infection. In this review, we showed that there is a direct association between the activation of ADCC and better clinical outcomes. This, in turn, suggests that ADCC could be harnessed to control HIV-1 infection. To this end, we addressed the passive administration of bNAbs capable of selectively activating ADCC responses to HIV-1 patients. Finally, we summarized the potential barriers that may impede the optimal activation of ADCC during HIV-1 infection and provided strategic solutions to overcome these barriers.
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Affiliation(s)
- Nizar Mohammad Abuharfeil
- Department of Applied Biological Sciences, College of Science and Arts, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Mahmoud Mohammad Yaseen
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid 22110. Jordan
| | - Fawzi M. Alsheyab
- Department of Applied Biological Sciences, College of Science and Arts, Jordan University of Science and Technology, Irbid 22110, Jordan
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18
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Veenhuis RT, Kwaa AK, Garliss CC, Latanich R, Salgado M, Pohlmeyer CW, Nobles CL, Gregg J, Scully EP, Bailey JR, Bushman FD, Blankson JN. Long-term remission despite clonal expansion of replication-competent HIV-1 isolates. JCI Insight 2018; 3:122795. [PMID: 30232278 DOI: 10.1172/jci.insight.122795] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022] Open
Abstract
Clonal expansion of T cells harboring replication-competent virus has recently been demonstrated in patients on suppressive antiretroviral therapy (ART) regimens. However, there has not been direct evidence of this phenomenon in settings of natural control, including in posttreatment controllers who maintain control of viral replication after treatment when ART is discontinued. We present a case of an individual who has had undetectable viral loads for more than 15 years following the cessation of ART. Using near-full-genome sequence analysis, we demonstrate that 9 of 12 replication-competent isolates cultured from this subject were identical and that this identity was maintained 6 months later. A similar pattern of replication-competent virus clonality was seen in a treatment-naive HLA-B*57 elite controller. In both cases, we show that CD8+ T cells are capable of suppressing the replication of the clonally expanded viruses in vitro. Our data suggest that, while clonal expansion of replication-competent virus can present a barrier to viral eradication, these viral isolates remain susceptible to HIV-specific immune responses and can be controlled in patients with long-term suppression of viral replication.
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Affiliation(s)
- Rebecca T Veenhuis
- Department of Medicine and.,Department of Molecular and Comparative Pathobiology, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | - Christopher L Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John Gregg
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | | | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Joel N Blankson
- Department of Medicine and.,Department of Molecular and Comparative Pathobiology, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Sharaf R, Lee GQ, Sun X, Etemad B, Aboukhater LM, Hu Z, Brumme ZL, Aga E, Bosch RJ, Wen Y, Namazi G, Gao C, Acosta EP, Gandhi RT, Jacobson JM, Skiest D, Margolis DM, Mitsuyasu R, Volberding P, Connick E, Kuritzkes DR, Lederman MM, Yu XG, Lichterfeld M, Li JZ. HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers. J Clin Invest 2018; 128:4074-4085. [PMID: 30024859 PMCID: PMC6118642 DOI: 10.1172/jci120549] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/03/2018] [Indexed: 02/03/2023] Open
Abstract
HIV posttreatment controllers (PTCs) represent a natural model of sustained HIV remission, but they are rare and little is known about their viral reservoir. We obtained 1,450 proviral sequences after near-full-length amplification for 10 PTCs and 16 posttreatment noncontrollers (NCs). Before treatment interruption, the median intact and total reservoir size in PTCs was 7-fold lower than in NCs, but the proportion of intact, defective, and total clonally expanded proviral genomes was not significantly different between the 2 groups. Quantification of total but not intact proviral genome copies predicted sustained HIV remission as 81% of NCs, but none of the PTCs had a total proviral genome greater than 4 copies per million peripheral blood mononuclear cells (PBMCs). The results highlight the restricted intact and defective HIV reservoir in PTCs and suggest that total proviral genome burden could act as the first biomarker for identifying PTCs. Total and defective but not intact proviral copy numbers correlated with levels of cell-associated HIV RNA, activated NK cell percentages, and both HIV-specific CD4+ and CD8+ responses. These results support the concept that defective HIV genomes can lead to viral antigen production and interact with both the innate and adaptive immune systems.
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Affiliation(s)
- Radwa Sharaf
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
| | - Guinevere Q. Lee
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Behzad Etemad
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Layla M. Aboukhater
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zixin Hu
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zabrina L. Brumme
- Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Evgenia Aga
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ronald J. Bosch
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ying Wen
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Golnaz Namazi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | | | - Rajesh T. Gandhi
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Daniel Skiest
- University of Massachusetts Medical School-Baystate, Springfield, Massachusetts, USA
| | | | | | - Paul Volberding
- Gladstone Center for AIDS Research, UCSF, San Francisco, California, USA
| | | | - Daniel R. Kuritzkes
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Xu G. Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mathias Lichterfeld
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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20
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Abstract
Impressive advances have been made in the treatment and management of HIV-1 infected individuals. Combination antiretroviral therapy (cART) has turned HIV-1 infection from an almost invariable deadly infectious disease, to a lifelong manageable infectious disease. However, a cure or vaccine has not been forthcoming. A major problem in HIV-1 infection is the persistent and latently infected cellular and tissue reservoirs. One of these reservoirs is the Gut Associated Lymphoid tissue (GALT), which has been the research focus of our group. Our group and others have shown that HIV-1 evolves differently in different parts of the gastro intestinal tract, which also appears to affect the development of antiretroviral drug resistance. The GALT is not the only reservoir. HIV-1 continues to persist and evolve in various other cell and tissue reservoirs despite intense and apparent successful antiretroviral therapy. Moreover, drug resistance mutations remain prevalent under therapy and successful viral suppression. In addition to finding a vaccine, the research on combating and eradicating the HIV-1 viral reservoirs has also been an important focus of HIV-1 cure strategies. We will discuss some of the research findings on reservoirs in the context of some of the HIV-1 cure approaches.
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Affiliation(s)
- Guido van Marle
- a Department of Microbiology Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Deirdre L Church
- b Department of Medicine, Cumming School of Medicine , University of Calgary , Calgary , Canada.,c Department of Pathology and Laboratory Medicine, Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Frank van der Meer
- d Faculty of Veterinary Medicine, Department of Ecosystem and Public Health , University of Calgary , Calgary , Canada
| | - M John Gill
- a Department of Microbiology Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada.,b Department of Medicine, Cumming School of Medicine , University of Calgary , Calgary , Canada
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21
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Latent HIV dynamics and implications for sustained viral suppression in the absence of antiretroviral therapy. J Virus Erad 2018. [DOI: 10.1016/s2055-6640(20)30250-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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22
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Abstract
OBJECTIVE Control HIV replication requires continuous combined antiretroviral therapy (cART) as discontinuation of cART results in a rapid viral rebound. However, a few individuals exist who took cART for several years and did not show the expected viral rebound after treatment cessation. Most post-treatment controllers (PTCs) are early treated individuals. We report three cases who started cART during chronic infection. DESIGN Patients were treated and monitored according to Italian guidelines. For the description of cases, the percentage of CD8CD38HLA*DR cells, CD8CD38HLA*DR cells, major histocompatibility complex genotyping, total HIV-DNA and plasma levels of anti-retroviral (ARV) drugs were performed. RESULTS Patients started therapy during chronic infection. Patient 26636 started her first ARV drug two years after diagnosis and patients 93016 and 50293 started cART with high viral loads and low CD4 cell counts. Time without cART was 13, 11 and 1.5 years, respectively. None presented any of the protective class I HLA alleles and patient 93016 has the HLA-B*35 allele that appears to be enriched in PTCs. Patients 93016 and 50293 had very low levels of CD8CD38HLA*DR cells (<5%) much lower than those of patient 26636 (27%). T-cell-associated HIV-DNA was 3.78, 3.48 and 3.13 log copies/10 CD4, respectively. CONCLUSION Patients like ours may advance our understanding of the characteristics for which individuals may be more likely to achieve ART-free remissions. Furthermore, our patients are among the few so far described who started cART during chronic infection extending the hope that a functional cure is possible even in this setting.
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Insights into the Impact of CD8 + Immune Modulation on Human Immunodeficiency Virus Evolutionary Dynamics in Distinct Anatomical Compartments by Using Simian Immunodeficiency Virus-Infected Macaque Models of AIDS Progression. J Virol 2017; 91:JVI.01162-17. [PMID: 28931681 DOI: 10.1128/jvi.01162-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/24/2017] [Indexed: 12/16/2022] Open
Abstract
A thorough understanding of the role of human immunodeficiency virus (HIV) intrahost evolution in AIDS pathogenesis has been limited by the need for longitudinally sampled viral sequences from the vast target space within the host, which are often difficult to obtain from human subjects. CD8+ lymphocyte-depleted macaques infected with simian immunodeficiency virus (SIV) provide an increasingly utilized model of pathogenesis due to clinical manifestations similar to those for HIV-1 infection and AIDS progression, as well as a characteristic rapid disease onset. Comparison of this model with SIV-infected non-CD8+ lymphocyte-depleted macaques also provides a unique opportunity to investigate the role of CD8+ cells in viral evolution and population dynamics throughout the duration of infection. Using several different phylogenetic methods, we analyzed viral gp120 sequences obtained from extensive longitudinal sampling of multiple tissues and enriched leukocyte populations from SIVmac251-infected macaques with or without CD8+ lymphocyte depletion. SIV evolutionary and selection patterns in non-CD8+ lymphocyte-depleted animals were characterized by sequential population turnover and continual viral adaptation, a scenario readily comparable to intrahost evolutionary patterns during human HIV infection in the absence of antiretroviral therapy. Alternatively, animals that were depleted of CD8+ lymphocytes exhibited greater variation in population dynamics among tissues and cell populations over the course of infection. Our findings highlight the major role for CD8+ lymphocytes in prolonging disease progression through continual control of SIV subpopulations from various anatomical compartments and the potential for greater independent viral evolutionary behavior among these compartments in response to immune modulation.IMPORTANCE Although developments in combined antiretroviral therapy (cART) strategies have successfully prolonged the time to AIDS onset in HIV-1-infected individuals, a functional cure has yet to be found. Improvement of drug interventions for a virus that is able to infect a wide range of tissues and cell types requires a thorough understanding of viral adaptation and infection dynamics within this target milieu. Although it is difficult to accomplish in the human host, longitudinal sampling of multiple anatomical locations is readily accessible in the SIV-infected macaque models of neuro-AIDS. The significance of our research is in identifying the impact of immune modulation, through differing immune selective pressures, on viral evolutionary behavior in a multitude of anatomical compartments. The results provide evidence encouraging the development of a more sophisticated model that considers a network of individual viral subpopulations within the host, with differing infection and transmission dynamics, which is necessary for more effective treatment strategies.
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25
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Schwartz C, Bouchat S, Marban C, Gautier V, Van Lint C, Rohr O, Le Douce V. On the way to find a cure: Purging latent HIV-1 reservoirs. Biochem Pharmacol 2017; 146:10-22. [PMID: 28687465 DOI: 10.1016/j.bcp.2017.07.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/03/2017] [Indexed: 12/29/2022]
Abstract
Introduction of cART in 1996 has drastically increased the life expectancy of people living with HIV-1. However, this treatment has not allowed cure as cessation of cART is associated with a rapid viral rebound. The main barrier to the eradication of the virus is related to the persistence of latent HIV reservoirs. Evidence is now accumulating that purging the HIV-1 reservoir might lead to a cure or a remission. The most studied strategy is the so called "shock and kill" therapy. This strategy is based on reactivation of dormant viruses from the latently-infected reservoirs (the shock) followed by the eradication of the reservoirs (the kill). This review focuses mainly on the recent advances made in the "shock and kill" therapy. We believe that a cure or a remission will come from combinatorial approaches i.e. combination of drugs to reactivate the dormant virus from all the reservoirs including the one located in sanctuaries, and combination of strategies boosting the immune system. Alternative strategies based on cell and gene therapy or based in inducing deep latency, which are evoked in this review reinforce the idea that at least a remission is attainable.
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Affiliation(s)
- Christian Schwartz
- University of Strasbourg, EA7292, DHPI, Institute of Parasitology and Tropical Pathology, Strasbourg, France; University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France.
| | - Sophie Bouchat
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Céline Marban
- University of Strasbourg, Inserm UMR 1121 Faculté de Chirurgie Dentaire Pavillon Leriche 1, place de l'Hôpital Strasbourg, France
| | - Virginie Gautier
- UCD, Centre for Research in Infectious Diseases (CRID), School of Medicine University College Dublin, Belfield, Dublin 4, Ireland
| | - Carine Van Lint
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Olivier Rohr
- University of Strasbourg, EA7292, DHPI, Institute of Parasitology and Tropical Pathology, Strasbourg, France; University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France
| | - Valentin Le Douce
- UCD, Centre for Research in Infectious Diseases (CRID), School of Medicine University College Dublin, Belfield, Dublin 4, Ireland
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Cytokines Elevated in HIV Elite Controllers Reduce HIV Replication In Vitro and Modulate HIV Restriction Factor Expression. J Virol 2017; 91:JVI.02051-16. [PMID: 28053103 DOI: 10.1128/jvi.02051-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/22/2016] [Indexed: 12/20/2022] Open
Abstract
A subset of HIV-infected individuals termed elite controllers (ECs) maintain CD4+ T cell counts and control viral replication in the absence of antiretroviral therapy (ART). Systemic cytokine responses may differentiate ECs from subjects with uncontrolled viral replication or from those who require ART to suppress viral replication. We measured 87 cytokines in four groups of women: 73 ECs, 42 with pharmacologically suppressed viremia (ART), 42 with uncontrolled viral replication (noncontrollers [NCs]), and 48 HIV-uninfected (NEG) subjects. Four cytokines were elevated in ECs but not NCs or ART subjects: CCL14, CCL21, CCL27, and XCL1. In addition, median stromal cell-derived factor-1 (SDF-1) levels were 43% higher in ECs than in NCs. The combination of the five cytokines suppressed R5 and X4 virus replication in resting CD4+ T cells, and individually SDF-1β, CCL14, and CCL27 suppressed R5 virus replication, while SDF-1β, CCL21, and CCL14 suppressed X4 virus replication. Functional studies revealed that the combination of the five cytokines upregulated CD69 and CCR5 and downregulated CXCR4 and CCR7 on CD4+ T cells. The CD69 and CXCR4 effects were driven by SDF-1, while CCL21 downregulated CCR7. The combination of the EC-associated cytokines induced expression of the anti-HIV host restriction factors IFITM1 and IFITM2 and suppressed expression of RNase L and SAMHD1. These results identify a set of cytokines that are elevated in ECs and define their effects on cellular activation, HIV coreceptor expression, and innate restriction factor expression. This cytokine pattern may be a signature characteristic of HIV-1 elite control, potentially important for HIV therapeutic and curative strategies.IMPORTANCE Approximately 1% of people infected with HIV control virus replication without taking antiviral medications. These subjects, termed elite controllers (ECs), are known to have stronger immune responses targeting HIV than the typical HIV-infected subject, but the exact mechanisms of how their immune responses control infection are not known. In this study, we identified five soluble immune signaling molecules (cytokines) in the blood that were higher in ECs than in subjects with typical chronic HIV infection. We demonstrated that these cytokines can activate CD4+ T cells, the target cells for HIV infection. Furthermore, these five EC-associated cytokines could change expression levels of intrinsic resistance factors, or molecules inside the target cell that fight HIV infection. This study is significant in that it identified cytokines elevated in subjects with a good immune response against HIV and defined potential mechanisms as to how these cytokines could induce resistance to the virus in target cells.
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