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Board NL, Yuan Z, Wu F, Moskovljevic M, Ravi M, Sengupta S, Mun SS, Simonetti FR, Lai J, Tebas P, Lynn K, Hoh R, Deeks SG, Siliciano JD, Montaner LJ, Siliciano RF. Bispecific antibodies promote natural killer cell-mediated elimination of HIV-1 reservoir cells. Nat Immunol 2024; 25:462-470. [PMID: 38278966 PMCID: PMC10907297 DOI: 10.1038/s41590-023-01741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/28/2023] [Indexed: 01/28/2024]
Abstract
The persistence of CD4+ T cells carrying latent human immunodeficiency virus-1 (HIV-1) proviruses is the main barrier to a cure. New therapeutics to enhance HIV-1-specific immune responses and clear infected cells will probably be necessary to achieve reduction of the latent reservoir. In the present study, we report two single-chain diabodies (scDbs) that target the HIV-1 envelope protein (Env) and the human type III Fcγ receptor (CD16). We show that the scDbs promoted robust and HIV-1-specific natural killer (NK) cell activation and NK cell-mediated lysis of infected cells. Cocultures of CD4+ T cells from people with HIV-1 on antiretroviral therapy (ART) with autologous NK cells and the scDbs resulted in marked elimination of reservoir cells that was dependent on latency reversal. Treatment of human interleukin-15 transgenic NSG mice with one of the scDbs after ART initiation enhanced NK cell activity and reduced reservoir size. Thus, HIV-1-specific scDbs merit further evaluation as potential therapeutics for clearance of the latent reservoir.
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Affiliation(s)
- Nathan L Board
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhe Yuan
- The Wistar Institute, Philadelphia, PA, USA
| | - Fengting Wu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Milica Moskovljevic
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Meghana Ravi
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Srona Sengupta
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sung Soo Mun
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francesco R Simonetti
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pablo Tebas
- Presbyterian Hospital-University of Pennsylvania Hospital, Philadelphia, PA, USA
| | - Kenneth Lynn
- Presbyterian Hospital-University of Pennsylvania Hospital, Philadelphia, PA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Janet D Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | | | - Robert F Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA.
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2
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Alves ALV, da Silva LS, Faleiros CA, Silva VAO, Reis RM. The Role of Ingenane Diterpenes in Cancer Therapy: From Bioactive Secondary Compounds to Small Molecules. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221105691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Diterpenes are a class of critical taxonomic markers of the Euphorbiaceae family, representing small compounds (eg, molecules) with a wide range of biological activities and multi-target therapeutic potential. Diterpenes can exert different activities, including antitumor and multi-drug resistance-reversing activities, and antiviral, immunomodulatory, and anti-inflammatory effects, mainly due to their great structural diversity. In particular, one polycyclic skeleton has been highlighted: ingenane. Besides this natural diterpene, promising polycyclic skeletons may be submitted to chemical modification—by in silico approaches, chemical reactions, or biotransformation—putatively providing more active analogs (eg, ingenol derivatives), which are currently under pre-clinical investigation. This review outlines the current mechanisms of action and potential therapeutic implications of ingenol diterpenes as small cancer molecules.
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Affiliation(s)
- Ana Laura V. Alves
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Luciane S. da Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Camila A. Faleiros
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Viviane A. O. Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Rui M. Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga, Portugal
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3
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Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. Pathogens 2022; 11:pathogens11070743. [PMID: 35889989 PMCID: PMC9320269 DOI: 10.3390/pathogens11070743] [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: 05/09/2022] [Revised: 06/11/2022] [Accepted: 06/25/2022] [Indexed: 01/25/2023] Open
Abstract
COVID-19 vaccines have been instrumental tools in reducing the impact of SARS-CoV-2 infections around the world by preventing 80% to 90% of hospitalizations and deaths from reinfection, in addition to preventing 40% to 65% of symptomatic illnesses. However, the simultaneous large-scale vaccination of the global population will indubitably unveil heterogeneity in immune responses as well as in the propensity to developing post-vaccine adverse events, especially in vulnerable individuals. Herein, we applied a systems biology workflow, integrating vaccine transcriptional signatures with chemogenomics, to study the pharmacological effects of mRNA vaccines. First, we derived transcriptional signatures and predicted their biological effects using pathway enrichment and network approaches. Second, we queried the Connectivity Map (CMap) to prioritize adverse events hypotheses. Finally, we accepted higher-confidence hypotheses that have been predicted by independent approaches. Our results reveal that the mRNA-based BNT162b2 vaccine affects immune response pathways related to interferon and cytokine signaling, which should lead to vaccine success, but may also result in some adverse events. Our results emphasize the effects of BNT162b2 on calcium homeostasis, which could be contributing to some frequently encountered adverse events related to mRNA vaccines. Notably, cardiac side effects were signaled in the CMap query results. In summary, our approach has identified mechanisms underlying both the expected protective effects of vaccination as well as possible post-vaccine adverse effects. Our study illustrates the power of systems biology approaches in improving our understanding of the comprehensive biological response to vaccination against COVID-19.
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Sengupta S, Board NL, Wu F, Moskovljevic M, Douglass J, Zhang J, Reinhold BR, Duke-Cohan J, Yu J, Reed MC, Tabdili Y, Azurmendi A, Fray EJ, Zhang H, Hsiue EHC, Jenike K, Ho YC, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S, Siliciano JD, Sadegh-Nasseri S, Reinherz EL, Siliciano RF. TCR-mimic bispecific antibodies to target the HIV-1 reservoir. Proc Natl Acad Sci U S A 2022; 119:e2123406119. [PMID: 35394875 PMCID: PMC9169739 DOI: 10.1073/pnas.2123406119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/04/2022] [Indexed: 12/12/2022] Open
Abstract
HIV-1 infection is incurable due to the persistence of the virus in a latent reservoir of resting memory CD4+ T cells. “Shock-and-kill” approaches that seek to induce HIV-1 gene expression, protein production, and subsequent targeting by the host immune system have been unsuccessful due to a lack of effective latency-reversing agents (LRAs) and kill strategies. In an effort to develop reagents that could be used to promote killing of infected cells, we constructed T cell receptor (TCR)-mimic antibodies to HIV-1 peptide-major histocompatibility complexes (pMHC). Using phage display, we panned for phages expressing antibody-like variable sequences that bound HIV-1 pMHC generated using the common HLA-A*02:01 allele. We targeted three epitopes in Gag and reverse transcriptase identified and quantified via Poisson detection mass spectrometry from cells infected in vitro with a pseudotyped HIV-1 reporter virus (NL4.3 dEnv). Sequences isolated from phages that bound these pMHC were cloned into a single-chain diabody backbone (scDb) sequence, such that one fragment is specific for an HIV-1 pMHC and the other fragment binds to CD3ε, an essential signal transduction subunit of the TCR. Thus, these antibodies utilize the sensitivity of T cell signaling as readouts for antigen processing and as agents to promote killing of infected cells. Notably, these scDbs are exquisitely sensitive and specific for the peptide portion of the pMHC. Most importantly, one scDb caused killing of infected cells presenting a naturally processed target pMHC. This work lays the foundation for a novel therapeutic killing strategy toward elimination of the HIV-1 reservoir.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Nathan L. Board
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Milica Moskovljevic
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Josephine Zhang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bruce R. Reinhold
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jonathan Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jeanna Yu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Madison C. Reed
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Yasmine Tabdili
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Emily J. Fray
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Katharine Jenike
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Janet D. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | - Ellis L. Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Robert F. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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5
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Okoye AA, Fromentin R, Takata H, Brehm JH, Fukazawa Y, Randall B, Pardons M, Tai V, Tang J, Smedley J, Axthelm M, Lifson JD, Picker LJ, Favre D, Trautmann L, Chomont N. The ingenol-based protein kinase C agonist GSK445A is a potent inducer of HIV and SIV RNA transcription. PLoS Pathog 2022; 18:e1010245. [PMID: 35041707 PMCID: PMC8797195 DOI: 10.1371/journal.ppat.1010245] [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: 08/11/2021] [Revised: 01/28/2022] [Accepted: 01/03/2022] [Indexed: 01/01/2023] Open
Abstract
Activation of the NF-κB signaling pathway by Protein Kinase C (PKC) agonists is a potent mechanism for human immunodeficiency virus (HIV) latency disruption in vitro. However, significant toxicity risks and the lack of evidence supporting their activity in vivo have limited further evaluation of PKC agonists as HIV latency-reversing agents (LRA) in cure strategies. Here we evaluated whether GSK445A, a stabilized ingenol-B derivative, can induce HIV/simian immunodeficiency virus (SIV) transcription and virus production in vitro and demonstrate pharmacological activity in nonhuman primates (NHP). CD4+ T cells from people living with HIV and from SIV+ rhesus macaques (RM) on antiretroviral therapy (ART) exposed in vitro to 25 nM of GSK445A produced cell-associated viral transcripts as well as viral particles at levels similar to those induced by PMA/Ionomycin, indicating that GSK445A can potently reverse HIV/SIV latency. Importantly, these concentrations of GSK445A did not impair the proliferation or survival of HIV-specific CD8+ T cells, but instead, increased their numbers and enhanced IFN-γ production in response to HIV peptides. In vivo, GSK445A tolerability was established in SIV-naïve RM at 15 μg/kg although tolerability was reduced in SIV-infected RM on ART. Increases in plasma viremia following GSK445A administration were suggestive of increased SIV transcription in vivo. Collectively, these results indicate that GSK445A is a potent HIV/SIV LRA in vitro and has a tolerable safety profile amenable for further evaluation in vivo in NHP models of HIV cure/remission. Antiretroviral therapy (ART) is not a definitive cure for HIV infection, in part, because the virus is able to integrate its genetic material in the host cell and remain in a dormant but fully replication-competent form during ART. These latently-infected cells can persist for long periods of time and remain hidden from the host’s immune system. If ART is stopped, the virus can reactivate from this pool of infected cells and resume HIV replication and disease progression. As such, finding and eliminating cells with latent HIV infection is priority for HIV cure research. One approach is to use compounds referred to as latency-reversing agents, that can induce HIV reactivation during ART. The goal of this approach is to facilitate elimination of infected cells by the virus itself once it reactivates or by the host’s immune system, once virus induction renders the cells detectable by the immune system, while also preventing the virus from infecting new cells due to the continued presence of ART. In this study we report on the activity of a novel latency-reversing agent called GSK445A, a potent activator of the enzyme protein kinase C (PKC). We show that GSK445A can induce HIV and simian immunodeficiency virus (SIV) latency reversal in vitro and has a tolerable saftey profile in nonhuman primates that should permit further testing of this PKC-agonist in strategies to cure HIV.
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Affiliation(s)
- Afam A Okoye
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Rémi Fromentin
- Centre de Recherche du CHUM, Montréal, Québec, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Québec, Canada
| | - Hiroshi Takata
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Jessica H Brehm
- ViiV Healthcare, Research Triangle Park, North Carolina, United States of America
| | - Yoshinori Fukazawa
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Bryan Randall
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Marion Pardons
- Centre de Recherche du CHUM, Montréal, Québec, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Québec, Canada
| | - Vincent Tai
- ViiV Healthcare, Research Triangle Park, North Carolina, United States of America
| | - Jun Tang
- ViiV Healthcare, Research Triangle Park, North Carolina, United States of America
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Michael Axthelm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - David Favre
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.,HIV Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Lydie Trautmann
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Nicolas Chomont
- Centre de Recherche du CHUM, Montréal, Québec, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Québec, Canada
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Hajjo R, Tropsha A. A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality. Pharm Res 2020; 37:212. [PMID: 33025261 PMCID: PMC7537965 DOI: 10.1007/s11095-020-02930-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/17/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE Coronavirus disease 2019 (COVID-19) is expected to continue to cause worldwide fatalities until the World population develops 'herd immunity', or until a vaccine is developed and used as a prevention. Meanwhile, there is an urgent need to identify alternative means of antiviral defense. Bacillus Calmette-Guérin (BCG) vaccine that has been recognized for its off-target beneficial effects on the immune system can be exploited to boast immunity and protect from emerging novel viruses. METHODS We developed and employed a systems biology workflow capable of identifying small-molecule antiviral drugs and vaccines that can boast immunity and affect a wide variety of viral disease pathways to protect from the fatal consequences of emerging viruses. RESULTS Our analysis demonstrates that BCG vaccine affects the production and maturation of naïve T cells resulting in enhanced, long-lasting trained innate immune responses that can provide protection against novel viruses. We have identified small-molecule BCG mimics, including antiviral drugs such as raltegravir and lopinavir as high confidence hits. Strikingly, our top hits emetine and lopinavir were independently validated by recent experimental findings that these compounds inhibit the growth of SARS-CoV-2 in vitro. CONCLUSIONS Our results provide systems biology support for using BCG and small-molecule BCG mimics as putative vaccine and drug candidates against emergent viruses including SARS-CoV-2.
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Affiliation(s)
- Rima Hajjo
- Department of Pharmacy - Computational Chemical Biology, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan.
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, UNC Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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7
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Campos Coelho AV, de Moura RR, Crovella S. Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents. Microorganisms 2020; 8:microorganisms8101505. [PMID: 33007800 PMCID: PMC7601709 DOI: 10.3390/microorganisms8101505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) causes a progressive depletion of CD4+ T cells, hampering immune function. Current experimental strategies to fight the virus focus on the reactivation of latent HIV-1 in the viral reservoir to make the virus detectable by the immune system, by searching for latency reversal agents (LRAs). We hypothesize that if common molecular pathways elicited by the presence of LRAs are known, perhaps new, more efficient, “shock-and-kill” strategies can be found. Thus, the objective of the present study is to re-evaluate RNA-Seq assays to find differentially expressed genes (DEGs) during latency reversal via transcriptome analysis. We selected six studies (45 samples altogether: 16 negative controls and 29 LRA-treated CD4+ T cells) and 11 LRA strategies through a systematic search in Gene Expression Omnibus (GEO) and PubMed databases. The raw reads were trimmed, counted, and normalized. Next, we detected consistent DEGs in these independent experiments. AZD5582, romidepsin, and suberanilohydroxamic acid (SAHA) were the LRAs that modulated most genes. We detected 948 DEGs shared by those three LRAs. Gene ontology analysis and cross-referencing with other sources of the literature showed enrichment of cell activation, differentiation and signaling, especially mitogen-activated protein kinase (MAPK) and Rho-GTPases pathways.
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Affiliation(s)
- Antonio Victor Campos Coelho
- Federal University of Pernambuco, Avenida da Engenharia, Cidade Universitária, Recife 50670-901, Brazil
- Correspondence: ; Tel.: +55-81-2126-8522
| | - Ronald Rodrigues de Moura
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (R.R.d.M.); (S.C.)
| | - Sergio Crovella
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (R.R.d.M.); (S.C.)
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
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8
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Jiang G, Maverakis E, Cheng MY, Elsheikh MM, Deleage C, Méndez-Lagares G, Shimoda M, Yukl SA, Hartigan-O’Connor DJ, Thompson GR, Estes JD, Wong JK, Dandekar S. Disruption of latent HIV in vivo during the clearance of actinic keratosis by ingenol mebutate. JCI Insight 2019; 4:126027. [PMID: 30944245 PMCID: PMC6483647 DOI: 10.1172/jci.insight.126027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/14/2019] [Indexed: 01/20/2023] Open
Abstract
Actinic keratosis (AK) is a precancerous skin lesion that is common in HIV-positive patients. Without effective treatment, AKs can progress to squamous cell carcinoma. Ingenol mebutate, a PKC agonist, is a US Food and Drug Administration-approved (FDA-approved) topical treatment for AKs. It can induce reactivation of latent HIV transcription in CD4+ T cells both in vitro and ex vivo. Although PKC agonists are known to be potent inducers of HIV expression from latency, their effects in vivo are not known because of the concerns of toxicity. Therefore, we sought to determine the effects of topical ingenol mebutate gel on the HIV transcription profile in HIV-infected individuals with AKs, specifically in the setting of suppressive antiretroviral therapy (ART). We found that AKs cleared following topical application of ingenol mebutate and detected marginal changes in immune activation in the peripheral blood and in skin biopsies. An overall increase in the level of HIV transcription initiation, elongation, and complete transcription was detected only in skin biopsies after the treatment. Our data demonstrate that application of ingenol mebutate to AKs in ART-suppressed HIV-positive patients can effectively cure AKs as well as disrupt HIV latency in the skin tissue microenvironment in vivo without causing massive immune activation.
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Affiliation(s)
- Guochun Jiang
- Department of Medical Microbiology and Immunology and
| | | | | | | | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | | | - Steven A. Yukl
- San Francisco Veterans Affairs (VA) Medical Center and UCSF, San Francisco, California, USA
| | | | | | - Jacob D. Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Joseph K. Wong
- San Francisco Veterans Affairs (VA) Medical Center and UCSF, San Francisco, California, USA
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9
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Interferon Alpha Enhances NK Cell Function and the Suppressive Capacity of HIV-Specific CD8 + T Cells. J Virol 2019; 93:JVI.01541-18. [PMID: 30404799 DOI: 10.1128/jvi.01541-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/29/2018] [Indexed: 12/23/2022] Open
Abstract
Current shock-and-kill strategies for the eradication of the HIV-1 reservoir have resulted in blips of viremia but not in a decrease in the size of the latent reservoir in patients on suppressive antiretroviral therapy (ART). This discrepancy could potentially be explained by an inability of the immune system to kill HIV-1-infected cells following the reversal of latency. Furthermore, some studies have suggested that certain latency-reversing agents (LRAs) may inhibit CD8+ T cell and natural killer (NK) cell responses. In this study, we tested the hypothesis that alpha interferon (IFN-α) could improve the function of NK cells from chronic progressors (CP) on ART. We show here that IFN-α treatment enhanced cytokine secretion, polyfunctionality, degranulation, and the cytotoxic potential of NK cells from healthy donors (HD) and CP. We also show that this cytokine enhanced the viral suppressive capacity of NK cells from HD and elite controllers or suppressors. Furthermore, IFN-α enhanced global CP CD8+ T cell cytokine responses and the suppressive capacity of ES CD8+ T cells. Our data suggest that IFN-α treatment may potentially be used as an immunomodulatory agent in HIV-1 cure strategies.IMPORTANCE Data suggest that HIV+ individuals unable to control infection fail to do so due to impaired cytokine production and/cytotoxic effector cell function. Consequently, the success of cure agendas such as the shock-and-kill strategy will probably depend on enhancing patient effector cell function. In this regard, NK cells are of particular interest since they complement the function of CD8+ T cells. Here, we demonstrate the ability of short-course alpha interferon (IFN-α) treatments to effectively enhance such effector functions in chronic progressor NK cells without inhibiting their general CD8+ T cell function. These results point to the possibility of exploring such short-course IFN-α treatments for the enhancement of effector cell function in HIV+ patients in future cure strategies.
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Dampier W, Sullivan NT, Mell JC, Pirrone V, Ehrlich GD, Chung CH, Allen AG, DeSimone M, Zhong W, Kercher K, Passic S, Williams JW, Szep Z, Khalili K, Jacobson JM, Nonnemacher MR, Wigdahl B. Broad-Spectrum and Personalized Guide RNAs for CRISPR/Cas9 HIV-1 Therapeutics. AIDS Res Hum Retroviruses 2018; 34:950-960. [PMID: 29968495 PMCID: PMC6238604 DOI: 10.1089/aid.2017.0274] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9 system has been used to excise the HIV-1 proviral genome from latently infected cells, potentially offering a cure for HIV-infected patients. Recent studies have shown that most published HIV-1 guide RNAs (gRNAs) do not account for the diverse viral quasispecies within or among patients, which continue to diversify with time even in long-term antiretroviral therapy (ART)-suppressed patients. Given this observation, proviral genomes were deep sequenced from 23 HIV-1-infected patients in the Drexel Medicine CNS AIDS Research and Eradication Study cohort at two different visits. Based on the spectrum of integrated proviral DNA polymorphisms observed, three gRNA design strategies were explored: based on the patient's own HIV-1 sequences (personalized), based on consensus sequences from a large sample of patients [broad-spectrum (BS)], or a combination of both approaches. Using a bioinformatic algorithm, the personalized gRNA design was predicted to cut 46 of 48 patient samples at 90% efficiency, whereas the top 4 BS gRNAs (BS4) were predicted to excise provirus from 44 of 48 patient samples with 90% efficiency. Using a mixed design with the top three BS gRNAs plus one personalized gRNA (BS3 + PS1) resulted in predicted excision of provirus from 45 of 48 patient samples with 90% efficiency. In summary, these studies used an algorithmic design strategy to identify potential BS gRNAs to target a spectrum of HIV-1 long teriminal repeat (LTR) quasispecies for use with a small HIV-1-infected population. This approach should advance CRISPR/Cas9 excision technology taking into account the extensive molecular heterogeneity of HIV-1 that persists in situ after prolonged ART.
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Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Neil T. Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Garth D. Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Otolaryngology—Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Mathew DeSimone
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Jean W. Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Zsofia Szep
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology, and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Jeffrey M. Jacobson
- Department of Neuroscience, Center for Neurovirology, and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Section of Infectious Disease, Department of Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
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11
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Clutton GT, Jones RB. Diverse Impacts of HIV Latency-Reversing Agents on CD8+ T-Cell Function: Implications for HIV Cure. Front Immunol 2018; 9:1452. [PMID: 29988382 PMCID: PMC6023971 DOI: 10.3389/fimmu.2018.01452] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022] Open
Abstract
Antiretroviral therapy regimens durably suppress HIV replication, but do not cure infection. This is partially attributable to the persistence of long-lived pools of resting CD4+ T-cells harboring latent replication-competent virus. Substantial clinical and pre-clinical research is currently being directed at purging this viral reservoir by combining pharmacological latency reversal with immune effectors, such as HIV-specific CD8+ T-cells, capable of eliminating reactivated targets-the so-called "shock-and-kill" approach. However, several studies indicate that the latency-reversing agents (LRAs) may affect CD8+ T-cell function. The current review aims to frame recent advances, and ongoing challenges, in implementing "shock-and-kill" strategies from the perspective of effectively harnessing CD8+ T-cells. We review and contextualize findings indicating that LRAs often have unintended impacts on CD8+ T-cell function, both detrimental and beneficial. We identify and attempt to bridge the gap between viral reactivation, as measured by the detection of RNA or protein, and bona fide presentation of viral antigens to CD8+ T-cells. Finally, we highlight factors on the effector (CD8+) and target (CD4+) cell sides that contribute to whether or not infected-cell recognition results in killing/elimination. These perspectives may contribute to an integrated view of "shock-and-kill," with implications for therapeutic development.
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Affiliation(s)
- Genevieve Tyndale Clutton
- Department of Microbiology and Immunology, UNC Chapel Hill School of Medicine, Chapel Hill, NC, United States
| | - R. Brad Jones
- Department of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, United States
- Infectious Disease Division, Weill Cornell Medical College, New York, NY, United States
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12
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Sengupta S, Siliciano RF. Targeting the Latent Reservoir for HIV-1. Immunity 2018; 48:872-895. [PMID: 29768175 PMCID: PMC6196732 DOI: 10.1016/j.immuni.2018.04.030] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 02/07/2023]
Abstract
Antiretroviral therapy can effectively block HIV-1 replication and prevent or reverse immunodeficiency in HIV-1-infected individuals. However, viral replication resumes within weeks of treatment interruption. The major barrier to a cure is a small pool of resting memory CD4+ T cells that harbor latent HIV-1 proviruses. This latent reservoir is now the focus of an intense international research effort. We describe how the reservoir is established, challenges involved in eliminating it, and pharmacologic and immunologic strategies for targeting this reservoir. The development of a successful cure strategy will most likely require understanding the mechanisms that maintain HIV-1 proviruses in a latent state and pathways that drive the proliferation of infected cells, which slows reservoir decay. In addition, a cure will require the development of effective immunologic approaches to eliminating infected cells. There is renewed optimism about the prospect of a cure, and the interventions discussed here could pave the way.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Graduate Program in Immunology and Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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Darcis G, Das AT, Berkhout B. Tackling HIV Persistence: Pharmacological versus CRISPR-Based Shock Strategies. Viruses 2018; 10:v10040157. [PMID: 29596334 PMCID: PMC5923451 DOI: 10.3390/v10040157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 02/07/2023] Open
Abstract
Jan Svoboda studied aspects of viral latency, in particular with respect to disease induction by avian RNA tumor viruses, which were later renamed as part of the extended retrovirus family. The course of retroviral pathogenesis is intrinsically linked to their unique property of integrating the DNA copy of the retroviral genome into that of the host cell, thus forming the provirus. Retroviral latency has recently become of major clinical interest to allow a better understanding of why we can effectively block the human immunodeficiency virus type 1 (HIV-1) in infected individuals with antiviral drugs, yet never reach a cure. We will discuss HIV-1 latency and its direct consequence—the formation of long-lasting HIV-1 reservoirs. We next focus on one of the most explored strategies in tackling HIV-1 reservoirs—the “shock and kill” strategy—which describes the broadly explored pharmacological way of kicking the latent provirus, with subsequent killing of the virus-producing cell by the immune system. We furthermore present how the clustered regularly interspaced palindromic repeats (CRISPR) and associated protein (Cas) system can be harnessed to reach the same objective by reactivating HIV-1 gene expression from latency. We will review the benefits and drawbacks of these different cure strategies.
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Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
- Infectious Diseases Department, Liège University Hospital, 4000 Liege, Belgium.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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14
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Abstract
Antiretroviral therapy (ART) has rendered HIV-1 infection a treatable illness; however, ART is not curative owing to the persistence of replication-competent, latent proviruses in long-lived resting T cells. Strategies that target these latently infected cells and allow immune recognition and clearance of this reservoir will be necessary to eradicate HIV-1 in infected individuals. This review describes current pharmacologic approaches to reactivate the latent reservoir so that infected cells can be recognized and targeted, with the ultimate goal of achieving an HIV-1 cure.
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Affiliation(s)
- Adam M Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112;
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