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Wang J, Yang J, Yang Z, Lu X, Jin C, Cheng L, Wu N. RbAp48, a novel inhibitory factor that regulates the transcription of human immunodeficiency virus type 1. Int J Mol Med 2016; 38:267-274. [PMID: 27222146 DOI: 10.3892/ijmm.2016.2598] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 05/10/2016] [Indexed: 11/06/2022] Open
Abstract
Retinoblastoma binding protein 4 (RbAp48) is a histone chaperone which has been suggested to play a role in gene silencing. However, the role of RbAp48 in human immunodeficiency virus type 1 (HIV-1) infection and gene replication has not been determined to date, to the best of our knowledge. For this purpose, we demonstrated in the present study that RbAp48 expression was upregulated by HIV-1 infection, whereas the knockdown of RbAp48 promoted HIV infection and the production of virus particles. The ectopic expression of RbAp48 inhibited HIV-1 expression, and this inhibition correlated with a marked decrease in the expression of HIV-1 genomic RNA and various RNA transcripts. Further experiments to determine the mechanism responsible for the inhibitory effects of RbAp48 revealed that the ectopic expression of RbAp48 repressed HIV-1 long terminal repeat (LTR)-mediated basal transcription as well as TNF-α- and phorbol 12-myristate 13-acetate (PMA)‑activated transcription. Furthermore, the results of the electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis revealed that RbAp48 binds to the HIV-1 LTR in vitro. Taken together, these findings demonstrate that, as a transcriptional cofactor, RbAp48 is likely to act as a potent antiretroviral defense.
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Affiliation(s)
- Juan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Jin Yang
- Department of Medicine, Blood Center of Zhejiang Province, Hangzhou, Zhejiang 330100, P.R. China
| | - Zongxing Yang
- Xixi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, P.R. China
| | - Xiangyun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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Rausell A, Muñoz M, Martinez R, Roger T, Telenti A, Ciuffi A. Innate immune defects in HIV permissive cell lines. Retrovirology 2016; 13:43. [PMID: 27350062 PMCID: PMC4924258 DOI: 10.1186/s12977-016-0275-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/14/2016] [Indexed: 11/29/2022] Open
Abstract
Background Primary CD4+ T cells and cell lines differ in their permissiveness to HIV infection. Impaired innate immunity may contribute to this different phenotype. Findings We used transcriptome profiling of 1503 innate immunity genes in primary CD4+ T cells and permissive cell lines. Two clusters of differentially expressed genes were identified: a set of 249 genes that were highly expressed in primary cells and minimally expressed in cell lines and a set of 110 genes with the opposite pattern. Specific to HIV, HEK293T, Jurkat, SupT1 and CEM cell lines displayed unique patterns of downregulation of genes involved in viral sensing and restriction. Activation of primary CD4+ T cells resulted in reversal of the pattern of expression of those sets of innate immunity genes. Functional analysis of prototypical innate immunity pathways of permissive cell lines confirmed impaired responses identified in transcriptome analyses. Conclusion Integrity of innate immunity genes and pathways needs to be considered in designing gain/loss functional genomic screens of viral infection. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0275-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio Rausell
- Clinical Bioinformatics lab, Imagine Institute, Paris Descartes University - Sorbonne Paris Cité, 75015, Paris, France.
| | - Miguel Muñoz
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Thierry Roger
- Infectious Diseases Service, Department of Medicine, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Amalio Telenti
- Genetic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
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Pine PS, Munro SA, Parsons JR, McDaniel J, Lucas AB, Lozach J, Myers TG, Su Q, Jacobs-Helber SM, Salit M. Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design. BMC Biotechnol 2016; 16:54. [PMID: 27342544 PMCID: PMC4921035 DOI: 10.1186/s12896-016-0281-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 06/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approaches included a modified Latin square design to provide a broad dynamic range of relative abundance with known differences between four complex pools of ERCC RNA transcripts spiked into a human liver total RNA background. RESULTS ERCC pools were analyzed on four different microarray platforms: Agilent 1- and 2-color, Illumina bead, and NIAID lab-made spotted microarrays; and two different second-generation sequencing platforms: the Life Technologies 5500xl and the Illumina HiSeq 2500. Individual ERCC controls were assessed for reproducible performance in signal response to concentration among the platforms. Most demonstrated linear behavior if they were not located near one of the extremes of the dynamic range. Performance issues with any individual ERCC transcript could be attributed to detection limitations, platform-specific target probe issues, or potential mixing errors. Collectively, these pools of spike-in RNA controls were evaluated for suitability as surrogates for endogenous transcripts to interrogate the performance of the RNA measurement process of each platform. The controls were useful for establishing the dynamic range of the assay, as well as delineating the useable region of that range where differential expression measurements, expressed as ratios, would be expected to be accurate. CONCLUSIONS The modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.
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Affiliation(s)
- P Scott Pine
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA.
| | - Sarah A Munro
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA
| | - Jerod R Parsons
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA
| | - Jennifer McDaniel
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA
| | - Anne Bergstrom Lucas
- Genomics Research and Development, Agilent Technologies, Santa Clara, CA, 95051, USA
| | | | - Timothy G Myers
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Qin Su
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Sarah M Jacobs-Helber
- AIBioTech, Inc., Richmond, VA, 23235, USA.,Present Address: GENETWORx, LLC., Glen Allen, VA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA
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54
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White CH, Moesker B, Ciuffi A, Beliakova-Bethell N. Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation. World J Clin Infect Dis 2016; 6:6-21. [DOI: 10.5495/wjcid.v6.i2.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/15/2016] [Accepted: 03/09/2016] [Indexed: 02/06/2023] Open
Abstract
Eradication of human immunodeficiency virus (HIV) in infected individuals is currently not possible because of the presence of the persistent cellular reservoir of latent infection. The identification of HIV latency biomarkers and a better understanding of the molecular mechanisms contributing to regulation of HIV expression might provide essential tools to eliminate these latently infected cells. This review aims at summarizing gene expression profiling and systems biology applications to studies of HIV latency and eradication. Studies comparing gene expression in latently infected and uninfected cells identify candidate latency biomarkers and novel mechanisms of latency control. Studies that profiled gene expression changes induced by existing latency reversing agents (LRAs) highlight uniting themes driving HIV reactivation and novel mechanisms that contribute to regulation of HIV expression by different LRAs. Among the reviewed gene expression studies, the common approaches included identification of differentially expressed genes and gene functional category assessment. Integration of transcriptomic data with other biological data types is presently scarce, and the field would benefit from increased adoption of these methods in future studies. In addition, designing prospective studies that use the same methods of data acquisition and statistical analyses will facilitate a more reliable identification of latency biomarkers using different model systems and the comparison of the effects of different LRAs on host factors with a role in HIV reactivation. The results from such studies would have the potential to significantly impact the process by which candidate drugs are selected and combined for future evaluations and advancement to clinical trials.
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55
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Jones RB, Mueller S, O’Connor R, Rimpel K, Sloan DD, Karel D, Wong HC, Jeng EK, Thomas AS, Whitney JB, Lim SY, Kovacs C, Benko E, Karandish S, Huang SH, Buzon MJ, Lichterfeld M, Irrinki A, Murry JP, Tsai A, Yu H, Geleziunas R, Trocha A, Ostrowski MA, Irvine DJ, Walker BD. A Subset of Latency-Reversing Agents Expose HIV-Infected Resting CD4+ T-Cells to Recognition by Cytotoxic T-Lymphocytes. PLoS Pathog 2016; 12:e1005545. [PMID: 27082643 PMCID: PMC4833318 DOI: 10.1371/journal.ppat.1005545] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 03/11/2016] [Indexed: 12/25/2022] Open
Abstract
Resting CD4+ T-cells harboring inducible HIV proviruses are a critical reservoir in antiretroviral therapy (ART)-treated subjects. These cells express little to no viral protein, and thus neither die by viral cytopathic effects, nor are efficiently cleared by immune effectors. Elimination of this reservoir is theoretically possible by combining latency-reversing agents (LRAs) with immune effectors, such as CD8+ T-cells. However, the relative efficacy of different LRAs in sensitizing latently-infected cells for recognition by HIV-specific CD8+ T-cells has not been determined. To address this, we developed an assay that utilizes HIV-specific CD8+ T-cell clones as biosensors for HIV antigen expression. By testing multiple CD8+ T-cell clones against a primary cell model of HIV latency, we identified several single agents that primed latently-infected cells for CD8+ T-cell recognition, including IL-2, IL-15, two IL-15 superagonists (IL-15SA and ALT-803), prostratin, and the TLR-2 ligand Pam3CSK4. In contrast, we did not observe CD8+ T-cell recognition of target cells following treatment with histone deacetylase inhibitors or with hexamethylene bisacetamide (HMBA). In further experiments we demonstrate that a clinically achievable concentration of the IL-15 superagonist ‘ALT-803’, an agent presently in clinical trials for solid and hematological tumors, primes the natural ex vivo reservoir for CD8+ T-cell recognition. Thus, our results establish a novel experimental approach for comparative evaluation of LRAs, and highlight ALT-803 as an LRA with the potential to synergize with CD8+ T-cells in HIV eradication strategies. Although modern therapies have greatly improved the lives of HIV-positive people with access to care, a cure remains elusive. This leaves these individuals burdened by a lifelong commitment to medication, and fails to fully restore health. Curing infection would likely require therapies that combine the ability to force the virus out the ‘latent state’ in which it hides, with immune responses able to kill unmasked infected cells, the so called “shock and kill” strategy. A critical aspect of this strategy is identifying drugs that are effective at shocking virus out of latency, known as latency reversing agents. In this study, we took the novel approach of using CD8+ T-cells, immune cells responsible for killing infected cells, as biosensors able to detect the unmasking of latently-infected cells. Using this method, we screened a panel of potential latency reversing agents. We found that while a subset of these agents exposed infected cells to the immune system, others did not. Our results establish a new method for screening potential latency reversing agents, and support the prioritization of the agents that were shown to be effective for combination with CD8+ T-cells in shock and kill strategies aimed at curing HIV infection.
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Affiliation(s)
- R. Brad Jones
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
- Department of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - Stefanie Mueller
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
| | - Rachel O’Connor
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Katherine Rimpel
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Derek D. Sloan
- Gilead Sciences, Foster City, California, United States of America
| | - Dan Karel
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Hing C. Wong
- Altor BioScience Corporation, Miramar, Florida, United States of America
| | - Emily K. Jeng
- Altor BioScience Corporation, Miramar, Florida, United States of America
| | - Allison S. Thomas
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Department of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - James B. Whitney
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - So-Yon Lim
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Colin Kovacs
- The Maple Leaf Medical Clinic, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erika Benko
- The Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Sara Karandish
- Department of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - Szu-Han Huang
- Department of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, D.C., United States of America
| | - Maria J. Buzon
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Mathias Lichterfeld
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Alivelu Irrinki
- Gilead Sciences, Foster City, California, United States of America
| | - Jeffrey P. Murry
- Gilead Sciences, Foster City, California, United States of America
| | - Angela Tsai
- Gilead Sciences, Foster City, California, United States of America
| | - Helen Yu
- Gilead Sciences, Foster City, California, United States of America
| | - Romas Geleziunas
- Gilead Sciences, Foster City, California, United States of America
| | - Alicja Trocha
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Mario A. Ostrowski
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Medical Institute, St. Michael’s Hospital, Toronto, Ontario, Canad
| | - Darrell J. Irvine
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States of America
| | - Bruce D. Walker
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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56
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Abstract
Current efforts toward achieving a cure for HIV are focused on developing strategies to eliminate latently infected CD4+ T cells, which represent the major barrier to virus eradication. Sensitive, precise, and practical assays that can reliably characterize and measure this HIV reservoir and can reliably measure the impact of a candidate treatment strategy are essential. PCR-based procedures for detecting integrated HIV DNA will overestimate the size of the reservoir by detecting replication-incompetent proviruses; however, viral outgrowth assays underestimate the size of the reservoir. Here, we describe the attributes and limitations of current procedures for measuring the HIV reservoir. Characterizing their relative merits will require rigorous evaluation of their performance characteristics (sensitivity, specificity, reproducibility, etc.) and their relationship to the results of clinical studies.
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Affiliation(s)
| | - Douglas D. Richman
- UCSD, La Jolla, California, USA
- VA San Diego Healthcare System, La Jolla, California, USA
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57
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Host Response in HIV Infection. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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58
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Wang C, Yang S, Lu H, You H, Ni M, Shan W, Lin T, Gao X, Chen H, Zhou Q, Xue Y. A Natural Product from Polygonum cuspidatum Sieb. Et Zucc. Promotes Tat-Dependent HIV Latency Reversal through Triggering P-TEFb's Release from 7SK snRNP. PLoS One 2015; 10:e0142739. [PMID: 26569506 PMCID: PMC4646521 DOI: 10.1371/journal.pone.0142739] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 10/25/2015] [Indexed: 01/22/2023] Open
Abstract
The latent reservoirs of HIV represent a major impediment to eradication of HIV/AIDS. To overcome this problem, agents that can activate latent HIV proviruses have been actively sought after, as they can potentially be used in combination with the highly active antiretroviral therapy (HAART) to eliminate the latent reservoirs. Although several chemical compounds have been shown to activate latency, they are of limited use due to high toxicity and poor clinical outcomes. In an attempt to identify natural products as effective latency activators from traditional Chinese medicinal herbs that have long been widely used in human population, we have isolated procyanidin C-13,3',3"-tri-O-gallate (named as REJ-C1G3) from Polygonum cuspidatum Sieb. et Zucc., that can activate HIV in latently infected Jurkat T cells. REJ-C1G3 preferentially stimulates HIV transcription in a process that depends on the viral encoded Tat protein and acts synergistically with prostratin (an activator of the NF-κB pathway) or JQ1 (an inhibitor of Brd4) to activate HIV latency. Our mechanistic analyses further show that REJ-C1G3 accomplishes these tasks by inducing the release of P-TEFb, a host cofactor essential for Tat-activation of HIV transcription, from the cellular P-TEFb reservoir 7SK snRNP.
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Affiliation(s)
- Cong Wang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shuiyuan Yang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Huasong Lu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Hongchao You
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Man Ni
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wenjun Shan
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ting Lin
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiang Gao
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Haifeng Chen
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qiang Zhou
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Yuhua Xue
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
- * E-mail:
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59
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A Subset of CD4/CD8 Double-Negative T Cells Expresses HIV Proteins in Patients on Antiretroviral Therapy. J Virol 2015; 90:2165-79. [PMID: 26537682 PMCID: PMC4810694 DOI: 10.1128/jvi.01913-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/21/2015] [Indexed: 12/21/2022] Open
Abstract
A major goal in HIV eradication research is characterizing the reservoir cells that harbor HIV in the presence of antiretroviral therapy (ART), which reseed viremia after treatment is stopped. In general, it is assumed that the reservoir consists of CD4+ T cells that express no viral proteins. However, recent findings suggest that this may be an overly simplistic view and that the cells that contribute to the reservoir may be a diverse population that includes both CD4+ and CD4− cells. In this study, we directly infected resting CD4+ T cells and used fluorescence-activated cell sorting (FACS) and fiber-optic array scanning technology (FAST) to identify and image cells expressing HIV Gag. We found that Gag expression from integrated proviruses occurred in resting cells that lacked surface CD4, likely resulting from Nef- and Env-mediated receptor internalization. We also extended our approach to detect cells expressing HIV proteins in patients suppressed on ART. We found evidence that rare Gag+ cells persist during ART and that these cells are often negative for CD4. We propose that these double-negative α/β T cells that express HIV protein may be a component of the long-lived reservoir.
IMPORTANCE A reservoir of infected cells persists in HIV-infected patients during antiretroviral therapy (ART) that leads to rebound of virus if treatment is stopped. In this study, we used flow cytometry and cell imaging to characterize protein expression in HIV-infected resting cells. HIV Gag protein can be directly detected in infected resting cells and occurs with simultaneous loss of CD4, consistent with the expression of additional viral proteins, such as Env and Nef. Gag+ CD4− cells can also be detected in suppressed patients, suggesting that a subset of infected cells express proteins during ART. Understanding the regulation of viral protein expression during ART will be key to designing effective strategies to eradicate HIV reservoirs.
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60
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Abstract
DESIGN Persistent latently infected CD4 T cells represent a major obstacle to HIV eradication. Histone deacetylase inhibitors (HDACis) are a proposed activation therapy. However, off-target effects on gene expression in host immune cells are poorly understood. We hypothesized that HDACi-modulated genes would be best identified with a dose-response analysis. METHODS Resting primary CD4 T cells were treated with 0.34, 1, 3, or 10 μmol/l of the HDACi, suberoylanilide hydroxamic acid (SAHA), for 24 h and subjected to microarray gene expression analysis. Genes with dose-correlated expression were filtered to identify a subset with consistent up or downregulation at each SAHA dose. Histone modifications were characterized in six SAHA dose-responsive genes by chromatin immunoprecipitation (ChIP-RT-qPCR). RESULTS A large number of genes were shown to be upregulated (N = 657) or downregulated (N = 725) by SAHA in a dose-responsive manner (FDR-corrected P-value ≤ 0.5, fold change ≥|2|). Several genes (e.g. CINNAL1, DPEP2, H1F0, IRGM, PHF15, and SELL) are potential in-vivo biomarkers of SAHA activity. SAHA dose-responsive genes included transcription factors, HIV restriction factors, histone methyltransferases, and host proteins that interact with HIV. Pathway analysis suggested net downregulation of T-cell activation with increasing SAHA dose. Histone acetylation was not correlated with host gene expression, but plausible alternative mechanisms for SAHA-modulated gene expression were identified. CONCLUSION Numerous genes in CD4 T cells are modulated by SAHA in a dose-responsive manner, including genes that may negatively influence HIV activation from latency. Our study suggests that SAHA influences gene expression through a confluence of several mechanisms, including histone modification, and altered expression and activity of transcription factors.
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61
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White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N. Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency. Antiviral Res 2015; 123:78-85. [PMID: 26343910 PMCID: PMC5606336 DOI: 10.1016/j.antiviral.2015.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/22/2015] [Accepted: 09/03/2015] [Indexed: 02/06/2023]
Abstract
Suberoylanilide hydroxamic acid (SAHA) has been assessed in clinical trials as part of a "shock and kill" strategy to cure HIV-infected patients. While it was effective at inducing expression of HIV RNA ("shock"), treatment with SAHA did not result in a reduction of reservoir size ("kill"). We therefore utilized a combined analysis of effects of SAHA on the host transcriptome and proteome to dissect its mechanisms of action that may explain its limited success in "shock and kill" strategies. CD4+ T cells from HIV seronegative donors were treated with 1μM SAHA or its solvent dimethyl sulfoxide (DMSO) for 24h. Protein expression and post-translational modifications were measured with iTRAQ proteomics using ultra high-precision two-dimensional liquid chromatography-tandem mass spectrometry. Gene expression was assessed by Illumina microarrays. Using limma package in the R computing environment, we identified 185 proteins, 18 phosphorylated forms, 4 acetylated forms and 2982 genes, whose expression was modulated by SAHA. A protein interaction network integrating these 4 data types identified the HIV transcriptional repressor HMGA1 to be upregulated by SAHA at the transcript, protein and acetylated protein levels. Further functional category assessment of proteins and genes modulated by SAHA identified gene ontology terms related to NFκB signaling, protein folding and autophagy, which are all relevant to HIV reactivation. In summary, SAHA modulated numerous host cell transcripts, proteins and post-translational modifications of proteins, which would be expected to have very mixed effects on the induction of HIV-specific transcription and protein function. Proteome profiling highlighted a number of potential counter-regulatory effects of SAHA with respect to viral induction, which transcriptome profiling alone would not have identified. These observations could lead to a more informed selection and design of other HDACi with a more refined targeting profile, and prioritization of latency reversing agents of other classes to be used in combination with SAHA to achieve more potent induction of HIV expression.
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Affiliation(s)
- Cory H White
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, USA; San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA
| | - Harvey E Johnston
- Cancer Sciences Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK; Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK
| | - Bastiaan Moesker
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK
| | - Antigoni Manousopoulou
- Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK
| | - David M Margolis
- Departments of Medicine, Microbiology and Immunology, Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Douglas D Richman
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Celsa A Spina
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Spiros D Garbis
- Cancer Sciences Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK; Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK.
| | - Christopher H Woelk
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK.
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Modeling the Effects of Vorinostat In Vivo Reveals both Transient and Delayed HIV Transcriptional Activation and Minimal Killing of Latently Infected Cells. PLoS Pathog 2015; 11:e1005237. [PMID: 26496627 PMCID: PMC4619772 DOI: 10.1371/journal.ppat.1005237] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/28/2015] [Indexed: 12/31/2022] Open
Abstract
Recent efforts to cure human immunodeficiency virus type-1 (HIV-1) infection have focused on developing latency reversing agents as a first step to eradicate the latent reservoir. The histone deacetylase inhibitor, vorinostat, has been shown to activate HIV RNA transcription in CD4+ T-cells and alter host cell gene transcription in HIV-infected individuals on antiretroviral therapy. In order to understand how latently infected cells respond dynamically to vorinostat treatment and determine the impact of vorinostat on reservoir size in vivo, we have constructed viral dynamic models of latency that incorporate vorinostat treatment. We fitted these models to data collected from a recent clinical trial in which vorinostat was administered daily for 14 days to HIV-infected individuals on suppressive ART. The results show that HIV transcription is increased transiently during the first few hours or days of treatment and that there is a delay before a sustained increase of HIV transcription, whose duration varies among study participants and may depend on the long term impact of vorinostat on host gene expression. Parameter estimation suggests that in latently infected cells, HIV transcription induced by vorinostat occurs at lower levels than in productively infected cells. Furthermore, the estimated loss rate of transcriptionally induced cells remains close to baseline in most study participants, suggesting vorinostat treatment does not induce latently infected cell killing and thus reduce the latent reservoir in vivo. Combination antiretroviral therapy (cART) for HIV infection must be taken for life due to the existence of long lived latently infected cells. Recent efforts have focused on developing latency reversing agents to eliminate latently infected cells by activating HIV production. In this work, we assess the impact of a latency reversing agent, vorinostat, by fitting dynamic models to data from a clinical trial. Results show that vorinostat treatment induces HIV transcription transiently and that the sustained induction of HIV transcription may depend on the temporal impact of vorinostat on host gene expression. Our results also suggest that vorinostat treatment is not sufficient to induce killing of latently infected cells in a majority of HIV-infected individuals on cART.
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63
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Abstract
Purpose of review HIV targets primary CD4+ T cells. The virus depends on the physiological state of its target cells for efficient replication, and, in turn, viral infection perturbs the cellular state significantly. Identifying the virus–host interactions that drive these dynamic changes is important for a better understanding of viral pathogenesis and persistence. The present review focuses on experimental and computational approaches to study the dynamics of viral replication and latency. Recent findings It was recently shown that only a fraction of the inducible latently infected reservoirs are successfully induced upon stimulation in ex-vivo models while additional rounds of stimulation make allowance for reactivation of more latently infected cells. This highlights the potential role of treatment duration and timing as important factors for successful reactivation of latently infected cells. The dynamics of HIV productive infection and latency have been investigated using transcriptome and proteome data. The cellular activation state has shown to be a major determinant of viral reactivation success. Mathematical models of latency have been used to explore the dynamics of the latent viral reservoir decay. Summary Timing is an important component of biological interactions. Temporal analyses covering aspects of viral life cycle are essential for gathering a comprehensive picture of HIV interaction with the host cell and untangling the complexity of latency. Understanding the dynamic changes tipping the balance between success and failure of HIV particle production might be key to eradicate the viral reservoir.
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Søgaard OS, Graversen ME, Leth S, Olesen R, Brinkmann CR, Nissen SK, Kjaer AS, Schleimann MH, Denton PW, Hey-Cunningham WJ, Koelsch KK, Pantaleo G, Krogsgaard K, Sommerfelt M, Fromentin R, Chomont N, Rasmussen TA, Østergaard L, Tolstrup M. The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo. PLoS Pathog 2015; 11:e1005142. [PMID: 26379282 PMCID: PMC4575032 DOI: 10.1371/journal.ppat.1005142] [Citation(s) in RCA: 434] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/11/2015] [Indexed: 02/06/2023] Open
Abstract
Pharmacologically-induced activation of replication competent proviruses from latency in the presence of antiretroviral treatment (ART) has been proposed as a step towards curing HIV-1 infection. However, until now, approaches to reverse HIV-1 latency in humans have yielded mixed results. Here, we report a proof-of-concept phase Ib/IIa trial where 6 aviremic HIV-1 infected adults received intravenous 5 mg/m2 romidepsin (Celgene) once weekly for 3 weeks while maintaining ART. Lymphocyte histone H3 acetylation, a cellular measure of the pharmacodynamic response to romidepsin, increased rapidly (maximum fold range: 3.7–7.7 relative to baseline) within the first hours following each romidepsin administration. Concurrently, HIV-1 transcription quantified as copies of cell-associated un-spliced HIV-1 RNA increased significantly from baseline during treatment (range of fold-increase: 2.4–5.0; p = 0.03). Plasma HIV-1 RNA increased from <20 copies/mL at baseline to readily quantifiable levels at multiple post-infusion time-points in 5 of 6 patients (range 46–103 copies/mL following the second infusion, p = 0.04). Importantly, romidepsin did not decrease the number of HIV-specific T cells or inhibit T cell cytokine production. Adverse events (all grade 1–2) were consistent with the known side effects of romidepsin. In conclusion, romidepsin safely induced HIV-1 transcription resulting in plasma HIV-1 RNA that was readily detected with standard commercial assays demonstrating that significant reversal of HIV-1 latency in vivo is possible without blunting T cell-mediated immune responses. These finding have major implications for future trials aiming to eradicate the HIV-1 reservoir. One proposed way of curing HIV is to activate virus transcription and kill latently infected cells while the presence of antiretroviral therapy prevents spreading the infection. Induction of global T cell activation by mitogenic or other potent activators effectively reverses HIV-1 from latency ex vivo, but such compounds are generally too toxic for clinical use. Therefore, investigating the capacity of small molecule latency reversing agents to induce production of virus without causing global T cell activation has been a top research priority for scientists in recent years. In the present clinical trial, we demonstrate that significant viral reactivation can be safely induced using the depsipeptide romidepsin (HDAC inhibitor) in long-term suppressed HIV-1 individuals on antiretroviral therapy. Following each romidepsin infusion, we observed clear increases in lymphocyte H3 acetylation, HIV-1 transcription, and plasma HIV-1 RNA. Importantly, this reversal of HIV-1 latency could be measured using standard clinical assays for detection of plasma HIV-1 RNA. Furthermore, romidepsin did not alter the proportion of HIV-specific T cells or inhibit T cell cytokine production which is critically important for future trials combining HDAC inhibitors with interventions (e.g. therapeutic HIV-1 vaccination) designed to enhance killing of latently infected cells.
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Affiliation(s)
- Ole S. Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- * E-mail:
| | - Mette E. Graversen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Steffen Leth
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Rikke Olesen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | | | - Sara K. Nissen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Sofie Kjaer
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mariane H. Schleimann
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Paul W. Denton
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute for Advanced Studies, Aarhus University, Denmark
| | - William J. Hey-Cunningham
- Kirby Institute, University of New South Wales Medicine, University of New South Wales Australia, Sydney, Australia
| | - Kersten K. Koelsch
- Kirby Institute, University of New South Wales Medicine, University of New South Wales Australia, Sydney, Australia
| | - Giuseppe Pantaleo
- Division of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | | | | | | | - Nicolas Chomont
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Faculty of Medicine, Montreal, Quebec, Canada
| | - Thomas A. Rasmussen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
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65
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Abstract
PURPOSE OF REVIEW To explore how ethical considerations, improved diagnostics and data from clinical trials might see the lowering of some of the barriers blocking a cure for HIV infection over the next 5 years. RECENT FINDINGS Despite the recent well publicized but eventually disappointing case reports, there remains only one successful HIV cure, the 'Berlin patient'. We will review the data suggesting that more potent agents might achieve in-vivo viral activation and explore the tantalizing phenomenon of 'posttreatment control' following treatment in primary HIV infection. We will also explore how new assays and novel interventions might move the field forward. SUMMARY There is a need for new agents that can be safely tested to impact the viral reservoir, a more meaningful understanding of how to assay patient samples, and research into mechanisms behind how the reservoir is established and impacted by therapy. With HIV+ve individuals responding so well to antiretroviral therapy, new trials must be tested hand-in-hand with guidance from patient representatives, especially with respect to determining the acceptable risk. The road to a cure is going to be difficult, but it is vital that inevitable disappointments do not detract from the final goal, which remains worth striving for.
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66
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Kakizoe Y, Nakaoka S, Beauchemin CAA, Morita S, Mori H, Igarashi T, Aihara K, Miura T, Iwami S. A method to determine the duration of the eclipse phase for in vitro infection with a highly pathogenic SHIV strain. Sci Rep 2015; 5:10371. [PMID: 25996439 PMCID: PMC4440524 DOI: 10.1038/srep10371] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 04/09/2015] [Indexed: 01/08/2023] Open
Abstract
The time elapsed between successful cell infection and the start of virus production is called the eclipse phase. Its duration is specific to each virus strain and, along with an effective virus production rate, plays a key role in infection kinetics. How the eclipse phase varies amongst cells infected with the same virus strain and therefore how best to mathematically represent its duration is not clear. Most mathematical models either neglect this phase or assume it is exponentially distributed, such that at least some if not all cells can produce virus immediately upon infection. Biologically, this is unrealistic (one must allow for the translation, transcription, export, etc. to take place), but could be appropriate if the duration of the eclipse phase is negligible on the time-scale of the infection. If it is not, however, ignoring this delay affects the accuracy of the mathematical model, its parameter estimates, and predictions. Here, we introduce a new approach, consisting in a carefully designed experiment and simple analytical expressions, to determine the duration and distribution of the eclipse phase in vitro. We find that the eclipse phase of SHIV-KS661 lasts on average one day and is consistent with an Erlang distribution.
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Affiliation(s)
- Yusuke Kakizoe
- Department of Biology, Kyushu University, Fukuoka 812-8581, Japan
| | - Shinji Nakaoka
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | | | - Satoru Morita
- Department of Mathematical and Systems Engineering, Shizuoka University, Shizuoka 432-8561, Japan
| | - Hiromi Mori
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | | | - Kazuyuki Aihara
- 1] Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan [2] Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-8656, Japan
| | - Tomoyuki Miura
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Shingo Iwami
- 1] Department of Biology, Kyushu University, Fukuoka 812-8581, Japan [2] PRESTO, JST, Kawaguchi, Saitama 3320012, Japan [3] CREST, JST, Kawaguchi, Saitama 3320012, Japan
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67
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Pino M, Erkizia I, Benet S, Erikson E, Fernández-Figueras MT, Guerrero D, Dalmau J, Ouchi D, Rausell A, Ciuffi A, Keppler OT, Telenti A, Kräusslich HG, Martinez-Picado J, Izquierdo-Useros N. HIV-1 immune activation induces Siglec-1 expression and enhances viral trans-infection in blood and tissue myeloid cells. Retrovirology 2015; 12:37. [PMID: 25947229 PMCID: PMC4423124 DOI: 10.1186/s12977-015-0160-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/24/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Myeloid cells are key players in the recognition and response of the host against invading viruses. Paradoxically, upon HIV-1 infection, myeloid cells might also promote viral pathogenesis through trans-infection, a mechanism that promotes HIV-1 transmission to target cells via viral capture and storage. The receptor Siglec-1 (CD169) potently enhances HIV-1 trans-infection and is regulated by immune activating signals present throughout the course of HIV-1 infection, such as interferon α (IFNα). RESULTS Here we show that IFNα-activated dendritic cells, monocytes and macrophages have an enhanced ability to capture and trans-infect HIV-1 via Siglec-1 recognition of viral membrane gangliosides. Monocytes from untreated HIV-1-infected individuals trans-infect HIV-1 via Siglec-1, but this capacity diminishes after effective antiretroviral treatment. Furthermore, Siglec-1 is expressed on myeloid cells residing in lymphoid tissues, where it can mediate viral trans-infection. CONCLUSIONS Siglec-1 on myeloid cells could fuel novel CD4(+) T-cell infections and contribute to HIV-1 dissemination in vivo.
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Affiliation(s)
- Maria Pino
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol IGTP, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Itziar Erkizia
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol IGTP, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Susana Benet
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol IGTP, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Elina Erikson
- Institute of Medical Virology, National Reference Center for Retroviruses, University of Frankfurt, Frankfurt, Germany. .,Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, Heidelberg, Germany.
| | | | | | - Judith Dalmau
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol IGTP, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Dan Ouchi
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol IGTP, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Antonio Rausell
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB) - Vital-IT, Lausanne, Switzerland.
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
| | - Oliver T Keppler
- Institute of Medical Virology, National Reference Center for Retroviruses, University of Frankfurt, Frankfurt, Germany.
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland. .,Current address: The J. Craig Venter Institute, La Jolla, CA, USA.
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, Heidelberg, Germany.
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol IGTP, Universitat Autònoma de Barcelona, Badalona, Spain. .,Institució Catalana de Recerca i Estudis Avançats ICREA, Barcelona, Spain. .,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.
| | - Nuria Izquierdo-Useros
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol IGTP, Universitat Autònoma de Barcelona, Badalona, Spain.
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68
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Abstract
Despite effective treatment, HIV is not completely eliminated from the infected organism because of the existence of viral reservoirs. A major reservoir consists of infected resting CD4+ T cells, mostly of memory type, that persist over time due to the stable proviral insertion and a long cellular lifespan. Resting cells do not produce viral particles and are protected from viral-induced cytotoxicity or immune killing. However, these latently infected cells can be reactivated by stochastic events or by external stimuli. The present review focuses on novel genome-wide technologies applied to the study of integration, transcriptome, and proteome characteristics and their recent contribution to the understanding of HIV latency.
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Affiliation(s)
- Angela Ciuffi
- Institute of Microbiology, University Hospital of Lausanne (CHUV), University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland,
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69
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Promoter Targeting RNAs: Unexpected Contributors to the Control of HIV-1 Transcription. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e222. [PMID: 25625613 PMCID: PMC4345301 DOI: 10.1038/mtna.2014.67] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 11/01/2014] [Indexed: 11/22/2022]
Abstract
In spite of prolonged and intensive treatment with combined antiretroviral therapy (cART), which efficiently suppresses plasma viremia, the integrated provirus of HIV-1 persists in resting memory CD4+ T cells as latent infection. Treatment with cART does not substantially reduce the burden of latent infection. Once cART is ceased, HIV-1 replication recrudesces from these reservoirs in the overwhelming majority of patients. There is increasing evidence supporting a role for noncoding RNAs (ncRNA), including microRNAs (miRNAs), antisense (as)RNAs, and short interfering (si)RNA in the regulation of HIV-1 transcription. This appears to be mediated by interaction with the HIV-1 promoter region. Viral miRNAs have the potential to act as positive or negative regulators of HIV transcription. Moreover, inhibition of virally encoded long-asRNA can induce positive transcriptional regulation, while antisense strands of siRNA targeting the NF-κB region suppress viral transcription. An in-depth understanding of the interaction between ncRNAs and the HIV-1 U3 promoter region may lead to new approaches for the control of HIV reservoirs. This review focuses on promoter associated ncRNAs, with particular emphasis on their role in determining whether HIV-1 establishes active or latent infection.
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70
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Del Prete GQ, Shoemaker R, Oswald K, Lara A, Trubey CM, Fast R, Schneider DK, Kiser R, Coalter V, Wiles A, Wiles R, Freemire B, Keele BF, Estes JD, Quiñones OA, Smedley J, Macallister R, Sanchez RI, Wai JS, Tan CM, Alvord WG, Hazuda DJ, Piatak M, Lifson JD. Effect of suberoylanilide hydroxamic acid (SAHA) administration on the residual virus pool in a model of combination antiretroviral therapy-mediated suppression in SIVmac239-infected indian rhesus macaques. Antimicrob Agents Chemother 2014; 58:6790-806. [PMID: 25182644 PMCID: PMC4249371 DOI: 10.1128/aac.03746-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/25/2014] [Indexed: 11/20/2022] Open
Abstract
Nonhuman primate models are needed for evaluations of proposed strategies targeting residual virus that persists in HIV-1-infected individuals receiving suppressive combination antiretroviral therapy (cART). However, relevant nonhuman primate (NHP) models of cART-mediated suppression have proven challenging to develop. We used a novel three-class, six-drug cART regimen to achieve durable 4.0- to 5.5-log reductions in plasma viremia levels and declines in cell-associated viral RNA and DNA in blood and tissues of simian immunodeficiency virus SIVmac239-infected Indian-origin rhesus macaques, then evaluated the impact of treatment with the histone deacetylase inhibitor (HDACi) suberoylanilide hydroxamic acid (SAHA; Vorinostat) on the residual virus pool. Ex vivo SAHA treatment of CD4(+) T cells obtained from cART-suppressed animals increased histone acetylation and viral RNA levels in culture supernatants. cART-suppressed animals each received 84 total doses of oral SAHA. We observed SAHA dose-dependent increases in acetylated histones with evidence for sustained modulation as well as refractoriness following prolonged administration. In vivo virologic activity was demonstrated based on the ratio of viral RNA to viral DNA in peripheral blood mononuclear cells, a presumptive measure of viral transcription, which significantly increased in SAHA-treated animals. However, residual virus was readily detected at the end of treatment, suggesting that SAHA alone may be insufficient for viral eradication in the setting of suppressive cART. The effects observed were similar to emerging data for repeat-dose SAHA treatment of HIV-infected individuals on cART, demonstrating the feasibility, utility, and relevance of NHP models of cART-mediated suppression for in vivo assessments of AIDS virus functional cure/eradication approaches.
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Affiliation(s)
- Gregory Q Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Abigail Lara
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Charles M Trubey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Randy Fast
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Douglas K Schneider
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rebecca Kiser
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Vicky Coalter
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Adam Wiles
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rodney Wiles
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Brandi Freemire
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jacob D Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Octavio A Quiñones
- Statistical Consulting, Data Management Services, Inc., Frederick, Maryland, USA
| | - Jeremy Smedley
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rhonda Macallister
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - John S Wai
- Merck Research Labs, West Point, Pennsylvania, USA
| | | | - W Gregory Alvord
- Statistical Consulting, Data Management Services, Inc., Frederick, Maryland, USA
| | | | - Michael Piatak
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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