1
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Ashokkumar M, Mei W, Peterson JJ, Harigaya Y, Murdoch DM, Margolis DM, Kornfein C, Oesterling A, Guo Z, Rudin CD, Jiang Y, Browne EP. Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae003. [PMID: 38902848 PMCID: PMC11189801 DOI: 10.1093/gpbjnl/qzae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/19/2023] [Indexed: 06/22/2024]
Abstract
Despite the success of antiretroviral therapy, human immunodeficiency virus (HIV) cannot be cured because of a reservoir of latently infected cells that evades therapy. To understand the mechanisms of HIV latency, we employed an integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) approach to simultaneously profile the transcriptomic and epigenomic characteristics of ∼ 125,000 latently infected primary CD4+ T cells after reactivation using three different latency reversing agents. Differentially expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor (TF) activities across the cell population. We identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%-79% accurate at predicting viral reactivation. Finally, we validated the role of two candidate HIV-regulating factors, FOXP1 and GATA3, in viral transcription. These data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.
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Affiliation(s)
- Manickam Ashokkumar
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wenwen Mei
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jackson J Peterson
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yuriko Harigaya
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David M Murdoch
- Department of Medicine, Duke University, Durham, NC 27708, USA
| | - David M Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caleb Kornfein
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Alex Oesterling
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Zhicheng Guo
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Cynthia D Rudin
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Yuchao Jiang
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Edward P Browne
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Mondal A, Sarkar A, Das D, Sengupta A, Kabiraj A, Mondal P, Nag R, Mukherjee S, Das C. Epigenetic orchestration of the DNA damage response: Insights into the regulatory mechanisms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:99-141. [PMID: 39179350 DOI: 10.1016/bs.ircmb.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
The DNA damage response (DDR) is a critical cellular mechanism that safeguards genome integrity and prevents the accumulation of harmful DNA lesions. Increasing evidence highlights the intersection between DDR signaling and epigenetic regulation, offering profound insights into various aspects of cellular function including oncogenesis. This comprehensive review explores the intricate relationship between the epigenetic modifications and DDR activation, with a specific focus on the impact of viral infections. Oncogenic viruses, such as human papillomavirus, hepatitis virus (HBV or HCV), and Epstein-Barr virus have been shown to activate the DDR. Consequently, these DNA damage events trigger a cascade of epigenetic alterations, including changes in DNA methylation patterns, histone modifications and the expression of noncoding RNAs. These epigenetic changes exert profound effects on chromatin structure, gene expression, and maintenance of genome stability. Importantly, elucidation of the viral-induced epigenetic alterations in the context of DDR holds significant implications for comprehending the complexity of cancer and provides potential targets for therapeutic interventions.
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Affiliation(s)
- Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | | | - Dipanwita Das
- Virus Unit [NICED-ICMR], ID and BG Hospital, Kolkata, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Aindrila Kabiraj
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Rachayita Nag
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India.
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3
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Reda O, Monde K, Sugata K, Rahman A, Sakhor W, Rajib SA, Sithi SN, Tan BJY, Niimura K, Motozono C, Maeda K, Ono M, Takeuchi H, Satou Y. HIV-Tocky system to visualize proviral expression dynamics. Commun Biol 2024; 7:344. [PMID: 38509308 PMCID: PMC10954732 DOI: 10.1038/s42003-024-06025-8] [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: 09/05/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
Determinants of HIV-1 latency establishment are yet to be elucidated. HIV reservoir comprises a rare fraction of infected cells that can survive host and virus-mediated killing. In vitro reporter models so far offered a feasible means to inspect this population, but with limited capabilities to dissect provirus silencing dynamics. Here, we describe a new HIV reporter model, HIV-Timer of cell kinetics and activity (HIV-Tocky) with dual fluorescence spontaneous shifting to reveal provirus silencing and reactivation dynamics. This unique feature allows, for the first time, identifying two latent populations: a directly latent, and a recently silenced subset, with the latter having integration features suggestive of stable latency. Our proposed model can help address the heterogeneous nature of HIV reservoirs and offers new possibilities for evaluating eradication strategies.
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Affiliation(s)
- Omnia Reda
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Microbiology Department, High Institute of Public Health, Alexandria University, Alexandria, Egypt
| | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenji Sugata
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Akhinur Rahman
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Wajihah Sakhor
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Sharmin Nahar Sithi
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Benjy Jek Yang Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Koki Niimura
- School of Medicine, Kumamoto University, Kumamoto, Japan
| | - Chihiro Motozono
- Division of Infection and Immunology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kenji Maeda
- Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, London, UK
| | - Hiroaki Takeuchi
- Department of High-risk Infectious Disease Control, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
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4
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Inderbitzin A, Loosli T, Opitz L, Rusert P, Metzner KJ. Transcriptome profiles of latently- and reactivated HIV-1 infected primary CD4+ T cells: A pooled data-analysis. Front Immunol 2022; 13:915805. [PMID: 36090997 PMCID: PMC9459035 DOI: 10.3389/fimmu.2022.915805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
The main obstacle to cure HIV-1 is the latent reservoir. Antiretroviral therapy effectively controls viral replication, however, it does not eradicate the latent reservoir. Latent CD4+ T cells are extremely rare in HIV-1 infected patients, making primary CD4+ T cell models of HIV-1 latency key to understanding latency and thus finding a cure. In recent years several primary CD4+ T cell models of HIV-1 latency were developed to study the underlying mechanism of establishing, maintaining and reversing HIV-1 latency. In the search of biomarkers, primary CD4+ T cell models of HIV-1 latency were used for bulk and single-cell transcriptomics. A wealth of information was generated from transcriptome analyses of different primary CD4+ T cell models of HIV-1 latency using latently- and reactivated HIV-1 infected primary CD4+ T cells. Here, we performed a pooled data-analysis comparing the transcriptome profiles of latently- and reactivated HIV-1 infected cells of 5 in vitro primary CD4+ T cell models of HIV-1 latency and 2 ex vivo studies of reactivated HIV-1 infected primary CD4+ T cells from HIV-1 infected individuals. Identifying genes that are differentially expressed between latently- and reactivated HIV-1 infected primary CD4+ T cells could be a more successful strategy to better understand and characterize HIV-1 latency and reactivation. We observed that natural ligands and coreceptors were predominantly downregulated in latently HIV-1 infected primary CD4+ T cells, whereas genes associated with apoptosis, cell cycle and HLA class II were upregulated in reactivated HIV-1 infected primary CD4+ T cells. In addition, we observed 5 differentially expressed genes that co-occurred in latently- and reactivated HIV-1 infected primary CD4+ T cells, one of which, MSRB2, was found to be differentially expressed between latently- and reactivated HIV-1 infected cells. Investigation of primary CD4+ T cell models of HIV-1 latency that mimic the in vivo state remains essential for the study of HIV-1 latency and thus providing the opportunity to compare the transcriptome profile of latently- and reactivated HIV-1 infected cells to gain insights into differentially expressed genes, which might contribute to HIV-1 latency.
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Affiliation(s)
- Anne Inderbitzin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zürich/University of Zurich, Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J. Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- *Correspondence: Karin J. Metzner,
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5
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Wu L, Pan T, Zhou M, Chen T, Wu S, Lv X, Liu J, Yu F, Guan Y, Liu B, Zhang W, Deng X, Chen Q, Liang A, Lin Y, Wang L, Tang X, Cai W, Li L, He X, Zhang H, Ma X. CBX4 contributes to HIV-1 latency by forming phase-separated nuclear bodies and SUMOylating EZH2. EMBO Rep 2022; 23:e53855. [PMID: 35642598 PMCID: PMC9253744 DOI: 10.15252/embr.202153855] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 04/17/2022] [Accepted: 05/18/2022] [Indexed: 09/13/2023] Open
Abstract
The retrovirus HIV-1 integrates into the host genome and establishes a latent viral reservoir that escapes immune surveillance. Molecular mechanisms of HIV-1 latency have been studied extensively to achieve a cure for the acquired immunodeficiency syndrome (AIDS). Latency-reversing agents (LRAs) have been developed to reactivate and eliminate the latent reservoir by the immune system. To develop more promising LRAs, it is essential to evaluate new therapeutic targets. Here, we find that CBX4, a component of the Polycomb Repressive Complex 1 (PRC1), contributes to HIV-1 latency in seven latency models and primary CD4+ T cells. CBX4 forms nuclear bodies with liquid-liquid phase separation (LLPS) properties on the HIV-1 long terminal repeat (LTR) and recruits EZH2, the catalytic subunit of PRC2. CBX4 SUMOylates EZH2 utilizing its SUMO E3 ligase activity, thereby enhancing the H3K27 methyltransferase activity of EZH2. Our results indicate that CBX4 acts as a bridge between the repressor complexes PRC1 and PRC2 that act synergistically to maintain HIV-1 latency. Dissolution of phase-separated CBX4 bodies could be a potential intervention to reactivate latent HIV-1.
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Affiliation(s)
- Liyang Wu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ting Pan
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenChina
| | - Mo Zhou
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Tao Chen
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Shiyu Wu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Xi Lv
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Jun Liu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Fei Yu
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yuanjun Guan
- Core Laboratory Platform for Medical ScienceZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Bingfeng Liu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Wanying Zhang
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Xiaohui Deng
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenChina
| | - Qianyu Chen
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Anqi Liang
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yingtong Lin
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | | | - Xiaoping Tang
- Department of Infectious DiseasesGuangzhou 8 People's HospitalGuangzhouChina
| | - Weiping Cai
- Department of Infectious DiseasesGuangzhou 8 People's HospitalGuangzhouChina
| | - Linghua Li
- Department of Infectious DiseasesGuangzhou 8 People's HospitalGuangzhouChina
| | - Xin He
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Hui Zhang
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Guangzhou LaboratoryGuangzhou International Bio‐IslandGuangzhouChina
| | - Xiancai Ma
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
- Guangzhou LaboratoryGuangzhou International Bio‐IslandGuangzhouChina
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6
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Kim EH, Manganaro L, Schotsaert M, Brown BD, Mulder LC, Simon V. Development of an HIV reporter virus that identifies latently infected CD4 + T cells. CELL REPORTS METHODS 2022; 2:100238. [PMID: 35784650 PMCID: PMC9243624 DOI: 10.1016/j.crmeth.2022.100238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/26/2022] [Accepted: 05/24/2022] [Indexed: 04/23/2023]
Abstract
There is no cure for HIV infection, as the virus establishes a latent reservoir, which escapes highly active antiretroviral treatments. One major obstacle is the difficulty identifying cells that harbor latent proviruses. We devised a single-round viral vector that carries a series of versatile reporter molecules that are expressed in an LTR-dependent or LTR-independent manner and make it possible to accurately distinguish productive from latent infection. Using primary human CD4+ T cells, we show that transcriptionally silent proviruses are found in more than 50% of infected cells. The latently infected cells harbor proviruses but lack evidence for multiple spliced transcripts. LTR-silent integrations occurred to variable degrees in all CD4+ T subsets examined, with CD4+ TEM and CD4+ TREG displaying the highest frequency of latent infections. This viral vector permits the interrogation of HIV latency at single-cell resolution, revealing mechanisms of latency establishment and allowing the characterization of effective latency-reversing agents.
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Affiliation(s)
- Eun Hye Kim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lara Manganaro
- INGM, Istituto Nazionale di Genetica Molecolare, ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian D. Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lubbertus C.F. Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine at Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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7
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Single-Cell Imaging Shows That the Transcriptional State of the HIV-1 Provirus and Its Reactivation Potential Depend on the Integration Site. mBio 2022; 13:e0000722. [PMID: 35708287 PMCID: PMC9426465 DOI: 10.1128/mbio.00007-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Current antiretroviral treatment fails to cure HIV-1 infection since latent provirus resides in long-lived cellular reservoirs, rebounding whenever therapy is discontinued. The molecular mechanisms underlying HIV-1 latency are complex where the possible link between integration and transcription is poorly understood. HIV-1 integration is targeted toward active chromatin by the direct interaction with a host protein, lens epithelium-derived growth factor (LEDGF/p75). LEDGINs are small-molecule inhibitors of the LEDGF/p75-integrase (IN) interaction that effectively inhibit and retarget HIV-1 integration out of preferred integration sites, resulting in residual provirus that is more latent. Here, we describe a single-cell branched DNA imaging method for simultaneous detection of viral DNA and RNA. We investigated how treatment with LEDGINs affects the location, transcription, and reactivation of HIV-1 in both cell lines and primary cells. This approach demonstrated that LEDGIN-mediated retargeting hampered the baseline transcriptional state and the transcriptional reactivation of the provirus, evidenced by the reduction in viral RNA expression per residual copy. Moreover, treatment of primary cells with LEDGINs induced an enrichment of provirus in deep latency. These results corroborate the impact of integration site selection for the HIV-1 transcriptional state and support block-and-lock functional cure strategies in which the latent reservoir is permanently silenced after retargeting.
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8
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Lindqvist B, Jütte BB, Love L, Assi W, Roux J, Sönnerborg A, Tezil T, Verdin E, Svensson JP. T cell stimulation remodels the latently HIV-1 infected cell population by differential activation of proviral chromatin. PLoS Pathog 2022; 18:e1010555. [PMID: 35666761 PMCID: PMC9203004 DOI: 10.1371/journal.ppat.1010555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/16/2022] [Accepted: 04/26/2022] [Indexed: 01/22/2023] Open
Abstract
The reservoir of latently HIV-1 infected cells is heterogeneous. To achieve an HIV-1 cure, the reservoir of activatable proviruses must be eliminated while permanently silenced proviruses may be tolerated. We have developed a method to assess the proviral nuclear microenvironment in single cells. In latently HIV-1 infected cells, a zinc finger protein tethered to the HIV-1 promoter produced a fluorescent signal as a protein of interest came in its proximity, such as the viral transactivator Tat when recruited to the nascent RNA. Tat is essential for viral replication. In these cells we assessed the proviral activation and chromatin composition. By linking Tat recruitment to proviral activity, we dissected the mechanisms of HIV-1 latency reversal and the consequences of HIV-1 production. A pulse of promoter-associated Tat was identified that contrasted to the continuous production of viral proteins. As expected, promoter H3K4me3 led to substantial expression of the provirus following T cell stimulation. However, the activation-induced cell cycle arrest and death led to a surviving cell fraction with proviruses encapsulated in repressive chromatin. Further, this cellular model was used to reveal mechanisms of action of small molecules. In a proof-of-concept study we determined the effect of modifying enhancer chromatin on HIV-1 latency reversal. Only proviruses resembling active enhancers, associated with H3K4me1 and H3K27ac and subsequentially recognized by BRD4, efficiently recruited Tat upon cell stimulation. Tat-independent HIV-1 latency reversal of unknown significance still occurred. We present a method for single cell assessment of the microenvironment of the latent HIV-1 proviruses, used here to reveal how T cell stimulation modulates the proviral activity and how the subsequent fate of the infected cell depends on the chromatin context.
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Affiliation(s)
- Birgitta Lindqvist
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Bianca B. Jütte
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Luca Love
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Wlaa Assi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Laboratory of Viral Infectious Diseases, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Julie Roux
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden, Division of Infectious Diseases, Department of Medicine Huddinge, I73, Karolinska University Hospital, Stockholm, Sweden
| | - Tugsan Tezil
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - J. Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- * E-mail:
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9
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Abstract
The development of therapies to eliminate the latent HIV-1 reservoir is hampered by our incomplete understanding of the biomolecular mechanism governing HIV-1 latency. To further complicate matters, recent single cell RNA-seq studies reported extensive heterogeneity between latently HIV-1-infected primary T cells, implying that latent HIV-1 infection can persist in greatly differing host cell environments. We here show that transcriptomic heterogeneity is also found between latently infected T cell lines, which allowed us to study the underlying mechanisms of intercell heterogeneity at high signal resolution. Latently infected T cells exhibited a de-differentiated phenotype, characterized by the loss of T cell-specific markers and gene regulation profiles reminiscent of hematopoietic stem cells (HSC). These changes had functional consequences. As reported for stem cells, latently HIV-1 infected T cells efficiently forced lentiviral superinfections into a latent state and favored glycolysis. As a result, metabolic reprogramming or cell re-differentiation destabilized latent infection. Guided by these findings, data-mining of single cell RNA-seq data of latently HIV-1 infected primary T cells from patients revealed the presence of similar dedifferentiation motifs. >20% of the highly detectable genes that were differentially regulated in latently infected cells were associated with hematopoietic lineage development (e.g. HUWE1, IRF4, PRDM1, BATF3, TOX, ID2, IKZF3, CDK6) or were hematopoietic markers (SRGN; hematopoietic proteoglycan core protein). The data add to evidence that the biomolecular phenotype of latently HIV-1 infected cells differs from normal T cells and strategies to address their differential phenotype need to be considered in the design of therapeutic cure interventions. IMPORTANCE HIV-1 persists in a latent reservoir in memory CD4 T cells for the lifetime of a patient. Understanding the biomolecular mechanisms used by the host cells to suppress viral expression will provide essential insights required to develop curative therapeutic interventions. Unfortunately, our current understanding of these control mechanisms is still limited. By studying gene expression profiles, we demonstrated that latently HIV-1-infected T cells have a de-differentiated T cell phenotype. Software-based data integration allowed for the identification of drug targets that would re-differentiate viral host cells and, in extension, destabilize latent HIV-1 infection events. The importance of the presented data lies within the clear demonstration that HIV-1 latency is a host cell phenomenon. As such, therapeutic strategies must first restore proper host cell functionality to accomplish efficient HIV-1 reactivation.
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10
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Buttler CA, Chuong EB. Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev 2022; 305:165-178. [PMID: 34816452 PMCID: PMC8766910 DOI: 10.1111/imr.13042] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023]
Abstract
In recent years, there has been significant progress toward understanding the transcriptional networks underlying mammalian immune responses, fueled by advances in regulatory genomic technologies. Epigenomic studies profiling immune cells have generated detailed genome-wide maps of regulatory elements that will be key to deciphering the regulatory networks underlying cellular immune responses and autoimmune disorders. Unbiased analyses of these genomic maps have uncovered endogenous retroviruses as an unexpected ally in the regulation of human immune systems. Despite their parasitic origins, studies are finding an increasing number of examples of retroviral sequences having been co-opted for beneficial immune function and regulation by the host cell. Here, we review how endogenous retroviruses have given rise to numerous regulatory elements that shape the epigenetic landscape of host immune responses. We will discuss the implications of these elements on the function, dysfunction, and evolution of innate immunity.
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11
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021. [PMID: 34728591 PMCID: PMC8550911 DOI: 10.1007/s12038-021-00215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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12
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Aso H, Nagaoka S, Kawakami E, Ito J, Islam S, Tan BJY, Nakaoka S, Ashizaki K, Shiroguchi K, Suzuki Y, Satou Y, Koyanagi Y, Sato K. Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In Vivo. Cell Rep 2021; 32:107887. [PMID: 32668246 DOI: 10.1016/j.celrep.2020.107887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
For eradication of HIV-1 infection, it is important to elucidate the detailed features and heterogeneity of HIV-1-infected cells in vivo. To reveal multiple characteristics of HIV-1-producing cells in vivo, we use a hematopoietic-stem-cell-transplanted humanized mouse model infected with GFP-encoding replication-competent HIV-1. We perform multiomics experiments using recently developed technology to identify the features of HIV-1-infected cells. Genome-wide HIV-1 integration-site analysis reveals that productive HIV-1 infection tends to occur in cells with viral integration into transcriptionally active genomic regions. Bulk transcriptome analysis reveals that a high level of viral mRNA is transcribed in HIV-1-infected cells. Moreover, single-cell transcriptome analysis shows the heterogeneity of HIV-1-infected cells, including CXCL13high cells and a subpopulation with low expression of interferon-stimulated genes, which can contribute to efficient viral spread in vivo. Our findings describe multiple characteristics of HIV-1-producing cells in vivo, which could provide clues for the development of an HIV-1 cure.
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Affiliation(s)
- Hirofumi Aso
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Shumpei Nagaoka
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Eiryo Kawakami
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan; Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba 2608670, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Saiful Islam
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Benjy Jek Yang Tan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 0600810, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Koichi Ashizaki
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan
| | - Katsuyuki Shiroguchi
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 5650874, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 2300045, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 2778561, Japan
| | - Yorifumi Satou
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan.
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13
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Janssens J, Bruggemans A, Christ F, Debyser Z. Towards a Functional Cure of HIV-1: Insight Into the Chromatin Landscape of the Provirus. Front Microbiol 2021; 12:636642. [PMID: 33868195 PMCID: PMC8044952 DOI: 10.3389/fmicb.2021.636642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Despite potent combination antiretroviral therapy, HIV-1 infection persists due to irreversible integration of the virus in long-living cells of the immune system. The main focus of HIV-1 cure strategies has been on HIV-1 eradication, yet without great success so far. Therefore, HIV-1 remission or a functional cure, whereby the virus is silenced rather than eradicated, is considered as an alternative strategy. Elite controllers, individuals who spontaneously control HIV-1, may point us the way toward a functional HIV-1 cure. In order to achieve such a cure, a profound understanding of the mechanisms controlling HIV-1 expression and silencing is needed. In recent years, evidence has grown that the site of integration as well as the chromatin landscape surrounding the integration site affects the transcriptional state of the provirus. Still, at present, the impact of integration site selection on the establishment and maintenance of the HIV-1 reservoirs remains poorly understood. The discovery of LEDGF/p75 as a binding partner of HIV-1 integrase has led to a better understanding of integration site selection. LEDGF/p75 is one of the important determinants of integration site selection and targets integration toward active genes. In this review, we will provide an overview of the most important determinants of integration site selection. Secondly, we will discuss the chromatin landscape at the integration site and its implications on HIV-1 gene expression and silencing. Finally, we will discuss how interventions that affect integration site selection or modifications of the chromatin could yield a functional cure of HIV-1 infection.
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Affiliation(s)
- Julie Janssens
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Anne Bruggemans
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
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14
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021; 46:94. [PMID: 34728591 PMCID: PMC8550911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/20/2021] [Indexed: 02/11/2023]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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Affiliation(s)
- Ramisetti Rajeev
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Ambey Prasad Dwivedi
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anunay Sinha
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Viplove Agarwaal
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | | | - Anjana Kar
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Institute of Microbial Technology (IMTech), Chandigarh, India
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15
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Vansant G, Chen HC, Zorita E, Trejbalová K, Miklík D, Filion G, Debyser Z. The chromatin landscape at the HIV-1 provirus integration site determines viral expression. Nucleic Acids Res 2020; 48:7801-7817. [PMID: 32597987 PMCID: PMC7641320 DOI: 10.1093/nar/gkaa536] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
HIV-1 persists lifelong in memory cells of the immune system as latent provirus that rebounds upon treatment interruption. Therefore, the latent reservoir is the main target for an HIV cure. Here, we studied the direct link between integration site and transcription using LEDGINs and Barcoded HIV-ensembles (B-HIVE). LEDGINs are antivirals that inhibit the interaction between HIV-1 integrase and the chromatin-tethering factor LEDGF/p75. They were used as a tool to retarget integration, while the effect on HIV expression was measured with B-HIVE. B-HIVE tracks insert-specific HIV expression by tagging a unique barcode in the HIV genome. We confirmed that LEDGINs retarget integration out of gene-dense and actively transcribed regions. The distance to H3K36me3, the marker recognized by LEDGF/p75, clearly increased. LEDGIN treatment reduced viral RNA expression and increased the proportion of silent provirus. Finally, silent proviruses obtained after LEDGIN treatment were located further away from epigenetic marks associated with active transcription. Interestingly, proximity to enhancers stimulated transcription irrespective of LEDGIN treatment, while the distance to H3K36me3 only changed after treatment with LEDGINs. The fact that proximity to these markers are associated with RNA expression support the direct link between provirus integration site and viral expression.
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Affiliation(s)
- Gerlinde Vansant
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Flanders, Belgium
| | - Heng-Chang Chen
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalunya, Spain
| | - Eduard Zorita
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalunya, Spain
| | - Katerina Trejbalová
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska, Prague, Czech Republic
| | - Dalibor Miklík
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska, Prague, Czech Republic
| | - Guillaume Filion
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalunya, Spain.,University Pompeu Fabra, Barcelona, Catalunya, Spain
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Flanders, Belgium
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16
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CBF-1 Promotes the Establishment and Maintenance of HIV Latency by Recruiting Polycomb Repressive Complexes, PRC1 and PRC2, at HIV LTR. Viruses 2020; 12:v12091040. [PMID: 32961937 PMCID: PMC7551090 DOI: 10.3390/v12091040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022] Open
Abstract
The C-promoter binding factor-1 (CBF-1) is a potent and specific inhibitor of the human immunodeficiency virus (HIV)-1 LTR promoter. Here, we demonstrate that the knockdown of endogenous CBF-1 in latently infected primary CD4+ T cells, using specific small hairpin RNAs (shRNA), resulted in the reactivation of latent HIV proviruses. Chromatin immunoprecipitation (ChIP) assays using latently infected primary T cells and Jurkat T-cell lines demonstrated that CBF-1 induces the establishment and maintenance of HIV latency by recruiting polycomb group (PcG/PRC) corepressor complexes or polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Knockdown of CBF-1 resulted in the dissociation of PRCs corepressor complexes enhancing the recruitment of RNA polymerase II (RNAP II) at HIV LTR. Knockdown of certain components of PRC1 and PRC2 also led to the reactivation of latent proviruses. Similarly, the treatment of latently infected primary CD4+ T cells with the PRC2/EZH2 inhibitor, 3-deazaneplanocin A (DZNep), led to their reactivation.
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17
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Turner AMW, Dronamraju R, Potjewyd F, James KS, Winecoff DK, Kirchherr JL, Archin NM, Browne EP, Strahl BD, Margolis DM, James LI. Evaluation of EED Inhibitors as a Class of PRC2-Targeted Small Molecules for HIV Latency Reversal. ACS Infect Dis 2020; 6:1719-1733. [PMID: 32347704 PMCID: PMC7359025 DOI: 10.1021/acsinfecdis.9b00514] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
A hallmark of human
immunodeficiency type-1 (HIV) infection is
the integration of the viral genome into host chromatin, resulting
in a latent reservoir that persists despite antiviral therapy or immune
response. Thus, key priorities toward eradication of HIV infection
are to understand the mechanisms that allow HIV latency and to develop
latency reversal agents (LRAs) that can facilitate the clearance of
latently infected cells. The repressive H3K27me3 histone mark, catalyzed
by the PRC2 complex, plays a pivotal role in transcriptional repression
at the viral promoter in both cell line and primary CD4+ T cell models
of latency. EZH2 inhibitors which block H3K27 methylation have been
shown to act as LRAs, suggesting other PRC2 components could also
be potential targets for latency reversal. EED, a core component of
PRC2, ensures the propagation of H3K27me3 by allosterically activating
EZH2 methyltransferase activity. Therefore, we sought to investigate
if inhibition of EED would also reverse latency. Inhibitors of EED,
EED226 and A-395, demonstrated latency reversal activity as single
agents, and this activity was further enhanced when used in combination
with other known LRAs. Loss of H3K27me3 following EED inhibition significantly
increased the levels of H3K27 acetylation globally and at the HIV
LTR. These results further confirm that PRC2 mediated repression plays
a significant role in the maintenance of HIV latency and suggest that
EED may serve as a promising new target for LRA development.
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Affiliation(s)
- Anne-Marie W. Turner
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Raghuvar Dronamraju
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Frances Potjewyd
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Katherine S. James
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Daniel K. Winecoff
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Jennifer L. Kirchherr
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Nancie M. Archin
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Edward P. Browne
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Brian D. Strahl
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - David M. Margolis
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, Chapel Hill, North Carolina 27599, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- UNC HIV Cure Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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18
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Abstract
Human immunodeficiency virus 1 (HIV-1) replicates through the integration of its viral DNA into the genome of human immune target cells. Chronically infected individuals thus carry a genomic burden of virus-derived sequences that persists through antiretroviral therapy. This burden consists of a small fraction of intact, but transcriptionally silenced, i.e. latent, viral genomes and a dominant fraction of defective sequences. Remarkably, all viral-derived sequences are subject to interaction with host cellular physiology at various levels. In this review, we focus on epigenetic aspects of this interaction. We provide a comprehensive overview of how epigenetic mechanisms contribute to establishment and maintenance of HIV-1 gene repression during latency. We furthermore summarize findings indicating that HIV-1 infection leads to changes in the epigenome of target and bystander immune cells. Finally, we discuss how an improved understanding of epigenetic features and mechanisms involved in HIV-1 infection could be exploited for clinical use.
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19
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Chromatin maturation of the HIV-1 provirus in primary resting CD4+ T cells. PLoS Pathog 2020; 16:e1008264. [PMID: 31999790 PMCID: PMC6991963 DOI: 10.1371/journal.ppat.1008264] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is a chronic condition, where viral DNA integrates into the genome. Latently infected cells form a persistent, heterogeneous reservoir that at any time can reactivate the integrated HIV-1. Here we confirmed that latently infected cells from HIV-1 positive study participants exhibited active HIV-1 transcription but without production of mature spliced mRNAs. To elucidate the mechanisms behind this we employed primary HIV-1 latency models to study latency establishment and maintenance. We characterized proviral transcription and chromatin development in cultures of resting primary CD4+ T-cells for four months after ex vivo HIV-1 infection. As heterochromatin (marked with H3K9me3 or H3K27me3) gradually stabilized, the provirus became less accessible with reduced activation potential. In a subset of infected cells, active marks (e.g. H3K27ac) and elongating RNAPII remained detectable at the latent provirus, despite prolonged proviral silencing. In many aspects, latent HIV-1 resembled an active enhancer in a subset of resting cells. The enhancer chromatin actively promoted latency and the enhancer-specific CBP/P300-inhibitor GNE049 was identified as a new latency reversal agent. The division of the latent reservoir according to distinct chromatin compositions with different reactivation potential enforces the notion that even though a relatively large set of cells contains the HIV-1 provirus, only a discrete subset is readily able to reactivate the provirus and spread the infection. HIV infection is a devastating disease affecting 35 million people worldwide. Current anti-retroviral treatment is highly effective and has made the HIV infection chronic. However, despite more effective treatments, the prospects of a cure are distant. The problem for an HIV cure is that, even though the virus particles are eradicated, the infected cells maintain the information of remake the virus. This information is integrated in the host cell as a provirus. The provirus switches between active and inactive states. Thereby, the infected cells evade both the immune system and death associated with massive viral production. We have characterized the composition of proviral chromatin and how it connects with transcription and viral production. In resting primary CD4+ T-cells, we follow the fate of the provirus starting at infection until latency is firmly established. Only in a fraction of intact proviruses were we able to reverse latency and that this was highly regulated by the chromatin composition. Whereas the proviruses encompassed in heterochromatin were refractory to activation, latent proviruses with “enhancer” characteristics were readily activated. Our study provides key insights as to detect the remaining HIV-1 infected cells capable of reseeding the infection, and the mechanisms whereby they are maintained.
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20
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Qu D, Sun WW, Li L, Ma L, Sun L, Jin X, Li T, Hou W, Wang JH. Long noncoding RNA MALAT1 releases epigenetic silencing of HIV-1 replication by displacing the polycomb repressive complex 2 from binding to the LTR promoter. Nucleic Acids Res 2019; 47:3013-3027. [PMID: 30788509 PMCID: PMC6451131 DOI: 10.1093/nar/gkz117] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/10/2019] [Accepted: 02/14/2019] [Indexed: 12/23/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) may either repress or activate HIV-1 replication and latency; however, specific mechanisms for their action are not always clear. In HIV-1 infected CD4+ T cells, we performed RNA-Sequencing (RNA-Seq) analysis and discovered an up-regulation of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), an lncRNA previously described in cancer cells that associate with cancer pathogenesis. Moreover, we found that MALAT1 promoted HIV-1 transcription and infection, as its knockdown by CRISPR/Cas9 markedly reduced the HIV-1 long terminal repeat (LTR)-driven gene transcription and viral replication. Mechanistically, through an association with chromatin modulator polycomb repressive complex 2 (PRC2), MALAT1 detached the core component enhancer of zeste homolog 2 (EZH2) from binding with HIV-1 LTR promoter, and thus removed PRC2 complex-mediated methylation of histone H3 on lysine 27 (H3K27me3) and relieved epigenetic silencing of HIV-1 transcription. Moreover, the reactivation of HIV-1 stimulated with latency reversal agents (LRAs) induced MALAT1 expression in latently infected cells. Successful combination antiretroviral therapy (cART) was accompanied by significantly diminished MALAT1 expression in patients, suggesting a positive correlation of MALAT1 expression with HIV-1 replication. Our data have identified MALAT1 as a promoter of HIV-1 transcription, and suggested that MALAT1 may be targeted for the development of new therapeutics.
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Affiliation(s)
- Di Qu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Wei-Wei Sun
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Li Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430070, China.,State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei 430070, China
| | - Li Ma
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Sun
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xia Jin
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wei Hou
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430070, China.,State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei 430070, China
| | - Jian-Hua Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100039, China
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21
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Cortés-Rubio CN, Salgado-Montes de Oca G, Prado-Galbarro FJ, Matías-Florentino M, Murakami-Ogasawara A, Kuri-Cervantes L, Carranco-Arenas AP, Ormsby CE, Cortés-Rubio IK, Reyes-Terán G, Ávila-Ríos S. Longitudinal variation in human immunodeficiency virus long terminal repeat methylation in individuals on suppressive antiretroviral therapy. Clin Epigenetics 2019; 11:134. [PMID: 31519219 PMCID: PMC6743183 DOI: 10.1186/s13148-019-0735-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/30/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Persistence of latent, replication-competent provirus in CD4+ T cells of human immunodeficiency virus (HIV)-infected individuals on antiretroviral treatment (ART) is the main obstacle for virus eradication. Methylation of the proviral 5' long terminal repeat (LTR) promoter region has been proposed as a possible mechanism contributing to HIV latency; however, conflicting observations exist regarding its relevance. We assessed 5'-LTR methylation profiles in total CD4+ T cells from blood of 12 participants on short-term ART (30 months) followed up for 2 years, and a cross-sectional group of participants with long-term ART (6-15 years), using next generation sequencing. We then looked for associations between specific 5'-LTR methylation patterns and baseline and follow-up clinical characteristics. RESULTS 5'-LTR methylation was observed in all participants and behaved dynamically. The number of 5'-LTR variants found per sample ranged from 1 to 13, with median sequencing depth of 16270× (IQR 4107×-46760×). An overall significant 5'-LTR methylation increase was observed at month 42 compared to month 30 (median CpG Methylation Index: 74.7% vs. 0%, p = 0.025). This methylation increase was evident in a subset of participants (methylation increase group), while the rest maintained fairly high and constant methylation (constant methylation group). Persons in the methylation increase group were younger, had higher CD4+ T cell gain, larger CD8% decrease, and larger CD4/CD8 ratio change after 48 months on ART (all p < 0.001). Using principal component analysis, the constant methylation and methylation increase groups showed low evidence of separation along time (factor 2: p = 0.04). Variance was largely explained (21%) by age, CD4+/CD8+ T cell change, and CD4+ T cell subpopulation proportions. Persons with long-term ART showed overall high methylation (median CpG Methylation Index: 78%; IQR 71-87%). No differences were observed in residual plasma viral load or proviral load comparing individuals on short-term (both at 30 or 42 months) and long-term ART. CONCLUSIONS Our study shows evidence that HIV 5'-LTR methylation in total CD4+ T cells is dynamic along time and that it can follow different temporal patterns that are associated with a combination of baseline and follow-up clinical characteristics. These observations may account for differences observed between previous contrasting studies.
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Affiliation(s)
- César N. Cortés-Rubio
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Gonzalo Salgado-Montes de Oca
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | | | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Ana P. Carranco-Arenas
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Christopher E. Ormsby
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | | | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
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22
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Wang J, Yang Z, Cheng L, Lu L, Pan K, Yang J, Wu N. Retinoblastoma binding protein 4 represses HIV-1 long terminal repeat-mediated transcription by recruiting NR2F1 and histone deacetylase. Acta Biochim Biophys Sin (Shanghai) 2019; 51:934-944. [PMID: 31435636 DOI: 10.1093/abbs/gmz082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Indexed: 01/22/2023] Open
Abstract
Human immunodeficiency virus (HIV) transcription is closely associated with chromatin remodeling. Retinoblastoma binding protein 4 (RBBP4) is a histone chaperone implicated in chromatin remodeling. However, the role of RBBP4 in HIV-1 infection and the underlying mechanism remain elusive. In the present study, we showed that RBBP4 plays a negative regulatory role during HIV-1 infection. RBBP4 expression was significantly increased in HIV-1-infected T cells. RBBP4 binds to the HIV-1 long terminal repeat (LTR), represses HIV-1 LTR-mediated transcription through recruiting nuclear receptor subfamily 2 group F member 1(NR2F1) and histone deacetylase 1 and 2 (HDAC1/2) to HIV-1 LTR, and further controls local histone 3 (H3) deacetylation and chromatin compaction. Furthermore, the occupancy of RBBP4, HDAC1/2, and NR2F1 on LTR in HIV-latent J-lat cells was significantly higher than that in HIV-1-activated cells. In conclusion, our results establish RBBP4 as a new potent antiretroviral factor, which may provide theoretical basis for the treatment of HIV in the future.
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Affiliation(s)
- Juan Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Zongxing Yang
- The Second Department of Infectious Disease, Xixi Hospital of Hangzhou, Hangzhou, China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lingna Lu
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Kenv Pan
- Department of Clinical Laboratory, Xixi Hospital of Hangzhou, Hangzhou, China
| | - Jin Yang
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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23
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Liu Y, Niu Y, Li L, Timani KA, He VL, Sanburns C, Xie J, He JJ. Tat expression led to increased histone 3 tri-methylation at lysine 27 and contributed to HIV latency in astrocytes through regulation of MeCP2 and Ezh2 expression. J Neurovirol 2019; 25:508-519. [PMID: 31020497 PMCID: PMC6750972 DOI: 10.1007/s13365-019-00751-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/03/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023]
Abstract
Astrocytes are susceptible to HIV infection and potential latent HIV reservoirs. Tat is one of three abundantly expressed HIV early genes in HIV-infected astrocytes and has been shown to be a major pathogenic factor for HIV/neuroAIDS. In this study, we sought to determine if and how Tat expression would affect HIV infection and latency in astrocytes. Using the glycoprotein from vesicular stomatitis virus-pseudotyped red-green HIV (RGH) reporter viruses, we showed that HIV infection was capable of establishing HIV latency in astrocytes. We also found that Tat expression decreased the generation of latent HIV-infected cells. Activation of latent HIV-infected astrocytes showed that treatment of GSK126, a selective inhibitor of methyltransferase enhancer of zeste homolog 2 (Ezh2) that is specifically responsible for tri-methylation of histone 3 lysine 27 (H3K27me3), led to activation of significantly more latent HIV-infected Tat-expressing astrocytes. Molecular analysis showed that H3K27me3, Ezh2, MeCP2, and Tat all exhibited a similar bimodal expression kinetics in the course of HIV infection and latency in astrocytes, although H3K27me3, Ezh2, and MeCP2 were expressed higher in Tat-expressing astrocytes and their expression were peaked immediately preceding Tat expression. Subsequent studies showed that Tat expression alone was sufficient to induce H3K27me3 expression, likely through its regulation of Ezh2 and MeCP2 expression. Taken together, these results showed for the first time that Tat expression induced H3K27me3 expression and contributed to HIV latency in astrocytes and suggest a new role and novel mechanism for Tat in HIV latency.
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Affiliation(s)
- Ying Liu
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA.
| | - Yinghua Niu
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Lu Li
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Khalid A Timani
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Victor L He
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Chris Sanburns
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Jiafeng Xie
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
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24
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Horsburgh BA, Palmer S. Measuring HIV Persistence on Antiretroviral Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1075:265-284. [PMID: 30030797 DOI: 10.1007/978-981-13-0484-2_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In order to determine if an eradication strategy for HIV is effective, it will be important to measure persistent replication-competent virus, the current barrier to a cure. Various assays are available that measure persistent virus, each with advantages and disadvantages that must be balanced in order to select the best assay for the experimental aim. Assays of free virus do not measure the latent form of the virus but can be utilised in conjunction with other assays in order to better understand HIV persistence on ART. The quantitative viral outgrowth assay (QVOA) is the gold standard assay for measuring persistent replication-competent virus, but it, along with assays that vary the classical QVOA method, underestimates the frequency of latently infected cells in blood due to the presence of non-induced yet intact and replication-competent proviruses. Assays that quantify or sequence specific genomic regions of HIV overestimate the size of the reservoir as they are unable to distinguish between intact and defective virus. As an alternative, sequencing the full-length integrated genome can better distinguish replication-competent provirus, but these methods may be expensive and time-consuming. Novel assays, and the application of these assays to novel questions, will be key to the development of future curative therapies for HIV.
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Affiliation(s)
- Bethany A Horsburgh
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia.
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
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25
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Spontaneous reactivation of latent HIV-1 promoters is linked to the cell cycle as revealed by a genetic-insulators-containing dual-fluorescence HIV-1-based vector. Sci Rep 2018; 8:10204. [PMID: 29977044 PMCID: PMC6033903 DOI: 10.1038/s41598-018-28161-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
Long-lived latently HIV-1-infected cells represent a barrier to cure. We developed a dual-fluorescence HIV-1-based vector containing a pair of genetic insulators flanking a constitutive fluorescent reporter gene to study HIV-1 latency. The protective effects of these genetic insulators are demonstrated through long-term (up to 394 days) stable fluorescence profiles in transduced SUP-T1 cells. Analysis of 1,941 vector integration sites confirmed reproduction of HIV-1 integration patterns. We sorted monoclonal cells representing latent HIV-1 infections and found that both vector integration sites and integrity of the vector genomes influence the reactivation potentials of latent HIV-1 promoters. Interestingly, some latent monoclonal cells exhibited a small cell subpopulation with a spontaneously reactivated HIV-1 promoter. Higher expression levels of genes involved in cell cycle progression are observed in these cell subpopulations compared to their counterparts with HIV-1 promoters that remained latent. Consistently, larger fractions of spontaneously reactivated cells are in the S and G2 phases of the cell cycle. Furthermore, genistein and nocodazole treatments of these cell clones, which halted cells in the G2 phase, resulted in a 1.4–2.9-fold increase in spontaneous reactivation. Taken together, our HIV-1 latency model reveals that the spontaneous reactivation of latent HIV-1 promoters is linked to the cell cycle.
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26
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McGettrick PMC, Barco EA, Kaminskiy G, Mallon PWG. The immune profile in HIV: A useful signature in future HIV research? Germs 2018; 8:54-57. [PMID: 29951377 DOI: 10.18683/germs.2018.1131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Padraig M C McGettrick
- MB BCh BAO, MRCPI, HIV Molecular Research Group, UCD School of Medicine, Catherine McAuely Education and Research Centre, Nelson Street, Dublin 7, Dublin, Ireland, Department of Infectious Diseases, Mater Misericordae University Hospital, Eccles Street, Dublin 7, Ireland
| | - Elena Alvarez Barco
- BSc, PhD, HIV Molecular Research Group, UCD School of Medicine, Catherine McAuely Education and Research Centre, Nelson Street, Dublin 7, Dublin, Ireland
| | - Greg Kaminskiy
- MD, National Medical Research Centre of Phthisiopulmonology and Infectious Diseases, Moscow, Russian Federation
| | - Patrick W G Mallon
- BSc FRACP MB BCh BAO PhD, HIV Molecular Research Group, UCD School of Medicine, Catherine McAuely Education and Research Centre, Nelson Street, Dublin 7, Dublin, Ireland, Department of Infectious Diseases, Mater Misericordae University Hospital, Eccles Street, Dublin 7, Ireland
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27
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Hofmann S, Dehn S, Businger R, Bolduan S, Schneider M, Debyser Z, Brack-Werner R, Schindler M. Dual role of the chromatin-binding factor PHF13 in the pre- and post-integration phases of HIV-1 replication. Open Biol 2018; 7:rsob.170115. [PMID: 29021215 PMCID: PMC5666080 DOI: 10.1098/rsob.170115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/08/2017] [Indexed: 12/23/2022] Open
Abstract
Viruses interact with multiple host cell factors. Some of these are required to promote viral propagation, others have roles in inhibiting infection. Here, we delineate the function of the cellular factor PHF13 (or SPOC1), a putative HIV-1 restriction factor. Early in the HIV-1 replication cycle PHF13 increased the number of integrated proviral copies and the number of infected cells. However, after HIV-1 integration, high levels of PHF13 suppressed viral gene expression. The antiviral activity of PHF13 is counteracted by the viral accessory protein Vpr, which mediates PHF13 degradation. Altogether, the transcriptional master regulator and chromatin binding protein PHF13 does not have purely repressive effects on HIV-1 replication, but also promotes viral integration. By the functional characterization of the dual role of PHF13 during the HIV-1 replication cycle, we reveal a surprising and intricate mechanism through which HIV-1 might regulate the switch from integration to viral gene expression. Furthermore, we identify PHF13 as a cellular target specifically degraded by HIV-1 Vpr.
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Affiliation(s)
- Stephan Hofmann
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Sandra Dehn
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Ramona Businger
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Bolduan
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Martha Schneider
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Leuven, Belgium
| | - Ruth Brack-Werner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Michael Schindler
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany .,Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
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28
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Kobayashi-Ishihara M, Terahara K, Martinez JP, Yamagishi M, Iwabuchi R, Brander C, Ato M, Watanabe T, Meyerhans A, Tsunetsugu-Yokota Y. HIV LTR-Driven Antisense RNA by Itself Has Regulatory Function and May Curtail Virus Reactivation From Latency. Front Microbiol 2018; 9:1066. [PMID: 29887842 PMCID: PMC5980963 DOI: 10.3389/fmicb.2018.01066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/04/2018] [Indexed: 01/21/2023] Open
Abstract
Latently infected T lymphocytes are an important barrier toward eliminating a persistent HIV infection. Here we describe an HIV-based recombinant fluorescent-lentivirus referred to as “rfl-HIV” that enables to analyze sense and antisense transcription by means of fluorescence reporter genes. This model virus exhibited similar transcriptional and functional properties of the antisense transcript as observed with a wild type HIV, and largely facilitated the generation of latently-infected T cells clones. We show that latently-infected cells can be divided into two types, those with and those without antisense transcription. Upon addition of latency reversal agents, only the cells that lack antisense transcripts are readily reactivated to transcribe HIV. Thus, antisense transcripts may exhibit a dominant suppressor activity and can lock an integrated provirus into a non-reactivatable state. These findings could have important implications for the development of strategies to eradicate HIV from infected individuals.
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Affiliation(s)
- Mie Kobayashi-Ishihara
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan.,Infection Biology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Kazutaka Terahara
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Javier P Martinez
- Infection Biology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Makoto Yamagishi
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryutaro Iwabuchi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Christian Brander
- IrsiCaixa - AIDS Research Institute, Badalona, Spain.,Universitat de Vic-Universitat Central de Catalunya, Vic, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshiki Watanabe
- Department of Advanced Medical Innovation, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Andreas Meyerhans
- Infection Biology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Yasuko Tsunetsugu-Yokota
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan.,Infection Biology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Department of Medical Technology, School of Human Sciences, Tokyo University of Technology, Tokyo, Japan
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29
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García M, Buzón MJ, Benito JM, Rallón N. Peering into the HIV reservoir. Rev Med Virol 2018; 28:e1981. [PMID: 29744964 DOI: 10.1002/rmv.1981] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 12/11/2022]
Abstract
The main obstacle to HIV eradication is the establishment of a long-term persistent HIV reservoir. Although several therapeutic approaches have been developed to reduce and eventually eliminate the HIV reservoir, only a few have achieved promising results. A better knowledge of the mechanisms involved in the establishment and maintenance of HIV reservoir is of utmost relevance for the design of new therapeutic strategies aimed at purging it with the ultimate goal of achieving HIV eradication or alternatively a functional cure. In this regard, it is also important to take a close look into the cellular HIV reservoirs other than resting memory CD4 T-cells with key roles in reservoir maintenance that have been recently described. Unraveling the special characteristics of these HIV cellular compartments could aid us in designing new therapeutic strategies to deplete the latent HIV reservoir.
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Affiliation(s)
- Marcial García
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | | | - José M Benito
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Norma Rallón
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
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30
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Ray S, Maulik U. Discovering Perturbation of Modular Structure in HIV Progression by Integrating Multiple Data Sources Through Non-Negative Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:869-877. [PMID: 28029629 DOI: 10.1109/tcbb.2016.2642184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information, and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified meta-modules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.
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31
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SUN2 Modulates HIV-1 Infection and Latency through Association with Lamin A/C To Maintain the Repressive Chromatin. mBio 2018; 9:mBio.02408-17. [PMID: 29717016 PMCID: PMC5930302 DOI: 10.1128/mbio.02408-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The postintegrational latency of HIV-1 is characterized by reversible silencing of long terminal repeat (LTR)-driven transcription of the HIV genome. It is known that the formation of repressive chromatin at the 5′-LTR of HIV-1 proviral DNA impedes viral transcription by blocking the recruitment of positive transcription factors. How the repressive chromatin is formed and modulated during HIV-1 infection remains elusive. Elucidation of which chromatin reassembly factor mediates the reorganization of chromatin is likely to facilitate the understanding of the host’s modulation of HIV-1 transcription and latency. Here we revealed that “Sad1 and UNC84 domain containing 2” (SUN2), an inner nuclear membrane protein, maintained the repressive chromatin and inhibited HIV LTR-driven transcription of proviral DNA through an association with lamin A/C. Specifically, lamin A/C tethered SUN2 to the nucleosomes 1 and 2 of the HIV-1 5′-LTR to block the initiation and elongation of HIV-1 transcription. SUN2 knockdown converted chromatin to an active form and thus enhanced the phosphorylation of RNA polymerase II and its recruitment to the 5′-LTR HIV-1 proviral DNA, leading to reactivation of HIV-1 from latency. Conversely, the exogenous factors such as tumor necrosis factor alpha (TNF-α) induced reactivation, and the replication of HIV-1 led to the disassociation between SUN2 and lamin A/C, suggesting that disruption of the association between SUN2 and lamin A/C to convert the repressive chromatin to the active form might be a prerequisite for the initiation of HIV-1 transcription and replication. Together, our findings indicate that SUN2 is a novel chromatin reassembly factor that helps to maintain chromatin in a repressive state and consequently inhibits HIV-1 transcription. Despite the successful use of scores of antiretroviral drugs, HIV latency poses a major impediment to virus eradication. Elucidation of the mechanism of latency facilitates the discovery of new therapeutic strategies. It has been known that the formation of repressive chromatin at the 5′-LTR of HIV-1 proviral DNA impedes viral transcription and maintains viral latency, but how the repressive chromatin is formed and modulated during HIV-1 infection remains elusive. In this study, we performed in-depth virological and cell biological studies and discovered that an inner nuclear membrane protein, SUN2, is a novel chromatin reassembly factor that maintains repressive chromatin and thus modulates HIV-1 transcription and latency: therefore, targeting SUN2 may lead to new strategies for HIV cure.
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32
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Pasquereau S, Kumar A, Abbas W, Herbein G. Counteracting Akt Activation by HIV Protease Inhibitors in Monocytes/Macrophages. Viruses 2018; 10:v10040190. [PMID: 29652795 PMCID: PMC5923484 DOI: 10.3390/v10040190] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 02/07/2023] Open
Abstract
Akt signaling plays a central role in many biological processes that are key players in human immunodeficiency virus 1 (HIV-1) pathogenesis. The persistence of latent reservoirs in successfully treated patients, mainly located in macrophages and latently infected resting CD4+ T cells, remains a major obstacle in HIV-1 eradication. We assessed the in vitro effects of an HIV protease inhibitor (PI) and a non-nucleoside reverse transcriptase inhibitor (NNRTI) on HIV-1 Nef-induced Akt activation in macrophages and on HIV-1 reactivation in U1 monocytoid cells. Ex vivo, we investigated the impact of combination antiretroviral therapy (cART) on Akt activation, as measured by flow cytometry, and on the viral reservoir size, quantified by qPCR, in monocytes and autologous resting CD4+ T cells from HIV-infected individuals (Trial registration: NCT02858414). We found that, in myeloid cells, both Akt activation and HIV-1 reactivation were inhibited by PI but not by NNRTI in vitro. Our results indicate that cART decreases Akt activation and reduces the size of the HIV reservoir in both monocytes and resting CD4+ T cells. Our study indicates that Akt activation could play a role in HIV reservoir formation, indicating that drugs which target Akt could be efficient for limiting its size in aviremic chronically infected patients.
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Affiliation(s)
- Sébastien Pasquereau
- Pathogens & Inflammation/EPILAB Laboratory, UPRES EA4266, University of Franche-Comté, COMUE Bourgogne Franche-Comté University, 25030 Besançon , France.
| | - Amit Kumar
- Pathogens & Inflammation/EPILAB Laboratory, UPRES EA4266, University of Franche-Comté, COMUE Bourgogne Franche-Comté University, 25030 Besançon , France.
| | - Wasim Abbas
- Pathogens & Inflammation/EPILAB Laboratory, UPRES EA4266, University of Franche-Comté, COMUE Bourgogne Franche-Comté University, 25030 Besançon , France.
| | - Georges Herbein
- Pathogens & Inflammation/EPILAB Laboratory, UPRES EA4266, University of Franche-Comté, COMUE Bourgogne Franche-Comté University, 25030 Besançon , France.
- Department of Virology, CHRU Besançon, 25030 Besançon, France.
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Khan S, Iqbal M, Tariq M, Baig SM, Abbas W. Epigenetic regulation of HIV-1 latency: focus on polycomb group (PcG) proteins. Clin Epigenetics 2018; 10:14. [PMID: 29441145 PMCID: PMC5800276 DOI: 10.1186/s13148-018-0441-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/05/2018] [Indexed: 01/10/2023] Open
Abstract
HIV-1 latency allows the virus to persist until reactivation, in a transcriptionally silent form in its cellular reservoirs despite the presence of effective cART. Such viral persistence represents a major barrier to HIV eradication since treatment interruption leads to rebound plasma viremia. Polycomb group (PcG) proteins have recently got a considerable attention in regulating HIV-1 post-integration latency as they are involved in the repression of proviral gene expression through the methylation of histones. This epigenetic regulation plays an important role in the establishment and maintenance of HIV-1 latency. In fact, PcG proteins act in complexes and modulate the epigenetic signatures of integrated HIV-1 promoter. Key role played by PcG proteins in the molecular control of HIV-1 latency has led to hypothesize that PcG proteins may represent a valuable target for future HIV-1 therapy in purging HIV-1 reservoirs. In this regard, various small molecules have been synthesized or explored to specifically block the epigenetic activity of PcG. In this review, we will highlight the possible therapeutic approaches to achieve either a functional or sterilizing cure of HIV-1 infection with special focus on histone methylation by PcG proteins together with current and novel pharmacological approaches to reactivate HIV-1 from latency that could ultimately lead towards a better clearance of viral latent reservoirs.
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Affiliation(s)
- Sheraz Khan
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Tariq
- Department of Biology (Epigenetics group), SBA School of Science and Engineering, LUMS, Lahore, 54792 Pakistan
| | - Shahid M. Baig
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Wasim Abbas
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
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34
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Wang X, Xu H. Potential Epigenetic Regulation in the Germinal Center Reaction of Lymphoid Tissues in HIV/SIV Infection. Front Immunol 2018; 9:159. [PMID: 29449847 PMCID: PMC5799247 DOI: 10.3389/fimmu.2018.00159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/18/2018] [Indexed: 01/08/2023] Open
Abstract
The production of high-affinity and broadly neutralizing antibodies plays a key role in the defense against pathogens. These antibody responses require effective germinal center (GC) reaction within anatomical niches of GCs, where follicular helper T (Tfh) cells provide cognate help to B cells for T cell-dependent antibody responses. Emerging evidences indicate that GC reaction in normal state and perhaps establishment of latent Tfh cell reservoir in HIV/SIV infection are tightly regulated by epigenetic histone modifications, which are responsible for activating or silencing chromatin. A better understanding of the mechanisms behind GC responses at cellular and molecular levels thus provides necessary knowledge for vaccination and immunotherapy. In this review, we discussed the epigenetic regulation of GC responses, especially for GC B and Tfh cell under normal state or HIV/SIV infection.
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Affiliation(s)
- Xiaolei Wang
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
| | - Huanbin Xu
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
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35
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Zhang Z, Nikolai BC, Gates LA, Jung SY, Siwak EB, He B, Rice AP, O'Malley BW, Feng Q. Crosstalk between histone modifications indicates that inhibition of arginine methyltransferase CARM1 activity reverses HIV latency. Nucleic Acids Res 2017. [PMID: 28637181 PMCID: PMC5766202 DOI: 10.1093/nar/gkx550] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, the gene expression status is strictly controlled by epigenetic modifications on chromatin. The repressive status of chromatin largely contributes to HIV latency. Studies have shown that modification of histone H3K27 acts as a key molecular switch for activation or suppression of many cellular genes. In this study, we found that K27-acetylated histone H3 specifically recruited Super Elongation Complex (SEC), the transcriptional elongation complex essential for HIV-1 long terminal repeat (LTR)-mediated and general cellular transcription. Interestingly, H3K27 acetylation further stimulates H3R26 methylation, which subsequently abrogates the recruitment of SEC, forming a negative feedback regulatory loop. Importantly, by inhibiting methyltransferase activity of CARM1, the enzyme responsible for H3R26 methylation, HIV-1 transcription is reactivated in several HIV latency cell models, including a primary resting CD4+ T cell model. When combined with other latency disrupting compounds such as JQ1 or vorinostat/SAHA, the CARM1 inhibitor achieved synergistic effects on HIV-1 activation. This study suggests that coordinated and dynamic modifications at histone H3K27 and H3R26 orchestrate HIV-1 LTR-mediated transcription, and potentially opens a new avenue to disrupt latent HIV-1 infection by targeting specific epigenetic enzymes.
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Affiliation(s)
- Zheng Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Bryan C Nikolai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Leah A Gates
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sung Yun Jung
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Edward B Siwak
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Bin He
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Medicine-Hematology & Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Andrew P Rice
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Qin Feng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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37
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Kohlscheen S, Bonig H, Modlich U. Promises and Challenges in Hematopoietic Stem Cell Gene Therapy. Hum Gene Ther 2017; 28:782-799. [DOI: 10.1089/hum.2017.141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Saskia Kohlscheen
- Research Group for Gene Modification in Stem Cells, Center for Cell and Gene Therapy Frankfurt, Paul-Ehrlich-Institute, Langen, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe University, Frankfurt, Germany
- German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt, Germany
- Department of Medicine/Division of Hematology, University of Washington, Seattle, Washington
| | - Ute Modlich
- Research Group for Gene Modification in Stem Cells, Center for Cell and Gene Therapy Frankfurt, Paul-Ehrlich-Institute, Langen, Germany
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38
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Abstract
Viral latency can be considered a metastable, nonproductive infection state that is capable of subsequent reactivation to repeat the infection cycle. Viral latent infections have numerous associated pathologies, including cancer, birth defects, neuropathy, cardiovascular disease, chronic inflammation, and immunological dysfunctions. The mechanisms controlling the establishment, maintenance, and reactivation from latency are complex and diversified among virus families, species, and strains. Yet, as examined in this review, common properties of latent viral infections can be defined. Eradicating latent virus has become an important but elusive challenge and will require a more complete understanding of the mechanisms controlling these processes.
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Unravelling HIV-1 Latency, One Cell at a Time. Trends Microbiol 2017; 25:932-941. [PMID: 28668335 DOI: 10.1016/j.tim.2017.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/22/2017] [Accepted: 06/01/2017] [Indexed: 12/14/2022]
Abstract
A single virus is capable of infecting and replicating in a single cell. Recent advances across single-cell omics technologies - genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics - will offer unprecedented opportunities to gain more insights into the various aspects of the life cycle of viruses and their impact on the host cell. Here, using the human immunodeficiency virus type 1 (HIV-1) as an example, we summarize the current knowledge and the future potential of single-cell omics in the investigation of an important aspect of the life cycle of HIV-1 that represents a major hurdle in achieving viral eradication, HIV-1 latency.
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40
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Turner AMW, Margolis DM. Chromatin Regulation and the Histone Code in HIV Latency
. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:229-243. [PMID: 28656010 PMCID: PMC5482300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The formation of a latent reservoir of Human Immunodeficiency Virus (HIV) infection hidden from immune clearance remains a significant obstacle to approaches to eradicate HIV infection. Towards an understanding of the mechanisms of HIV persistence, there is a growing body of work implicating epigenetic regulation of chromatin in establishment and maintenance of this latent reservoir. Here we discuss recent advances in the field of chromatin regulation, specifically in our understanding of the histone code, and how these discoveries relate to our current knowledge of the chromatin mechanisms linked to HIV transcriptional repression and the reversal of latency. We also examine mechanisms unexplored in the context of HIV latency and briefly discuss current therapies aimed at the induction of proviral expression within latently infected cells. We aim to emphasize that a greater understanding of the epigenetic mechanisms which govern HIV latency could lead to new therapeutic targets for latency reversal and clearance cure strategies.
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Affiliation(s)
- Anne-Marie W. Turner
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - David M. Margolis
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC,To whom all correspondence should be addressed: David Margolis, University of North Carolina at Chapel Hill, 2016 Genetic Medicine Building, CB#7042, 120 Mason Farm Road, Chapel Hill, NC, 27599-7435, Tel: (919) 966-6388, .
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41
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Manjili MH. Tumor Dormancy and Relapse: From a Natural Byproduct of Evolution to a Disease State. Cancer Res 2017; 77:2564-2569. [PMID: 28507050 PMCID: PMC5459601 DOI: 10.1158/0008-5472.can-17-0068] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/22/2017] [Accepted: 03/10/2017] [Indexed: 12/24/2022]
Abstract
Species evolve by mutations and epigenetic changes acting on individuals in a population; tumors evolve by similar mechanisms at a cellular level in a tissue. This article reviews growing evidence about tumor dormancy and suggests that (i) cellular malignancy is a natural byproduct of evolutionary mechanisms, such as gene mutations and epigenetic modifications, which is manifested in the form of tumor dormancy in healthy individuals as well as in cancer survivors; (ii) cancer metastasis could be an early dissemination event that could occur during malignant dormancy even before primary cancer is clinically detectable; and (iii) chronic inflammation is a key factor in awakening dormant malignant cells at the primary site, leading to primary cancer development, and at distant sites, leading to advanced stage diseases. On the basis of this evidence, it is reasonable to propose that we are all cancer survivors rather than cancer-free individuals because of harboring dormant malignant cells in our organs. A better understanding of local and metastatic tumor dormancy could lead to novel cancer therapeutics for the prevention of cancer. Cancer Res; 77(10); 2564-9. ©2017 AACR.
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Affiliation(s)
- Masoud H Manjili
- Department of Microbiology & Immunology, VCU School of Medicine, Massey Cancer Center, Richmond, Virginia.
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42
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Ackloo S, Brown PJ, Müller S. Chemical probes targeting epigenetic proteins: Applications beyond oncology. Epigenetics 2017; 12:378-400. [PMID: 28080202 PMCID: PMC5453191 DOI: 10.1080/15592294.2017.1279371] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/23/2016] [Accepted: 01/02/2017] [Indexed: 12/15/2022] Open
Abstract
Epigenetic chemical probes are potent, cell-active, small molecule inhibitors or antagonists of specific domains in a protein; they have been indispensable for studying bromodomains and protein methyltransferases. The Structural Genomics Consortium (SGC), comprising scientists from academic and pharmaceutical laboratories, has generated most of the current epigenetic chemical probes. Moreover, the SGC has shared about 4 thousand aliquots of these probes, which have been used primarily for phenotypic profiling or to validate targets in cell lines or primary patient samples cultured in vitro. Epigenetic chemical probes have been critical tools in oncology research and have uncovered mechanistic insights into well-established targets, as well as identify new therapeutic starting points. Indeed, the literature primarily links epigenetic proteins to oncology, but applications in inflammation, viral, metabolic and neurodegenerative diseases are now being reported. We summarize the literature of these emerging applications and provide examples where existing probes might be used.
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Affiliation(s)
- Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straβe 15, Frankfurt am Main, Germany
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43
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Chen HC, Martinez JP, Zorita E, Meyerhans A, Filion GJ. Position effects influence HIV latency reversal. Nat Struct Mol Biol 2016; 24:47-54. [PMID: 27870832 DOI: 10.1038/nsmb.3328] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
The main obstacle to curing HIV is the presence of latent proviruses in the bodies of infected patients. The partial success of reactivation therapies suggests that the genomic context of integrated proviruses can interfere with treatment. Here we developed a method called Barcoded HIV ensembles (B-HIVE) to map the chromosomal locations of thousands of individual proviruses while tracking their transcriptional activities in an infected cell population. B-HIVE revealed that, in Jurkat cells, the expression of HIV is strongest close to endogenous enhancers. The insertion site also affects the response to latency-reversing agents, because we found that phytohemagglutinin and vorinostat reactivated proviruses inserted at distinct genomic locations. From these results, we propose that combinations of drugs targeting all areas of the genome will be most effective. Overall, our data suggest that the insertion context of HIV is a critical determinant of the viral response to reactivation therapies.
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Affiliation(s)
- Heng-Chang Chen
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,University Pompeu Fabra, Barcelona, Spain
| | - Javier P Martinez
- Infection Biology Group, Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Eduard Zorita
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,University Pompeu Fabra, Barcelona, Spain
| | - Andreas Meyerhans
- Infection Biology Group, Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Guillaume J Filion
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,University Pompeu Fabra, Barcelona, Spain
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44
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The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 328:197-252. [PMID: 28069134 DOI: 10.1016/bs.ircmb.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.
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45
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Melkova Z, Shankaran P, Madlenakova M, Bodor J. Current views on HIV-1 latency, persistence, and cure. Folia Microbiol (Praha) 2016; 62:73-87. [PMID: 27709447 DOI: 10.1007/s12223-016-0474-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/20/2016] [Indexed: 01/01/2023]
Abstract
HIV-1 infection cannot be cured as it persists in latently infected cells that are targeted neither by the immune system nor by available therapeutic approaches. Consequently, a lifelong therapy suppressing only the actively replicating virus is necessary. The latent reservoir has been defined and characterized in various experimental models and in human patients, allowing research and development of approaches targeting individual steps critical for HIV-1 latency establishment, maintenance, and reactivation. However, additional mechanisms and processes driving the remaining low-level HIV-1 replication in the presence of the suppressive therapy still remain to be identified and targeted. Current approaches toward HIV-1 cure involve namely attempts to reactivate and purge HIV latently infected cells (so-called "shock and kill" strategy), as well as approaches involving gene therapy and/or gene editing and stem cell transplantation aiming at generation of cells resistant to HIV-1. This review summarizes current views and concepts underlying different approaches aiming at functional or sterilizing cure of HIV-1 infection.
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Affiliation(s)
- Zora Melkova
- Department of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studnickova 7, 128 00, Prague 2, Czech Republic. .,BIOCEV, Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec, Průmyslová 595, 252 50, Vestec, Czech Republic.
| | - Prakash Shankaran
- Department of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studnickova 7, 128 00, Prague 2, Czech Republic
| | - Michaela Madlenakova
- Department of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studnickova 7, 128 00, Prague 2, Czech Republic.,BIOCEV, Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Josef Bodor
- BIOCEV, Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec, Průmyslová 595, 252 50, Vestec, Czech Republic
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Kumar A, Abbas W, Colin L, Khan KA, Bouchat S, Varin A, Larbi A, Gatot JS, Kabeya K, Vanhulle C, Delacourt N, Pasquereau S, Coquard L, Borch A, König R, Clumeck N, De Wit S, Rohr O, Rouzioux C, Fulop T, Van Lint C, Herbein G. Tuning of AKT-pathway by Nef and its blockade by protease inhibitors results in limited recovery in latently HIV infected T-cell line. Sci Rep 2016; 6:24090. [PMID: 27076174 PMCID: PMC4831010 DOI: 10.1038/srep24090] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/18/2016] [Indexed: 12/14/2022] Open
Abstract
Akt signaling plays a central role in many biological processes, which are key players in human immunodeficiency virus 1 (HIV-1) pathogenesis. We found that Akt interacts with HIV-1 Nef protein. In primary T cells treated with exogenous Nef or acutely infected with Nef-expressing HIV-1 in vitro, Akt became phosphorylated on serine473 and threonine308. In vitro, Akt activation mediated by Nef in T-cells was blocked by HIV protease inhibitors (PI), but not by reverse transcriptase inhibitors (RTI). Ex vivo, we found that the Akt pathway is hyperactivated in peripheral blood lymphocytes (PBLs) from cART naïve HIV-1-infected patients. PBLs isolated from PI-treated patients, but not from RTI-treated patients, exhibited decreased Akt activation, T-cell proliferation and IL-2 production. We found that PI but not RTI can block HIV-1 reactivation in latently infected J-Lat lymphoid cells stimulated with various stimuli. Using luciferase measurement, we further confirmed that Nef-mediated reactivation of HIV-1 from latency in 1G5 cells was blocked by PI parallel to decreased Akt activation. Our results indicate that PI-mediated blockade of Akt activation could impact the HIV-1 reservoir and support the need to further assess the therapeutic use of HIV-1 PI in order to curtail latently infected cells in HIV-1-infected patients.
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Affiliation(s)
- Amit Kumar
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Wasim Abbas
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Laurence Colin
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Kashif Aziz Khan
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Sophie Bouchat
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Audrey Varin
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Anis Larbi
- Department of Medicine, University of Sherbrooke, Sherbrooke, Canada
| | - Jean-Stéphane Gatot
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Kabamba Kabeya
- Department of Infectious Diseases, CHU St-Pierre, ULB, Bruxelles, Belgium
| | - Caroline Vanhulle
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Nadège Delacourt
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Sébastien Pasquereau
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Laurie Coquard
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Alexandra Borch
- Research Group "Host-Pathogen Interactions", Paul-Ehrlich-Institute, Langen, Germany
| | - Renate König
- Research Group "Host-Pathogen Interactions", Paul-Ehrlich-Institute, Langen, Germany.,Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA; German Center for Infection Research (DZIF), Langen, Germany
| | - Nathan Clumeck
- Department of Infectious Diseases, CHU St-Pierre, ULB, Bruxelles, Belgium
| | - Stephane De Wit
- Department of Infectious Diseases, CHU St-Pierre, ULB, Bruxelles, Belgium
| | - Olivier Rohr
- Institut de Parasitologie et Pathologie Tropicale, University of Strasbourg, Strasbourg, France
| | - Christine Rouzioux
- Department of Virology, Paris University, EA7327 Paris Descartes, APHP Necker Hospital, Paris, France
| | - Tamas Fulop
- Department of Medicine, University of Sherbrooke, Sherbrooke, Canada
| | - Carine Van Lint
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Georges Herbein
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
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Bire S, Casteret S, Piégu B, Beauclair L, Moiré N, Arensbuger P, Bigot Y. Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2. PLoS Genet 2016; 12:e1005902. [PMID: 26939020 PMCID: PMC4777549 DOI: 10.1371/journal.pgen.1005902] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/05/2016] [Indexed: 12/31/2022] Open
Abstract
Transposable elements are driving forces for establishing genetic innovations such as transcriptional regulatory networks in eukaryotic genomes. Here, we describe a silencer situated in the last 300 bp of the Mos1 transposase open reading frame (ORF) which functions in vertebrate and arthropod cells. Functional silencers are also found at similar locations within three other animal mariner elements, i.e. IS630-Tc1-mariner (ITm) DD34D elements, Himar1, Hsmar1 and Mcmar1. These silencers are able to impact eukaryotic promoters monitoring strong, moderate or low expression as well as those of mariner elements located upstream of the transposase ORF. We report that the silencing involves at least two transcription factors (TFs) that are conserved within animal species, NFAT-5 and Alx1. These cooperatively act with YY1 to trigger the silencing activity. Four other housekeeping transcription factors (TFs), neuron restrictive silencer factor (NRSF), GAGA factor (GAF) and GTGT factor (GTF), were also found to have binding sites within mariner silencers but their impact in modulating the silencer activity remains to be further specified. Interestingly, an NRSF binding site was found to overlap a 30 bp motif coding a highly conserved PHxxYSPDLAPxD peptide in mariner transposases. We also present experimental evidence that silencing is mainly achieved by co-opting the host Polycomb Repressive Complex 2 pathway. However, we observe that when PRC2 is impaired another host silencing pathway potentially takes over to maintain weak silencer activity. Mariner silencers harbour features of Polycomb Response Elements, which are probably a way for mariner elements to self-repress their transcription and mobility in somatic and germinal cells when the required TFs are expressed. At the evolutionary scale, mariner elements, through their exaptation, might have been a source of silencers playing a role in the chromatin configuration in eukaryotic genomes. Transposons are mobile DNA sequences that have long co-evolved with the genome of their hosts. Consequently, they are involved in the generation of mutations, as well as the creation of genes and regulatory networks. Controlling the transposon activity, and consequently its negative effects on both the host soma and germ line, is a challenge for the survival of both the host and the transposon. To silence transposons, hosts often use defence mechanisms involving DNA methylation and RNA interference pathways. Here we show that mariner transposons can self-regulate their activity by using a silencer element located in their DNA sequence. The silencer element interferes with host housekeeping protein transcription factors involved in the polycomb silencing pathways. As the regulation of chromatin configuration by polycomb is an important regulator of animal development, our findings open the possibility that mariner silencers might have been exapted during animal evolution to participate in certain regulation pathways of their hosts. Since some of the TFs involved in mariner silencer activity play a role at different stages of nervous system development and neuron differentiation, it might be possible that mariner transposons can be active during some steps of cell differentiation. Interestingly, mariner transposons (i.e. IS630-Tc1-mariner (ITm) DD34D transposons) have so far only been found in genomes of animals having a nervous system.
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Affiliation(s)
- Solenne Bire
- PRC, UMR INRA-CNRS 7247, PRC, Nouzilly, France
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | | | | | | | | | - Peter Arensbuger
- Biological Sciences Department, California State Polytechnic University, Pomona, California, United States of America
| | - Yves Bigot
- PRC, UMR INRA-CNRS 7247, PRC, Nouzilly, France
- * E-mail:
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Small Molecule Inhibitors of BAF; A Promising Family of Compounds in HIV-1 Latency Reversal. EBioMedicine 2015; 3:108-121. [PMID: 26870822 PMCID: PMC4739437 DOI: 10.1016/j.ebiom.2015.11.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 11/19/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022] Open
Abstract
Persistence of latently infected cells in presence of Anti-Retroviral Therapy presents the main obstacle to HIV-1 eradication. Much effort is thus placed on identification of compounds capable of HIV-1 latency reversal in order to render infected cells susceptible to viral cytopathic effects and immune clearance. We identified the BAF chromatin remodeling complex as a key player required for maintenance of HIV-1 latency, highlighting its potential as a molecular target for inhibition in latency reversal. Here, we screened a recently identified panel of small molecule inhibitors of BAF (BAFi's) for potential to activate latent HIV-1. Latency reversal was strongly induced by BAFi's Caffeic Acid Phenethyl Ester and Pyrimethamine, two molecules previously characterized for clinical application. BAFi's reversed HIV-1 latency in cell line based latency models, in two ex vivo infected primary cell models of latency, as well as in HIV-1 infected patient's CD4 + T cells, without inducing T cell proliferation or activation. BAFi-induced HIV-1 latency reversal was synergistically enhanced upon PKC pathway activation and HDAC-inhibition. Therefore BAFi's constitute a promising family of molecules for inclusion in therapeutic combinatorial HIV-1 latency reversal. BAF complex inhibitors (BAFi's) activate latent HIV-1 in cell line models of latency. BAFi's in combination with HDAC inhibitors and PKC activators synergistically activate latent HIV-1. The BAFi's PYR and CAPE reverse HIV-1 latency in primary cell models of latency and in cells obtained from HIV-1 patients.
Access to Combination antiretroviral therapy (cART) has made HIV-1 infection a chronic disease. However, cART is not curative, as a small number of infected cells harboring silent virus with potential to renew the infection persist despite cART. Efforts to cure HIV-1 include activation of these latent cells, making them susceptible to immune clearance. Here we describe the activity of BAF inhibitors in HIV-1 activation in in vitro models of HIV-1 latency as well as in cells obtained from HIV-1 infected patient volunteers. Our data highlight the clinical potential of BAF inhibitors for inclusion in combinatorial therapy to reverse HIV-1 latency.
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Key Words
- BAF complex
- BAF, BRG-Brahma Associated Factors
- BAF250a, BAF Associated Factor 250 a
- BAFi, BAF inhibitor
- BRG-1, Brahma Related Gene 1
- CAPE, caffeic acid phenetyl esther
- ChIP, Chromatin Immunoprecipitation
- Chromatin remodeling
- CycA, Cyclophilin A
- DHS-1, DNase Hypersensitive Site 1
- ES cells, embryonic stem cells
- FAIRE, Formaldehyde Assisted Isolation of Regulatory Elements
- FBS, Fetal Bovine Serum
- GFP, Green Fluorescent Protein
- HDAC, histone deacetylase
- HIV
- HIV-1, human immunodeficiency virus type 1
- IFNß, Interferon beta
- IL10, Interleukin 10
- IL12, Interleukin 12
- IL4, Interleukin 4
- IL6, Interleukin 6
- INI-1, Integrase Interactor 1
- IRES, Internal Ribosome Entry Site
- IκB-α, Inhibitor of NF-κB – alpha
- LRA, latency reversal agent
- LTR, Long Terminal Repeat
- Latency
- MIP26, Major Intrinsic Protein
- MMP9, Matrix Metallopeptidase 9
- NF-κB, Nuclear Factor Kappa-light-chain-enhancer of activated B cells
- PBMC, peripheral blood mononuclear cell
- PBS, Phosphate Buffered Saline
- PKC, Protein Kinase C
- PYR, Pyrimethamine
- RT-qPCR, Reverse Transcriptase, quantitative Polymerase Chain Reaction
- SAHA, Suberoylanilide Hydroxamic Acid
- SD, Standard Deviation
- SOCS3, Suppressor Of Cytokine Signaling 3
- TGF-ß, Transforming Growth Factor beta
- TLR2, Toll-like Receptor 2
- bp, base pairs
- cART, combination Antiretroviral Therapy
- latency reversal agents
- nuc, nucleosome
- siRNA, small interfering RNA
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Liu C, Ma X, Liu B, Chen C, Zhang H. HIV-1 functional cure: will the dream come true? BMC Med 2015; 13:284. [PMID: 26588898 PMCID: PMC4654816 DOI: 10.1186/s12916-015-0517-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 02/07/2023] Open
Abstract
The reservoir of human immunodeficiency virus type 1 (HIV-1), a long-lived pool of latently infected cells harboring replication-competent viruses, is the major obstacle to curing acquired immune deficiency syndrome (AIDS). Although the combination antiretroviral therapy (cART) can successfully suppress HIV-1 viremia and significantly delay the progression of the disease, it cannot eliminate the viral reservoir and the patient must continue to take anti-viral medicines for life. Currently, the appearance of the 'Berlin patient', the 'Boston patients', and the 'Mississippi baby' have inspired many therapeutic strategies for HIV-1 aimed at curing efforts. However, the specific eradication of viral latency and the recovery and optimization of the HIV-1-specific immune surveillance are major challenges to achieving such a cure. Here, we summarize recent studies addressing the mechanisms underlying the viral latency and define two categories of viral reservoir: 'shallow' and 'deep'. We also present the current strategies and recent advances in the development of a functional cure for HIV-1, focusing on full/partial replacement of the immune system, 'shock and kill', and 'permanent silencing' approaches.
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Affiliation(s)
- Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Xiancai Ma
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Bingfeng Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Cancan Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
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H3K27 Demethylation at the Proviral Promoter Sensitizes Latent HIV to the Effects of Vorinostat in Ex Vivo Cultures of Resting CD4+ T Cells. J Virol 2015; 89:8392-405. [PMID: 26041287 DOI: 10.1128/jvi.00572-15] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/26/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Histone methyltransferase inhibitors (HMTis) and histone deacetylase inhibitors (HDACis) are reported to synergistically induce the expression of latent human immunodeficiency virus type 1 (HIV-1), but studies have largely been performed with cell lines. As specific and potent HMTis directed at EZH1 (enhancer of zeste 2 Polycomb repressive complex 2 subunit 1)/EZH2 are now in human testing, we wished to rigorously test such an inhibitor in a primary resting T-cell model of HIV latency. We found that GSK343, a potent and selective EZH2/EZH1 inhibitor, reduced trimethylation of histone 3 at lysine 27 (H3K27) of the HIV provirus in resting cells. Remarkably, this epigenetic change was not associated with increased proviral expression in latently infected resting cells. However, following the reduction in H3K27 at the HIV long terminal repeat (LTR), subsequent exposure to the HDACi suberoylanilide hydroxamic acid or vorinostat (VOR) resulted in increases in HIV gag RNA and HIV p24 antigen production that were up to 2.5-fold greater than those induced by VOR alone. Therefore, in primary resting CD4(+) T cells, true mechanistic synergy in the reversal of HIV latency may be achieved by the combination of HMTis and HDACis. Although other cellular effects of EZH2 inhibition may contribute to the sensitization of the HIV LTR to subsequent exposure to VOR, and to increase viral antigen production, this synergistic effect is directly associated with H3K27 demethylation at nucleosome 1 (Nuc-1). Based upon our findings, the combination of HMTis and HDACis should be considered for testing in animal models or clinical trials. IMPORTANCE Demethylation of H3K27 mediated by the histone methyltransferase inhibitor GSK343 in primary resting T cells is slow, occurring over 96 h, but by itself does not result in a significant upregulation of cell-associated HIV RNA expression or viral antigen production. However, following H3K27 demethylation, latent viral expression within infected primary resting CD4(+) T cells is synergistically increased upon exposure to the histone deacetylase inhibitor vorinostat. Demethylation at H3K27 sensitizes the HIV promoter to the effects of an HDACi and provides a proof-of-concept for the testing of combination epigenetic approaches to disrupt latent HIV infection, a necessary step toward the eradication of HIV infection.
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