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Sun Y, Wang L. Development of Anti-HIV Therapeutics: From Conventional Drug Discovery to Cutting-Edge Technology. Pharmaceuticals (Basel) 2024; 17:887. [PMID: 39065738 PMCID: PMC11280173 DOI: 10.3390/ph17070887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
The efforts to discover HIV therapeutics have continued since the first human immunodeficiency virus (HIV) infected patient was confirmed in the 1980s. Ten years later, the first HIV drug, zidovudine (AZT), targeting HIV reverse transcriptase, was developed. Meanwhile, scientists were enlightened to discover new drugs that target different HIV genes, like integrase, protease, and host receptors. Combination antiretroviral therapy (cART) is the most feasible medical intervention to suppress the virus in people with HIV (PWH) and control the epidemic. ART treatment has made HIV a chronic infection rather than a fatal disease, but ART does not eliminate latent reservoirs of HIV-1 from the host cells; strict and life-long adherence to ART is required for the therapy to be effective in patients. In this review, we first discussed the scientific history of conventional HIV drug discovery since scientists need to develop more and more drugs to solve drug-resistant issues and release the side effects. Then, we summarized the novel research technologies, like gene editing, applied to HIV treatment and their contributions to eliminating HIV as a complementary therapy.
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Affiliation(s)
| | - Lingyun Wang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA;
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2
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Roesmann F, Müller L, Klaassen K, Heß S, Widera M. Interferon-Regulated Expression of Cellular Splicing Factors Modulates Multiple Levels of HIV-1 Gene Expression and Replication. Viruses 2024; 16:938. [PMID: 38932230 PMCID: PMC11209495 DOI: 10.3390/v16060938] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Type I interferons (IFN-Is) are pivotal in innate immunity against human immunodeficiency virus I (HIV-1) by eliciting the expression of IFN-stimulated genes (ISGs), which encompass potent host restriction factors. While ISGs restrict the viral replication within the host cell by targeting various stages of the viral life cycle, the lesser-known IFN-repressed genes (IRepGs), including RNA-binding proteins (RBPs), affect the viral replication by altering the expression of the host dependency factors that are essential for efficient HIV-1 gene expression. Both the host restriction and dependency factors determine the viral replication efficiency; however, the understanding of the IRepGs implicated in HIV-1 infection remains greatly limited at present. This review provides a comprehensive overview of the current understanding regarding the impact of the RNA-binding protein families, specifically the two families of splicing-associated proteins SRSF and hnRNP, on HIV-1 gene expression and viral replication. Since the recent findings show specifically that SRSF1 and hnRNP A0 are regulated by IFN-I in various cell lines and primary cells, including intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs), we particularly discuss their role in the context of the innate immunity affecting HIV-1 replication.
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Affiliation(s)
- Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Katleen Klaassen
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Stefanie Heß
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
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3
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Berman RE, Dampier W, Nonnemacher MR, Wigdahl B. What's in a cure: designing a broad-spectrum HIV gene therapy. Curr Opin HIV AIDS 2024; 19:150-156. [PMID: 38547339 PMCID: PMC11188629 DOI: 10.1097/coh.0000000000000846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PURPOSE OF REVIEW The leading gene editing strategy for a human immunodeficiency virus type 1 (HIV-1) cure involves the delivery of SaCas9 and two guide RNAs (gRNAs) in an adeno-associated viral (AAV) vector. As a dual-component system, CRISPR is targeted to a genetic locus through the choice of a Cas effector and gRNA protospacer design pair. As CRISPR research has expanded in recent years, these components have been investigated for utilization in cure strategies, which will be discussed in this article. RECENT FINDINGS Type II SpCas9 and SaCas9 have been the leading Cas effectors across gene editing therapeutics to date. Additionally, extensive research has expanded the potential to multiplex gRNAs and target them effectively to the highly genetically diverse HIV-1 provirus. More recently, the Type V family of Cas12 effectors opens a new opportunity to use a smaller Cas protein for packaging into an AAV vector with multiplexed gRNAs. SUMMARY In understanding the individual components of a CRISPR/Cas therapeutic cure for HIV-1, it is important to know that the currently used strategies can be improved upon. Future areas will include alternative smaller Cas effectors, multiplexed gRNAs designs, and/or alternative delivery modalities.
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Affiliation(s)
- Rachel E. Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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4
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Klute S, Sparrer KMJ. Friends and Foes: The Ambivalent Role of Autophagy in HIV-1 Infection. Viruses 2024; 16:500. [PMID: 38675843 PMCID: PMC11054699 DOI: 10.3390/v16040500] [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: 02/28/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Autophagy has emerged as an integral part of the antiviral innate immune defenses, targeting viruses or their components for lysosomal degradation. Thus, successful viruses, like pandemic human immunodeficiency virus 1 (HIV-1), evolved strategies to counteract or even exploit autophagy for efficient replication. Here, we provide an overview of the intricate interplay between autophagy and HIV-1. We discuss the impact of autophagy on HIV-1 replication and report in detail how HIV-1 manipulates autophagy in infected cells and beyond. We also highlight tissue and cell-type specifics in the interplay between autophagy and HIV-1. In addition, we weigh exogenous modulation of autophagy as a putative double-edged sword against HIV-1 and discuss potential implications for future antiretroviral therapy and curative approaches. Taken together, we consider both antiviral and proviral roles of autophagy to illustrate the ambivalent role of autophagy in HIV-1 pathogenesis and therapy.
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5
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Hudait A, Voth GA. HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex. Proc Natl Acad Sci U S A 2024; 121:e2313737121. [PMID: 38241438 PMCID: PMC10823262 DOI: 10.1073/pnas.2313737121] [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: 08/10/2023] [Accepted: 12/06/2023] [Indexed: 01/21/2024] Open
Abstract
Nuclear import and uncoating of the viral capsid are critical steps in the HIV-1 life cycle that serve to transport and release genomic material into the nucleus. Viral core import involves translocating the HIV-1 capsid at the nuclear pore complex (NPC). Notably, the central channel of the NPC appears to often accommodate and allow passage of intact HIV-1 capsid, though mechanistic details of the process remain to be fully understood. Here, we investigate the molecular interactions that operate in concert between the HIV-1 capsid and the NPC that regulate capsid translocation through the central channel. To this end, we develop a "bottom-up" coarse-grained (CG) model of the human NPC from recently released cryo-electron tomography structure and then construct composite membrane-embedded CG NPC models. We find that successful translocation from the cytoplasmic side to the NPC central channel is contingent on the compatibility of the capsid morphology and channel dimension and the proper orientation of the capsid approach to the channel from the cytoplasmic side. The translocation dynamics is driven by maximizing the contacts between phenylalanine-glycine nucleoporins at the central channel and the capsid. For the docked intact capsids, structural analysis reveals correlated striated patterns of lattice disorder likely related to the intrinsic capsid elasticity. Uncondensed genomic material inside the docked capsid augments the overall lattice disorder of the capsid. Our results suggest that the intrinsic "elasticity" can also aid the capsid to adapt to the stress and remain structurally intact during translocation.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
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6
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Thenin-Houssier S, Machida S, Jahan C, Bonnet-Madin L, Abbou S, Chen HC, Tesfaye R, Cuvier O, Benkirane M. POLE3 is a repressor of unintegrated HIV-1 DNA required for efficient virus integration and escape from innate immune sensing. SCIENCE ADVANCES 2023; 9:eadh3642. [PMID: 37922361 PMCID: PMC10624344 DOI: 10.1126/sciadv.adh3642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Unintegrated retroviral DNA is transcriptionally silenced by host chromatin silencing factors. Here, we used the proteomics of isolated chromatin segments method to reveal viral and host factors associated with unintegrated HIV-1DNA involved in its silencing. By gene silencing using siRNAs, 46 factors were identified as potential repressors of unintegrated HIV-1DNA. Knockdown and knockout experiments revealed POLE3 as a transcriptional repressor of unintegrated HIV-1DNA. POLE3 maintains unintegrated HIV-1DNA in a repressive chromatin state, preventing RNAPII recruitment to the viral promoter. POLE3 and the recently identified host factors mediating unintegrated HIV-1 DNA silencing, CAF1 and SMC5/SMC6/SLF2, show specificity toward different forms of unintegrated HIV-1DNA. Loss of POLE3 impaired HIV-1 replication, suggesting that repression of unintegrated HIV-1DNA is important for optimal viral replication. POLE3 depletion reduces the integration efficiency of HIV-1. POLE3, by maintaining a repressive chromatin structure of unintegrated HIV-1DNA, ensures HIV-1 escape from innate immune sensing in primary CD4+ T cells.
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Affiliation(s)
- Suzie Thenin-Houssier
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Shinichi Machida
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Cyprien Jahan
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Lucie Bonnet-Madin
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Scarlette Abbou
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Heng-Chang Chen
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Robel Tesfaye
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Cuvier
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Monsef Benkirane
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
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7
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D’Orso I, Forst CV. Mathematical Models of HIV-1 Dynamics, Transcription, and Latency. Viruses 2023; 15:2119. [PMID: 37896896 PMCID: PMC10612035 DOI: 10.3390/v15102119] [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: 08/31/2023] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
HIV-1 latency is a major barrier to curing infections with antiretroviral therapy and, consequently, to eliminating the disease globally. The establishment, maintenance, and potential clearance of latent infection are complex dynamic processes and can be best described with the help of mathematical models followed by experimental validation. Here, we review the use of viral dynamics models for HIV-1, with a focus on applications to the latent reservoir. Such models have been used to explain the multi-phasic decay of viral load during antiretroviral therapy, the early seeding of the latent reservoir during acute infection and the limited inflow during treatment, the dynamics of viral blips, and the phenomenon of post-treatment control. Finally, we discuss that mathematical models have been used to predict the efficacy of potential HIV-1 cure strategies, such as latency-reversing agents, early treatment initiation, or gene therapies, and to provide guidance for designing trials of these novel interventions.
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Affiliation(s)
- Iván D’Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Christian V. Forst
- Department of Genetics and Genomic Sciences, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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8
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Cabrera-Rodríguez R, Pérez-Yanes S, Lorenzo-Sánchez I, Trujillo-González R, Estévez-Herrera J, García-Luis J, Valenzuela-Fernández A. HIV Infection: Shaping the Complex, Dynamic, and Interconnected Network of the Cytoskeleton. Int J Mol Sci 2023; 24:13104. [PMID: 37685911 PMCID: PMC10487602 DOI: 10.3390/ijms241713104] [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: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
HIV-1 has evolved a plethora of strategies to overcome the cytoskeletal barrier (i.e., actin and intermediate filaments (AFs and IFs) and microtubules (MTs)) to achieve the viral cycle. HIV-1 modifies cytoskeletal organization and dynamics by acting on associated adaptors and molecular motors to productively fuse, enter, and infect cells and then traffic to the cell surface, where virions assemble and are released to spread infection. The HIV-1 envelope (Env) initiates the cycle by binding to and signaling through its main cell surface receptors (CD4/CCR5/CXCR4) to shape the cytoskeleton for fusion pore formation, which permits viral core entry. Then, the HIV-1 capsid is transported to the nucleus associated with cytoskeleton tracks under the control of specific adaptors/molecular motors, as well as HIV-1 accessory proteins. Furthermore, HIV-1 drives the late stages of the viral cycle by regulating cytoskeleton dynamics to assure viral Pr55Gag expression and transport to the cell surface, where it assembles and buds to mature infectious virions. In this review, we therefore analyze how HIV-1 generates a cell-permissive state to infection by regulating the cytoskeleton and associated factors. Likewise, we discuss the relevance of this knowledge to understand HIV-1 infection and pathogenesis in patients and to develop therapeutic strategies to battle HIV-1.
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Affiliation(s)
- Romina Cabrera-Rodríguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Silvia Pérez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Iria Lorenzo-Sánchez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
- Analysis Department, Faculty of Mathematics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain
| | - Judith Estévez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Jonay García-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
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9
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Borrmann H, Ulkar G, Kliszczak AE, Ismed D, Schilling M, Magri A, Harris JM, Balfe P, Vasudevan S, Borrow P, Zhuang X, McKeating JA. Molecular components of the circadian clock regulate HIV-1 replication. iScience 2023; 26:107007. [PMID: 37534138 PMCID: PMC10391662 DOI: 10.1016/j.isci.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/26/2023] [Indexed: 08/04/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) causes major health burdens worldwide and still lacks curative therapies and vaccines. Circadian rhythms are endogenous daily oscillations that coordinate an organism's response to its environment and invading pathogens. Peripheral viral loads of HIV-1 infected patients show diurnal variation; however, the underlying mechanisms remain unknown. Here, we demonstrate a role for the cell-intrinsic clock to regulate rhythmic HIV-1 replication in circadian-synchronized systems. Silencing the circadian activator Bmal1 abolishes this phenotype, and we observe BMAL1 binding to the HIV-1 promoter. Importantly, we show differential binding of the nuclear receptors REV-ERB and ROR to the HIV-long terminal repeat at different circadian times, demonstrating a dynamic interplay in time-of-day regulation of HIV-1 transcription. Bioinformatic analysis shows circadian regulation of host factors that control HIV-1 replication, providing an additional mechanism for rhythmic viral replication. This study increases our understanding of the circadian regulation of HIV-1, which can ultimately inform new therapies.
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Affiliation(s)
- Helene Borrmann
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Görkem Ulkar
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Anna E. Kliszczak
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dini Ismed
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mirjam Schilling
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Andrea Magri
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - James M. Harris
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jane A. McKeating
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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10
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Rheinberger M, Costa AL, Kampmann M, Glavas D, Shytaj IL, Sreeram S, Penzo C, Tibroni N, Garcia-Mesa Y, Leskov K, Fackler OT, Vlahovicek K, Karn J, Lucic B, Herrmann C, Lusic M. Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains. Cell Rep 2023; 42:112110. [PMID: 36790927 DOI: 10.1016/j.celrep.2023.112110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
HIV-1 encounters the hierarchically organized host chromatin to stably integrate and persist in anatomically distinct latent reservoirs. The contribution of genome organization in HIV-1 infection has been largely understudied across different HIV-1 targets. Here, we determine HIV-1 integration sites (ISs), associate them with chromatin and expression signatures at different genomic scales in a microglia cell model, and profile them together with the primary T cell reservoir. HIV-1 insertions into introns of actively transcribed genes with IS hotspots in genic and super-enhancers, characteristic of blood cells, are maintained in the microglia cell model. Genome organization analysis reveals dynamic CCCTC-binding factor (CTCF) clusters in cells with active and repressed HIV-1 transcription, whereas CTCF removal impairs viral integration. We identify CTCF-enriched topologically associated domain (TAD) boundaries with signatures of transcriptionally active chromatin as HIV-1 integration determinants in microglia and CD4+ T cells, highlighting the importance of host genome organization in HIV-1 infection.
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Affiliation(s)
- Mona Rheinberger
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Ana Luisa Costa
- Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, 69120 Heidelberg, Germany
| | - Martin Kampmann
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Dunja Glavas
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Iart Luca Shytaj
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Sheetal Sreeram
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Carlotta Penzo
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Nadine Tibroni
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Yoelvis Garcia-Mesa
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Konstantin Leskov
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany.
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, 69120 Heidelberg, Germany.
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany.
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11
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Ajoge HO, Renner TM, Bélanger K, Greig M, Dankar S, Kohio HP, Coleman MD, Ndashimye E, Arts EJ, Langlois MA, Barr SD. Antiretroviral APOBEC3 cytidine deaminases alter HIV-1 provirus integration site profiles. Nat Commun 2023; 14:16. [PMID: 36627271 PMCID: PMC9832166 DOI: 10.1038/s41467-022-35379-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/30/2022] [Indexed: 01/12/2023] Open
Abstract
APOBEC3 (A3) proteins are host-encoded deoxycytidine deaminases that provide an innate immune barrier to retroviral infection, notably against HIV-1. Low levels of deamination are believed to contribute to the genetic evolution of HIV-1, while intense catalytic activity of these proteins can induce catastrophic hypermutation in proviral DNA leading to near-total HIV-1 restriction. So far, little is known about how A3 cytosine deaminases might impact HIV-1 proviral DNA integration sites in human chromosomal DNA. Using a deep sequencing approach, we analyze the influence of catalytic active and inactive APOBEC3F and APOBEC3G on HIV-1 integration site selections. Here we show that DNA editing is detected at the extremities of the long terminal repeat regions of the virus. Both catalytic active and non-catalytic A3 mutants decrease insertions into gene coding sequences and increase integration sites into SINE elements, oncogenes and transcription-silencing non-B DNA features. Our data implicates A3 as a host factor influencing HIV-1 integration site selection and also promotes what appears to be a more latent expression profile.
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Affiliation(s)
- Hannah O Ajoge
- Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, London, ON, Canada
| | - Tyler M Renner
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kasandra Bélanger
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Matthew Greig
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Samar Dankar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hinissan P Kohio
- Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, London, ON, Canada
| | - Macon D Coleman
- Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, London, ON, Canada
| | - Emmanuel Ndashimye
- Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, London, ON, Canada
| | - Eric J Arts
- Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, London, ON, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Ottawa Center for Infection, Immunity and Inflammation (CI3), Ottawa, ON, Canada.
| | - Stephen D Barr
- Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, London, ON, Canada.
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12
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Mohamed H, Berman R, Connors J, Haddad EK, Miller V, Nonnemacher MR, Dampier W, Wigdahl B, Krebs FC. Immunomodulatory Effects of Non-Thermal Plasma in a Model for Latent HIV-1 Infection: Implications for an HIV-1-Specific Immunotherapy. Biomedicines 2023; 11:122. [PMID: 36672628 PMCID: PMC9856147 DOI: 10.3390/biomedicines11010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
In people living with HIV-1 (PLWH), antiretroviral therapy (ART) eventually becomes necessary to suppress the emergence of human immunodeficiency virus type 1 (HIV-1) replication from latent reservoirs because HIV-1-specific immune responses in PLWH are suboptimal. Immunotherapies that enhance anti-HIV-1 immune responses for better control of virus reemergence from latent reservoirs are postulated to offer ART-free control of HIV-1. Toward the goal of developing an HIV-1-specific immunotherapy based on non-thermal plasma (NTP), the early immunological responses to NTP-exposed latently infected T lymphocytes were examined. Application of NTP to the J-Lat T-lymphocyte cell line (clones 10.6 and 15.4) stimulated monocyte recruitment and macrophage maturation, which are key steps in initiation of an immune response. In contrast, CD8+ T lymphocytes in a mixed lymphocyte reaction assay were not stimulated by the presence of NTP-exposed J-Lat cells. Furthermore, co-culture of NTP-exposed J-Lat cells with mature phagocytes did not modulate their antigen presentation to primary CD8+ T lymphocytes (cross-presentation). However, reactivation from latency was stimulated in a clone-specific manner by NTP. Overall, these studies, which demonstrated that ex vivo application of NTP to latently infected lymphocytes can stimulate key immune cell responses, advance the development of an NTP-based immunotherapy that will provide ART-free control of HIV-1 reactivation in PLWH.
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Affiliation(s)
- Hager Mohamed
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Rachel Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Jennifer Connors
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Division of Infectious Diseases & HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Elias K. Haddad
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Division of Infectious Diseases & HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Vandana Miller
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Fred C. Krebs
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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13
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Friedman MJ, Lee H, Kwon YC, Oh S. Dynamics of Viral and Host 3D Genome Structure upon Infection. J Microbiol Biotechnol 2022; 32:1515-1526. [PMID: 36398441 PMCID: PMC9843816 DOI: 10.4014/jmb.2208.08020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022]
Abstract
Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including transcriptional regulation of gene expression. Like other host cellular mechanisms, viral pathogens utilize and modulate host chromatin architecture and its regulatory machinery to control features of their life cycle, such as lytic versus latent status. Combined with previous research focusing on individual loci, recent global genomic studies employing conformational assays coupled with high-throughput sequencing technology have informed models for host and, in some cases, viral 3D chromosomal structure re-organization during infection and the contribution of these alterations to virus-mediated diseases. Here, we review recent discoveries and progress in host and viral chromatin structural dynamics during infection, focusing on a subset of DNA (human herpesviruses and HPV) as well as RNA (HIV, influenza virus and SARS-CoV-2) viruses. An understanding of how host and viral genomic structure affect gene expression in both contexts and ultimately viral pathogenesis can facilitate the development of novel therapeutic strategies.
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Affiliation(s)
- Meyer J. Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Haram Lee
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
| | - Young-Chan Kwon
- Center for Convergent Research of Emerging Virus Infections, Korean Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Soohwan Oh
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
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14
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HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA. J Virol 2022; 96:e0101122. [PMID: 36094316 PMCID: PMC9517705 DOI: 10.1128/jvi.01011-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HIV-1 DNA is preferentially integrated into chromosomal hot spots by the preintegration complex (PIC). To understand the mechanism, we measured the DNA integration activity of PICs-extracted from infected cells-and intasomes, biochemically assembled PIC substructures using a number of relevant target substrates. We observed that PIC-mediated integration into human chromatin is preferred compared to genomic DNA. Surprisingly, nucleosomes lacking histone modifications were not preferred integration compared to the analogous naked DNA. Nucleosomes containing the trimethylated histone 3 lysine 36 (H3K36me3), an epigenetic mark linked to active transcription, significantly stimulated integration, but the levels remained lower than the naked DNA. Notably, H3K36me3-modified nucleosomes with linker DNA optimally supported integration mediated by the PIC but not by the intasome. Interestingly, optimal intasome-mediated integration required the cellular cofactor LEDGF. Unexpectedly, LEDGF minimally affected PIC-mediated integration into naked DNA but blocked integration into nucleosomes. The block for the PIC-mediated integration was significantly relieved by H3K36me3 modification. Mapping the integration sites in the preferred substrates revealed that specific features of the nucleosome-bound DNA are preferred for integration, whereas integration into naked DNA was random. Finally, biochemical and genetic studies demonstrate that DNA condensation by the H1 protein dramatically reduces integration, providing further evidence that features inherent to the open chromatin are preferred for HIV-1 integration. Collectively, these results identify the optimal target substrate for HIV-1 integration, report a mechanistic link between H3K36me3 and integration preference, and importantly, reveal distinct mechanisms utilized by the PIC for integration compared to the intasomes. IMPORTANCE HIV-1 infection is dependent on integration of the viral DNA into the host chromosomes. The preintegration complex (PIC) containing the viral DNA, the virally encoded integrase (IN) enzyme, and other viral/host factors carries out HIV-1 integration. HIV-1 integration is not dependent on the target DNA sequence, and yet the viral DNA is selectively inserted into specific "hot spots" of human chromosomes. A growing body of literature indicates that structural features of the human chromatin are important for integration targeting. However, the mechanisms that guide the PIC and enable insertion of the PIC-associated viral DNA into specific hot spots of the human chromosomes are not fully understood. In this study, we describe a biochemical mechanism for the preference of the HIV-1 DNA integration into open chromatin. Furthermore, our study defines a direct role for the histone epigenetic mark H3K36me3 in HIV-1 integration preference and identify an optimal substrate for HIV-1 PIC-mediated viral DNA integration.
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15
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Kalhori MR, Soleimani M, Yari K, Moradi M, Kalhori AA. MiR-1290: a potential therapeutic target for regenerative medicine or diagnosis and treatment of non-malignant diseases. Clin Exp Med 2022:10.1007/s10238-022-00854-9. [PMID: 35802264 DOI: 10.1007/s10238-022-00854-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
Abstract
MicroRNAs are a set of small non-coding RNAs that could change gene expression with post-transcriptional regulation. MiRNAs have a significant role in regulating molecular signaling pathways and innate and adaptive immune system activity. Moreover, miRNAs can be utilized as a powerful instrument for tissue engineers and regenerative medicine by altering the expression of genes and growth factors. MiR-1290, which was first discovered in human embryonic stem cells, is one of those miRNAs that play an essential role in developing the fetal nervous system. This review aims to discuss current findings on miR-1290 in different human pathologies and determine whether manipulation of miR-1290 could be considered a possible therapeutic strategy to treat different non-malignant diseases. The results of these studies suggest that the regulation of miR-1290 may be helpful in the treatment of some bacterial (leprosy) and viral infections (HIV, influenza A, and Borna disease virus). Also, adjusting the expression of miR-1290 in non-infectious diseases such as celiac disease, necrotizing enterocolitis, polycystic ovary syndrome, pulmonary fibrosis, ankylosing spondylitis, muscle atrophy, sarcopenia, and ischemic heart disease can help to treat these diseases better. In addition to acting as a biomarker for the diagnosis of non-malignant diseases (such as NAFLD, fetal growth, preeclampsia, down syndrome, chronic rhinosinusitis, and oral lichen planus), the miR-1290 can also be used as a valuable instrument in tissue engineering and reconstructive medicine. Consequently, it is suggested that the regulation of miR-1290 could be considered a possible therapeutic target in the treatment of non-malignant diseases in the future.
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Affiliation(s)
- Mohammad Reza Kalhori
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kheirollah Yari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mahmoudreza Moradi
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amir Ali Kalhori
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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16
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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Heterogeneity of Latency Establishment in the Different Human CD4
+
T Cell Subsets Stimulated with IL-15. J Virol 2022; 96:e0037922. [PMID: 35499323 PMCID: PMC9131862 DOI: 10.1128/jvi.00379-22] [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: 11/29/2022] Open
Abstract
HIV integrates into the host genome, creating a viral reservoir of latently infected cells that persists despite effective antiretroviral treatment. CD4-positive (CD4+) T cells are the main contributors to the HIV reservoir. CD4+ T cells are a heterogeneous population, and the mechanisms of latency establishment in the different subsets, as well as their contribution to the reservoir, are still unclear. In this study, we analyzed HIV latency establishment in different CD4+ T cell subsets stimulated with interleukin 15 (IL-15), a cytokine that increases both susceptibility to infection and reactivation from latency. Using a dual-reporter virus that allows discrimination between latent and productive infection at the single-cell level, we found that IL-15-treated primary human CD4+ T naive and CD4+ T stem cell memory (TSCM) cells are less susceptible to HIV infection than CD4+ central memory (TCM), effector memory (TEM), and transitional memory (TTM) cells but are also more likely to harbor transcriptionally silent provirus. The propensity of these subsets to harbor latent provirus compared to the more differentiated memory subsets was independent of differential expression of pTEFb components. Microscopy analysis of NF-κB suggested that CD4+ T naive cells express smaller amounts of nuclear NF-κB than the other subsets, partially explaining the inefficient long terminal repeat (LTR)-driven transcription. On the other hand, CD4+ TSCM cells display similar levels of nuclear NF-κB to CD4+ TCM, CD4+ TEM, and CD4+ TTM cells, indicating the availability of transcription initiation and elongation factors is not solely responsible for the inefficient HIV gene expression in the CD4+ TSCM subset. IMPORTANCE The formation of a latent reservoir is the main barrier to HIV cure. Here, we investigated how HIV latency is established in different CD4+ T cell subsets in the presence of IL-15, a cytokine that has been shown to efficiently induce latency reversal. We observed that, even in the presence of IL-15, the less differentiated subsets display lower levels of productive HIV infection than the more differentiated subsets. These differences were not related to different expression of pTEFb, and modest differences in NF-κB were observed for CD4+ T naive cells only, implying the involvement of other mechanisms. Understanding the molecular basis of latency establishment in different CD4+ T cell subsets might be important for tailoring specific strategies to reactivate HIV transcription in all the CD4+ T subsets that compose the latent reservoir.
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18
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Xufré C, González T, Leal L, Trubey CM, Lifson JD, Gatell JM, Alcamí J, Climent N, García F, Sánchez-Palomino S. Highly Efficient Autologous HIV-1 Isolation by Coculturing Macrophage With Enriched CD4 + T Cells From HIV-1 Patients. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2022; 2:869431. [PMID: 35967461 PMCID: PMC9364968 DOI: 10.3389/fviro.2022.869431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We described a novel HIV autologous isolation method based in coculturing macrophages and CD4+T-cell-enriched fractions from peripheral blood collected from antiretroviral-treated (ART) HIV patients. This method allows the isolation of high viral titers of autologous viruses, over 1010HIV RNA copies/ml, and reduces the time required to produce necessary amounts for virus for use as antigens presented by monocyte-derived myeloid cells in HIV therapeutic vaccine approaches. By applying these high titer and autologous virus produced in the patient-derived cells, we intended to elicit a boost of the immunological system response in HIV therapeutic vaccines in clinical trials.
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Affiliation(s)
- Cristina Xufré
- AIDS Research Group, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Tanía González
- AIDS Research Group, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) of Infectious Diseases, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Lorna Leal
- AIDS Research Group, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
- Infectious Diseases Service, Hospital Clinic, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Charles M. Trubey
- AIDS and Cancer Virus Program Inc., Frederick National Laboratory, Frederick, MD, United States
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program Inc., Frederick National Laboratory, Frederick, MD, United States
| | - José María Gatell
- AIDS Research Group, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - José Alcamí
- AIDS Research Group, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) of Infectious Diseases, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Núria Climent
- AIDS Research Group, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) of Infectious Diseases, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Felipe García
- Centro de Investigación Biomédica en Red (CIBER) of Infectious Diseases, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Sonsoles Sánchez-Palomino
- AIDS Research Group, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) of Infectious Diseases, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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19
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Chai H, Gu Q, Hughes J, Robertson DL. In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS Comput Biol 2022; 18:e1009720. [PMID: 35134057 PMCID: PMC8856524 DOI: 10.1371/journal.pcbi.1009720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 02/18/2022] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) continues to be a major cause of disease and premature death. As with all viruses, HIV-1 exploits a host cell to replicate. Improving our understanding of the molecular interactions between virus and human host proteins is crucial for a mechanistic understanding of virus biology, infection and host antiviral activities. This knowledge will potentially permit the identification of host molecules for targeting by drugs with antiviral properties. Here, we propose a data-driven approach for the analysis and prediction of the HIV-1 interacting proteins (VIPs) with a focus on the directionality of the interaction: host-dependency versus antiviral factors. Using support vector machine learning models and features encompassing genetic, proteomic and network properties, our results reveal some significant differences between the VIPs and non-HIV-1 interacting human proteins (non-VIPs). As assessed by comparison with the HIV-1 infection pathway data in the Reactome database (sensitivity > 90%, threshold = 0.5), we demonstrate these models have good generalization properties. We find that the ‘direction’ of the HIV-1-host molecular interactions is also predictable due to different characteristics of ‘forward’/pro-viral versus ‘backward’/pro-host proteins. Additionally, we infer the previously unknown direction of the interactions between HIV-1 and 1351 human host proteins. A web server for performing predictions is available at http://hivpre.cvr.gla.ac.uk/.
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Affiliation(s)
- Haiting Chai
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- * E-mail:
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20
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Antiviral Activity and Resistance Profile of the Novel HIV-1 Non-Catalytic Site Integrase Inhibitor, JTP-0157602. J Virol 2022; 96:e0184321. [PMID: 35045265 DOI: 10.1128/jvi.01843-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 integrase (IN) is an essential enzyme for viral replication. Non-catalytic site integrase inhibitors (NCINIs) are allosteric HIV-1 IN inhibitors and a potential new class of antiretrovirals. In this report, we identified a novel NCINI, JTP-0157602, with an original scaffold. JTP-0157602 exhibited potent antiviral activity against HIV-1 and showed a serum-shifted EC90 of 138 nM, which is comparable to the FDA-approved IN strand transfer inhibitors (INSTIs). This compound was fully potent against a wide range of recombinant viruses with IN polymorphisms, including amino acids 124/125, a hot spot of IN polymorphisms. In addition, JTP-0157602 retained potent antiviral activity against a broad panel of recombinant viruses with INSTI-related resistant mutations, including multiple substitutions that emerged in clinical studies of INSTIs. Resistance selection experiments of JTP-0157602 led to the emergence of A128T and T174I mutations, which are located at the lens epithelium-derived growth factor/p75 binding pocket of IN. JTP-0157602 inhibited HIV-1 replication mainly during the late-phase of the replication cycle, and HIV-1 virions produced by reactivation from HIV-1 latently-infected Jurkat cells in the presence of JTP-0157602 were non-infectious. These results suggest that JTP-0157602 and analog compounds can be used to treat HIV-1 infectious diseases. IMPORTANCE Non-catalytic site integrase inhibitors (NCINIs) are allosteric HIV-1 integrase (IN) inhibitors that bind to the lens epithelium-derived growth factor (LEDGF)/p75 binding pocket of IN. NCINIs are expected to be a new class of anti-HIV-1 agents. In this study, we present a novel NCINI, JTP-0157602, which has potent activity against a broad range of HIV-1 strains with IN polymorphisms. Furthermore, JTP-0157602 shows strong antiviral activity against IN strand transfer inhibitor-resistant mutations, suggesting JTP-0157602 and its analogs are potential agents to treat HIV-1 infections. Structural modeling indicated that JTP-0157602 binds to the LEDGF/p75 binding pocket of IN, and the results of in vitro resistance induction revealed the JTP-0157602-resistance mechanism of HIV-1. These data shed light on developing novel NCINIs, which exhibit potent activity against HIV-1 with broad IN polymorphisms and multi-drug resistant HIV-1 variants.
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21
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Koonin EV, Dolja VV, Krupovic M, Kuhn JH. Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiol Mol Biol Rev 2021; 85:e0019320. [PMID: 34468181 PMCID: PMC8483706 DOI: 10.1128/mmbr.00193-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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22
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Lau CY, Adan MA, Maldarelli F. Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. Viruses 2021; 13:2512. [PMID: 34960781 PMCID: PMC8708047 DOI: 10.3390/v13122512] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antiretroviral therapy (ART) effectively reduces cycles of viral replication but does not target proviral populations in cells that persist for prolonged periods and that can undergo clonal expansion. Consequently, chronic human immunodeficiency virus (HIV) infection is sustained during ART by a reservoir of long-lived latently infected cells and their progeny. This proviral landscape undergoes change over time on ART. One of the forces driving change in the landscape is the clonal expansion of infected CD4 T cells, which presents a key obstacle to HIV eradication. Potential mechanisms of clonal expansion include general immune activation, antigenic stimulation, homeostatic proliferation, and provirus-driven clonal expansion, each of which likely contributes in varying, and largely unmeasured, amounts to maintaining the reservoir. The role of clinical events, such as infections or neoplasms, in driving these mechanisms remains uncertain, but characterizing these forces may shed light on approaches to effectively eradicate HIV. A limited number of individuals have been cured of HIV infection in the setting of bone marrow transplant; information from these and other studies may identify the means to eradicate or control the virus without ART. In this review, we describe the mechanisms of HIV-1 persistence and clonal expansion, along with the attempts to modify these factors as part of reservoir reduction and cure strategies.
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Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
- Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
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23
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Shen Q, Wu C, Freniere C, Tripler TN, Xiong Y. Nuclear Import of HIV-1. Viruses 2021; 13:2242. [PMID: 34835048 PMCID: PMC8619967 DOI: 10.3390/v13112242] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
The delivery of the HIV-1 genome into the nucleus is an indispensable step in retroviral infection of non-dividing cells, but the mechanism of HIV-1 nuclear import has been a longstanding debate due to controversial experimental evidence. It was commonly believed that the HIV-1 capsid would need to disassemble (uncoat) in the cytosol before nuclear import because the capsid is larger than the central channel of nuclear pore complexes (NPCs); however, increasing evidence demonstrates that intact, or nearly intact, HIV-1 capsid passes through the NPC to enter the nucleus. With the protection of the capsid, the HIV-1 core completes reverse transcription in the nucleus and is translocated to the integration site. Uncoating occurs while, or after, the viral genome is released near the integration site. These independent discoveries reveal a compelling new paradigm of this important step of the HIV-1 life cycle. In this review, we summarize the recent studies related to HIV-1 nuclear import, highlighting the spatial-temporal relationship between the nuclear entry of the virus core, reverse transcription, and capsid uncoating.
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Affiliation(s)
| | | | | | | | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; (Q.S.); (C.W.); (C.F.); (T.N.T.)
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24
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Abstract
To infect nondividing cells, HIV-1 needs to cross the nuclear membrane. The importin transportin-SR2 (TRN-SR2 or transportin-3) has been proposed to mediate HIV-1 nuclear import, but the detailed mechanism remains unresolved. The direct interaction of TRN-SR2 with HIV-1 integrase (IN) has been proposed to drive HIV-1 nuclear import. Alternatively, TRN-SR2 may play an indirect role by mediating nuclear import of cleavage and polyadenylation specificity factor 6 (CPSF6). To unravel the role of TRN-SR2, we designed CRISPR/Cas9 guide RNAs targeting different exons of TNPO3. Although this approach failed to generate full knockouts, monoallelic knockout clones were generated with indel mutations. HIV-1 replication was hampered in those clones at the level of HIV-1 nuclear import without an effect on the cellular distribution of the TRN-SR2 cargoes CPSF6 or alternative splicing factor1/pre-mRNA splicing factor SF2 (ASF/SF2). Recombinant ΔV105 TRN-SR2 expressed in clone 15.15 was 2-fold impaired for interaction with HIV-1 IN and classified as an interaction mutant. Our data support a model whereby TRN-SR2 acts as a cofactor of HIV-1 nuclear import without compromising the nuclear import of cellular cargoes. CRISPR/Cas9-induced mutagenesis can be used as a method to generate interface mutants to characterize host factors of human pathogens. IMPORTANCE Combination antiretroviral therapy (cART) effectively controls HIV-1 by reducing viral loads, but it does not cure the infection. Lifelong treatment with cART is a prerequisite for sustained viral suppression. The rapid emergence of drug-resistant viral strains drives the necessity to discover new therapeutic targets. The nuclear import of HIV-1 is crucial in the HIV-1 replication cycle, but the detailed mechanism remains incompletely understood. This study provides evidence that TRN-SR2 directly mediates HIV-1 nuclear import via the interaction with HIV-1 integrase. The interaction between those proteins is therefore a promising target toward a rational drug design which could lead to new therapeutic strategies due to the bottleneck nature of HIV-1 nuclear import.
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25
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Segura J, He B, Ireland J, Zou Z, Shen T, Roth G, Sun PD. The Role of L-Selectin in HIV Infection. Front Microbiol 2021; 12:725741. [PMID: 34659153 PMCID: PMC8511817 DOI: 10.3389/fmicb.2021.725741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
HIV envelope glycoprotein is the most heavily glycosylated viral protein complex identified with over 20 glycans on its surface. This glycan canopy is thought to primarily shield the virus from host immune recognition as glycans are poor immunogens in general, however rare HIV neutralizing antibodies nevertheless potently recognize the glycan epitopes. While CD4 and chemokine receptors have been known as viral entry receptor and coreceptor, for many years the role of viral glycans in HIV entry was controversial. Recently, we showed that HIV envelope glycan binds to L-selectin in solution and on CD4 T lymphocytes. The viral glycan and L-selectin interaction functions to facilitate the viral adhesion and entry. Upon entry, infected CD4 T lymphocytes are stimulated to progressively shed L-selectin and suppressing this lectin receptor shedding greatly reduced HIV viral release and caused aggregation of diminutive virus-like particles within experimental infections and from infected primary T lymphocytes derived from both viremic and aviremic individuals. As shedding of L-selectin is mediated by ADAM metalloproteinases downstream of host-cell stimulation, these findings showed a novel mechanism for HIV viral release and offer a potential new class of anti-HIV compounds.
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Affiliation(s)
- Jason Segura
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Biao He
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Joanna Ireland
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Zhongcheng Zou
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Thomas Shen
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Gwynne Roth
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Peter D Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
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26
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Yang X, Huang T, Wang T, Gao H, Zhang H, Peng W, Zhao J, Hu S, Lu P, Hong Z, Li B, Deng K. MAT2A-Mediated S-Adenosylmethionine Level in CD4 + T Cells Regulates HIV-1 Latent Infection. Front Immunol 2021; 12:745784. [PMID: 34616406 PMCID: PMC8488394 DOI: 10.3389/fimmu.2021.745784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 12/02/2022] Open
Abstract
Antiretroviral drugs effectively halt HIV-1 replication and disease progression, however, due to the presence of a stable viral latent reservoir, the infection cannot be cured by antiretroviral drugs alone. Elucidating the molecular mechanisms underlying HIV-1 latent infection remains a critical hurdle that precludes the development of novel therapeutic strategies aiming for a potential functional cure. Cellular metabolism has been reported to affect HIV-1 replication in CD4+ T cells, but it remains largely unclear whether it is involved in the regulation of HIV-1 latency. Here, we performed a sub-pooled CRISPR library knockout screen targeting 1773 metabolic-related genes in a cell model of HIV-1 latent infection and found that Methionine Adenosyltransferase 2A (MAT2A) contributes to HIV-1 latency. MAT2A knockout enhanced the reactivation of latent HIV-1 while MAT2A overexpression did the opposite. Mechanistically, MAT2A modulates HIV-1 latency through S-Adenosylmethionine (SAM)-mediated one-carbon flux. MAT2A knockout resulted in a significant downregulation of DNA and histone methylation at the HIV-1 5’-LTR. Importantly, we found that the plasma level of SAM is positively correlated with HIV-1 DNA in PBMCs from ART-treated infected individuals, suggesting SAM could serve as a potential biomarker for the latent viral reservoir. Overall, this study reveals an important role of MAT2A-mediated one-carbon metabolism in regulating HIV-1 latency and provides a promising target for the development of new strategies for a functional cure of HIV-1.
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Affiliation(s)
- Xiaofan Yang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ting Huang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Tiantian Wang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongbo Gao
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Haitao Zhang
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Wen Peng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jiacong Zhao
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shujing Hu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Panpan Lu
- School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Zhongsi Hong
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Bo Li
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kai Deng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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27
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Forte G, Michieletto D, Marenduzzo D, Orlandini E. Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids. J R Soc Interface 2021; 18:20210229. [PMID: 34428944 PMCID: PMC8385341 DOI: 10.1098/rsif.2021.0229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We theoretically study the integration of short viral DNA in a DNA braid made up by two entwined double-stranded DNA molecules. We show that the statistics of single integration events substantially differ in the straight and buckled, or plectonemic, phase of the braid and are more likely in the latter. We further discover that integration is most likely close to plectoneme tips, where the larger bending energy helps overcome the associated energy barrier and that successive integration events are spatio-temporally correlated, suggesting a potential mechanistic explanation of clustered integration sites in host genomes. The braid geometry we consider provides a novel experimental set-up to quantify integration in a supercoiled substrate in vitro, and to better understand the role of double-stranded DNA topology during this process.
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Affiliation(s)
- G Forte
- SUPA, School of Physics and Astronomy, Peter Guthrie Tait Road, University of Edinburgh, Edinburgh EH9 3FD, UK.,MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - D Michieletto
- SUPA, School of Physics and Astronomy, Peter Guthrie Tait Road, University of Edinburgh, Edinburgh EH9 3FD, UK.,MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, Peter Guthrie Tait Road, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - E Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universitá degli Studi di Padova, 35131 Padova, Italy
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28
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Sonti S, Sharma AL, Tyagi M. HIV-1 persistence in the CNS: Mechanisms of latency, pathogenesis and an update on eradication strategies. Virus Res 2021; 303:198523. [PMID: 34314771 DOI: 10.1016/j.virusres.2021.198523] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/14/2021] [Accepted: 07/17/2021] [Indexed: 12/20/2022]
Abstract
Despite four decades of research into the human immunodeficiency virus (HIV-1), a successful strategy to eradicate the virus post-infection is lacking. The major reason for this is the persistence of the virus in certain anatomical reservoirs where it can become latent and remain quiescent for as long as the cellular reservoir is alive. The Central Nervous System (CNS), in particular, is an intriguing anatomical compartment that is tightly regulated by the blood-brain barrier. Targeting the CNS viral reservoir is a major challenge owing to the decreased permeability of drugs into the CNS and the cellular microenvironment that facilitates the compartmentalization and evolution of the virus. Therefore, despite effective antiretroviral (ARV) treatment, virus persists in the CNS, and leads to neurological and neurocognitive deficits. To date, viral eradication strategies fail to eliminate the virus from the CNS. To facilitate the improvement of the existing elimination strategies, as well as the development of potential therapeutic targets, the aim of this review is to provide an in-depth understanding of HIV latency in CNS and the onset of HIV-1 associated neurological disorders.
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Affiliation(s)
- Shilpa Sonti
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | | | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.
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29
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Retrieval of vector integration sites from cell-free DNA. Nat Med 2021; 27:1458-1470. [PMID: 34140705 DOI: 10.1038/s41591-021-01389-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/07/2021] [Indexed: 12/23/2022]
Abstract
Gene therapy (GT) has rapidly attracted renewed interest as a treatment for otherwise incurable diseases, with several GT products already on the market and many more entering clinical testing for selected indications. Clonal tracking techniques based on vector integration enable monitoring of the fate of engineered cells in the blood of patients receiving GT and allow assessment of the safety and efficacy of these procedures. However, owing to the limited number of cells that can be tested and the impracticality of studying cells residing in peripheral organs without performing invasive biopsies, this approach provides only a partial snapshot of the clonal repertoire and dynamics of genetically modified cells and reduces the predictive power as a safety readout. In this study, we developed liquid biopsy integration site sequencing, or LiBIS-seq, a polymerase chain reaction technique optimized to quantitatively retrieve vector integration sites from cell-free DNA released into the bloodstream by dying cells residing in several tissues. This approach enabled longitudinal monitoring of in vivo liver-directed GT and clonal tracking in patients receiving hematopoietic stem cell GT, improving our understanding of the clonal composition and turnover of genetically modified cells in solid tissues and, in contrast to conventional analyses based only on circulating blood cells, enabling earlier detection of vector-marked clones that are aberrantly expanding in peripheral tissues.
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30
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Salahong T, Schwartz C, Sungthong R. Are BET Inhibitors yet Promising Latency-Reversing Agents for HIV-1 Reactivation in AIDS Therapy? Viruses 2021; 13:v13061026. [PMID: 34072421 PMCID: PMC8228869 DOI: 10.3390/v13061026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
AIDS first emerged decades ago; however, its cure, i.e., eliminating all virus sources, is still unachievable. A critical burden of AIDS therapy is the evasive nature of HIV-1 in face of host immune responses, the so-called "latency." Recently, a promising approach, the "Shock and Kill" strategy, was proposed to eliminate latently HIV-1-infected cell reservoirs. The "Shock and Kill" concept involves two crucial steps: HIV-1 reactivation from its latency stage using a latency-reversing agent (LRA) followed by host immune responses to destroy HIV-1-infected cells in combination with reinforced antiretroviral therapy to kill the progeny virus. Hence, a key challenge is to search for optimal LRAs. Looking at epigenetics of HIV-1 infection, researchers proved that some bromodomains and extra-terminal motif protein inhibitors (BETis) are able to reactivate HIV-1 from latency. However, to date, only a few BETis have shown HIV-1-reactivating functions, and none of them have yet been approved for clinical trial. In this review, we aim to demonstrate the epigenetic roles of BETis in HIV-1 infection and HIV-1-related immune responses. Possible future applications of BETis and their HIV-1-reactivating properties are summarized and discussed.
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Affiliation(s)
- Thanarat Salahong
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Christian Schwartz
- Research Unit 7292, DHPI, IUT Louis Pasteur, University of Strasbourg, 67300 Schiltigheim, France
- Correspondence: (C.S.); (R.S.)
| | - Rungroch Sungthong
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
- Laboratory of Hydrology and Geochemistry of Strasbourg, University of Strasbourg, UMR 7517 CNRS/EOST, 67084 Strasbourg CEDEX, France
- Correspondence: (C.S.); (R.S.)
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31
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Müller TG, Zila V, Peters K, Schifferdecker S, Stanic M, Lucic B, Laketa V, Lusic M, Müller B, Kräusslich HG. HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells. eLife 2021; 10:64776. [PMID: 33904396 PMCID: PMC8169111 DOI: 10.7554/elife.64776] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
HIV-1 replication commences inside the cone-shaped viral capsid, but timing, localization, and mechanism of uncoating are under debate. We adapted a strategy to visualize individual reverse-transcribed HIV-1 cDNA molecules and their association with viral and cellular proteins using fluorescence and correlative-light-and-electron-microscopy (CLEM). We specifically detected HIV-1 cDNA inside nuclei, but not in the cytoplasm. Nuclear cDNA initially co-localized with a fluorescent integrase fusion (IN-FP) and the viral CA (capsid) protein, but cDNA-punctae separated from IN-FP/CA over time. This phenotype was conserved in primary HIV-1 target cells, with nuclear HIV-1 complexes exhibiting strong CA-signals in all cell types. CLEM revealed cone-shaped HIV-1 capsid-like structures and apparently broken capsid-remnants at the position of IN-FP signals and elongated chromatin-like structures in the position of viral cDNA punctae lacking IN-FP. Our data argue for nuclear uncoating by physical disruption rather than cooperative disassembly of the CA-lattice, followed by physical separation from the pre-integration complex.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kyra Peters
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sandra Schifferdecker
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mia Stanic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bojana Lucic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
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32
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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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33
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Abstract
Exogenous retroviruses are RNA viruses that require reverse transcription for their replication. Among these viruses, human immunodeficiency virus (HIV) is infectious to humans and causes the development of acquired immune deficiency syndrome (AIDS). There are also endogenous retroelements that require reverse transcription for their retrotransposition, among which the type 1 long interspersed element (LINE-1) is the only type of retroelement that can replicate autonomously. It was once believed that retroviruses like HIV and retroelements like LINE-1 share similarities in processes such as reverse transcription and integration. Accordingly, many HIV suppressors are also potent LINE-1 inhibitors. However, in many cases, one suppressor uses two or more distinct mechanisms to repress HIV and LINE-1. In this review, we discuss some of these suppressors, focusing on their alternative mechanisms opposing the replication of HIV and LINE-1. Based on the differences in HIV and LINE-1 activity, the subcellular localization of these suppressors, and the impact of LINE-1 retrotransposition on human cells, we propose possible reasons for the inhibition of HIV and LINE-1 through different pathways by these suppressors, with the hope of accelerating future studies in associated research fields.
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Affiliation(s)
- Juan Du
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, China
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, China
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34
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Zila V, Margiotta E, Turoňová B, Müller TG, Zimmerli CE, Mattei S, Allegretti M, Börner K, Rada J, Müller B, Lusic M, Kräusslich HG, Beck M. Cone-shaped HIV-1 capsids are transported through intact nuclear pores. Cell 2021; 184:1032-1046.e18. [PMID: 33571428 PMCID: PMC7895898 DOI: 10.1016/j.cell.2021.01.025] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/20/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle.
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Affiliation(s)
- Vojtech Zila
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Erica Margiotta
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Beata Turoňová
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christian E Zimmerli
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Simone Mattei
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland; European Molecular Biology Laboratory, Imaging Center, 69117 Heidelberg, Germany
| | - Matteo Allegretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany
| | - Jona Rada
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany.
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Max Planck Institute of Biophysics, Department of Molecular Sociology, 60438 Frankfurt, Germany.
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35
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Bonnet A, Lesage P. Light and shadow on the mechanisms of integration site selection in yeast Ty retrotransposon families. Curr Genet 2021; 67:347-357. [PMID: 33590295 DOI: 10.1007/s00294-021-01154-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/21/2022]
Abstract
Transposable elements are ubiquitous in genomes. Their successful expansion depends in part on their sites of integration in their host genome. In Saccharomyces cerevisiae, evolution has selected various strategies to target the five Ty LTR-retrotransposon families into gene-poor regions in a genome, where coding sequences occupy 70% of the DNA. The integration of Ty1/Ty2/Ty4 and Ty3 occurs upstream and at the transcription start site of the genes transcribed by RNA polymerase III, respectively. Ty5 has completely different integration site preferences, targeting heterochromatin regions. Here, we review the history that led to the identification of the cellular tethering factors that play a major role in anchoring Ty retrotransposons to their preferred sites. We also question the involvement of additional factors in the fine-tuning of the integration site selection, with several studies converging towards an importance of the structure and organization of the chromatin.
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Affiliation(s)
- Amandine Bonnet
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France.
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36
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Zeng X, Zhao L, Shen C, Zhou Y, Li G, Sung WK. HIVID2: an accurate tool to detect virus integrations in the host genome. Bioinformatics 2021; 37:1821-1827. [PMID: 33453108 DOI: 10.1093/bioinformatics/btab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/27/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Virus integration in the host genome is frequently reported to be closely associated with many human diseases, and the detection of virus integration is a critically challenging task. However, most existing tools show limited specificity and sensitivity. Therefore, the objective of this study is to develop a method for accurate detection of virus integration into host genomes. RESULTS Herein, we report a novel method termed HIVID2 that is a significant upgrade of HIVID. HIVID2 performs a paired-end combination (PE-combination) for potentially integrated reads. The resulting sequences are then remapped onto the reference genomes, and both split and discordant chimeric reads are used to identify accurate integration breakpoints with high confidence. HIVID2 represents a great improvement in specificity and sensitivity, and predicts breakpoints closer to the real integrations, compared with existing methods. The advantage of our method was demonstrated using both simulated and real data sets. HIVID2 uncovered novel integration breakpoints in well-known cervical cancer-related genes, including FHIT and LRP1B, which was verified using protein expression data. In addition, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations. By analyzing the simulated data and real data tests, we demonstrated that HIVID2 is not only more accurate than HIVID but also better than other existing programs with respect to both sensitivity and specificity. We believe that HIVID2 will help in enhancing future research associated with virus integration. AVAILABILITY HIVID2 can be accessed at https://github.com/zengxi-hada/HIVID2/. CONTACT Xi Zeng (zengxi@mail.hzau.edu.cn), Linghao Zhao (michael_yifan@126.com). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Linghao Zhao
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Chenhang Shen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Zhou
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.,Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore.,Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
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37
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Lämmle CA, Varady A, Müller TG, Sturtzel C, Riepl M, Mathes B, Eichhorst J, Sporbert A, Lehmann M, Kräusslich HG, Distel M, Broichhagen J. Photocaged Hoechst Enables Subnuclear Visualization and Cell Selective Staining of DNA in vivo. Chembiochem 2020; 22:548-556. [PMID: 32974998 PMCID: PMC7894298 DOI: 10.1002/cbic.202000465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/17/2020] [Indexed: 12/19/2022]
Abstract
Selective targeting of DNA by means of fluorescent labeling has become a mainstay in the life sciences. While genetic engineering serves as a powerful technique and allows the visualization of nucleic acid by using DNA‐targeting fluorescent fusion proteins in a cell‐type‐ and subcellular‐specific manner, it relies on the introduction of foreign genes. On the other hand, DNA‐binding small fluorescent molecules can be used without genetic engineering, but they are not spatially restricted. Herein, we report a photocaged version of the DNA dye Hoechst33342 (pcHoechst), which can be uncaged by using UV to blue light for the selective staining of chromosomal DNA in subnuclear regions of live cells. Expanding its application to a vertebrate model organism, we demonstrate uncaging in epithelial cells and short‐term cell tracking in vivo in zebrafish. We envision pcHoechst as a valuable tool for targeting and interrogating DNA with precise spatiotemporal resolution in living cells and wild‐type organisms.
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Affiliation(s)
- Carina A Lämmle
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Adam Varady
- St. Anna Children's Cancer Research Institute, Innovative Cancer Models, Zimmermannplatz 10, 1090, Vienna, Austria
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute, Innovative Cancer Models, Zimmermannplatz 10, 1090, Vienna, Austria.,Zebrafish Platform Austria for preclinical drug screening (ZANDR), Zimmermannplatz 10, 1090, Vienna, Austria
| | - Michael Riepl
- St. Anna Children's Cancer Research Institute, Innovative Cancer Models, Zimmermannplatz 10, 1090, Vienna, Austria
| | - Bettina Mathes
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Jenny Eichhorst
- Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Anje Sporbert
- Advanced Light Microscopy, Max Delbrück Centrum for Molecular Medicine Berlin in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Martin Distel
- St. Anna Children's Cancer Research Institute, Innovative Cancer Models, Zimmermannplatz 10, 1090, Vienna, Austria.,Zebrafish Platform Austria for preclinical drug screening (ZANDR), Zimmermannplatz 10, 1090, Vienna, Austria
| | - Johannes Broichhagen
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany.,Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
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38
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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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Abstract
Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. However, viruses have evolved countermeasures that prevent the epigenetic silencing of their genes during lytic replication, and they can also take advantage of epigenetic silencing to establish latent infections. By contrast, the various covalent modifications added to RNAs, termed epitranscriptomic modifications, can positively regulate mRNA translation and/or stability, and both DNA and RNA viruses have evolved to utilize epitranscriptomic modifications as a means to maximize viral gene expression. As a consequence, both chromatin and RNA modifications could serve as novel targets for the development of antivirals. In this Review, we discuss how host epigenetic and epitranscriptomic processes regulate viral gene expression at the levels of chromatin and RNA function, respectively, and explore how viruses modify, avoid or utilize these processes in order to regulate viral gene expression.
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40
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Shukla A, Ramirez NGP, D’Orso I. HIV-1 Proviral Transcription and Latency in the New Era. Viruses 2020; 12:v12050555. [PMID: 32443452 PMCID: PMC7291205 DOI: 10.3390/v12050555] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Three decades of extensive work in the HIV field have revealed key viral and host cell factors controlling proviral transcription. Various models of transcriptional regulation have emerged based on the collective information from in vitro assays and work in both immortalized and primary cell-based models. Here, we provide a recount of the past and current literature, highlight key regulatory aspects, and further describe potential limitations of previous studies. We particularly delve into critical steps of HIV gene expression including the role of the integration site, nucleosome positioning and epigenomics, and the transition from initiation to pausing and pause release. We also discuss open questions in the field concerning the generality of previous regulatory models to the control of HIV transcription in patients under suppressive therapy, including the role of the heterogeneous integration landscape, clonal expansion, and bottlenecks to eradicate viral persistence. Finally, we propose that building upon previous discoveries and improved or yet-to-be discovered technologies will unravel molecular mechanisms of latency establishment and reactivation in a “new era”.
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Hu H, Xiao A, Zhang S, Li Y, Shi X, Jiang T, Zhang L, Zhang L, Zeng J. DeepHINT: understanding HIV-1 integration via deep learning with attention. Bioinformatics 2020; 35:1660-1667. [PMID: 30295703 DOI: 10.1093/bioinformatics/bty842] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/07/2018] [Accepted: 10/04/2018] [Indexed: 01/20/2023] Open
Abstract
MOTIVATION Human immunodeficiency virus type 1 (HIV-1) genome integration is closely related to clinical latency and viral rebound. In addition to human DNA sequences that directly interact with the integration machinery, the selection of HIV integration sites has also been shown to depend on the heterogeneous genomic context around a large region, which greatly hinders the prediction and mechanistic studies of HIV integration. RESULTS We have developed an attention-based deep learning framework, named DeepHINT, to simultaneously provide accurate prediction of HIV integration sites and mechanistic explanations of the detected sites. Extensive tests on a high-density HIV integration site dataset showed that DeepHINT can outperform conventional modeling strategies by automatically learning the genomic context of HIV integration from primary DNA sequence alone or together with epigenetic information. Systematic analyses on diverse known factors of HIV integration further validated the biological relevance of the prediction results. More importantly, in-depth analyses of the attention values output by DeepHINT revealed intriguing mechanistic implications in the selection of HIV integration sites, including potential roles of several DNA-binding proteins. These results established DeepHINT as an effective and explainable deep learning framework for the prediction and mechanistic study of HIV integration. AVAILABILITY AND IMPLEMENTATION DeepHINT is available as an open-source software and can be downloaded from https://github.com/nonnerdling/DeepHINT. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hailin Hu
- School of Medicine, Tsinghua University, Beijing, China
| | - An Xiao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Sai Zhang
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yangyang Li
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA.,Bioinformatics Division, BNRIST/Department of Computer Science and Technology, Tsinghua University, Beijing, China.,Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Lei Zhang
- School of Medicine, Tsinghua University, Beijing, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
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42
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Exploring histone loading on HIV DNA reveals a dynamic nucleosome positioning between unintegrated and integrated viral genome. Proc Natl Acad Sci U S A 2020; 117:6822-6830. [PMID: 32161134 PMCID: PMC7104181 DOI: 10.1073/pnas.1913754117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The biology of HIV DNA, from its synthesis to its integration into the host genome, remains poorly understood. Here we show that in the nucleus, histones are rapidly loaded on newly synthesized unintegrated HIV DNA. Interestingly, the chromatin architecture around the HIV long terminal repeat (LTR) is different in unintegrated and integrated HIV DNA. Specifically, a nucleosome present only on the DNase hypersensitive site of unintegrated HIV DNA contributes to the transcriptional silencing of unintegrated HIV DNA by preventing RNAPII recruitment. The aim of the present study was to understand the biology of unintegrated HIV-1 DNA and reveal the mechanisms involved in its transcriptional silencing. We found that histones are loaded on HIV-1 DNA after its nuclear import and before its integration in the host genome. Nucleosome positioning analysis along the unintegrated and integrated viral genomes revealed major differences in nucleosome density and position. Indeed, in addition to the well-known nucleosomes Nuc0, Nuc1, and Nuc2 loaded on integrated HIV-1 DNA, we also found NucDHS, a nucleosome that covers the DNase hypersensitive site, in unintegrated viral DNA. In addition, unintegrated viral DNA-associated Nuc0 and Nuc2 were positioned slightly more to the 5′ end relative to their position in integrated DNA. The presence of NucDHS in the proximal region of the long terminal repeat (LTR) promoter was associated with the absence of RNAPII and of the active histone marks H3K4me3 and H3ac at the LTR. Conversely, analysis of integrated HIV-1 DNA showed a loss of NucDHS, loading of RNAPII, and enrichment in active histone marks within the LTR. We propose that unintegrated HIV-1 DNA adopts a repressive chromatin structure that competes with the transcription machinery, leading to its silencing.
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43
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Wang W, Fasolino M, Cattau B, Goldman N, Kong W, Frederick MA, McCright SJ, Kiani K, Fraietta JA, Vahedi G. Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels. Proc Natl Acad Sci U S A 2020; 117:5442-5452. [PMID: 32094195 PMCID: PMC7071901 DOI: 10.1073/pnas.1919259117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chimeric antigen receptor (CAR)-T immunotherapy has yielded impressive results in several B cell malignancies, establishing itself as a powerful means to redirect the natural properties of T lymphocytes. In this strategy, the T cell genome is modified by the integration of lentiviral vectors encoding CAR that direct tumor cell killing. However, this therapeutic approach is often limited by the extent of CAR-T cell expansion in vivo. A major outstanding question is whether or not CAR-T integration itself enhances the proliferative competence of individual T cells by rewiring their regulatory landscape. To address this question, it is critical to define the identity of an individual CAR-T cell and simultaneously chart where the CAR-T vector integrates into the genome. Here, we report the development of a method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.
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Affiliation(s)
- Wenliang Wang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Maria Fasolino
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Benjamin Cattau
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Naomi Goldman
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Weimin Kong
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Megan A Frederick
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Sam J McCright
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Karun Kiani
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Joseph A Fraietta
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104;
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
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Abstract
For several decades, retroviral core uncoating has been thought to occur in the cytoplasm in coordination with reverse transcription, and while some recent studies have concluded that HIV-1 uncoating occurs at the nuclear envelope during nuclear import, none have concluded that uncoating occurs in the nucleus. Here, we developed methods to study HIV-1 uncoating by direct labeling and quantification of the viral capsid protein associated with infectious viral cores that produced transcriptionally active proviruses. We find that infectious viral cores in the nuclei of infected cells are largely intact and uncoat near their integration sites just before integration. These unexpected findings fundamentally change our understanding of HIV-1 postentry replication events. HIV-1 capsid core disassembly (uncoating) must occur before integration of viral genomic DNA into the host chromosomes, yet remarkably, the timing and cellular location of uncoating is unknown. Previous studies have proposed that intact viral cores are too large to fit through nuclear pores and uncoating occurs in the cytoplasm in coordination with reverse transcription or at the nuclear envelope during nuclear import. The capsid protein (CA) content of the infectious viral cores is not well defined because methods for directly labeling and quantifying the CA in viral cores have been unavailable. In addition, it has been difficult to identify the infectious virions because only one of ∼50 virions in infected cells leads to productive infection. Here, we developed methods to analyze HIV-1 uncoating by direct labeling of CA with GFP and to identify infectious virions by tracking viral cores in living infected cells through viral DNA integration and proviral DNA transcription. Astonishingly, our results show that intact (or nearly intact) viral cores enter the nucleus through a mechanism involving interactions with host protein cleavage and polyadenylation specificity factor 6 (CPSF6), complete reverse transcription in the nucleus before uncoating, and uncoat <1.5 h before integration near (<1.5 μm) their genomic integration sites. These results fundamentally change our current understanding of HIV-1 postentry replication events including mechanisms of nuclear import, uncoating, reverse transcription, integration, and evasion of innate immunity.
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45
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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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46
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Vansant G, Bruggemans A, Janssens J, Debyser Z. Block-And-Lock Strategies to Cure HIV Infection. Viruses 2020; 12:E84. [PMID: 31936859 PMCID: PMC7019976 DOI: 10.3390/v12010084] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Today HIV infection cannot be cured due to the presence of a reservoir of latently infected cells inducing a viral rebound upon treatment interruption. Hence, the latent reservoir is considered as the major barrier for an HIV cure. So far, efforts to completely eradicate the reservoir via a shock-and-kill approach have proven difficult and unsuccessful. Therefore, more research has been done recently on an alternative block-and-lock functional cure strategy. In contrast to the shock-and-kill strategy that aims to eradicate the entire reservoir, block-and-lock aims to permanently silence all proviruses, even after treatment interruption. HIV silencing can be achieved by targeting different factors of the transcription machinery. In this review, we first describe the underlying mechanisms of HIV transcription and silencing. Next, we give an overview of the different block-and-lock strategies under investigation.
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Affiliation(s)
- Gerlinde Vansant
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit, Leuven, 3000 Flanders, Belgium
| | - Anne Bruggemans
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit, Leuven, 3000 Flanders, Belgium
| | - Julie Janssens
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit, Leuven, 3000 Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit, Leuven, 3000 Flanders, Belgium
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Mușat MG, Nițulescu GM, Surleac M, Tsatsakis A, Spandidos DA, Margină D. HIV‑1 integrase inhibitors targeting various DDE transposases: Retroviral integration versus RAG‑mediated recombination (Review). Mol Med Rep 2019; 20:4749-4762. [PMID: 31702817 PMCID: PMC6854553 DOI: 10.3892/mmr.2019.10777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Transposases are ubiquitous mobile genetic elements responsible for genome development, driving rearrangements, such as insertions, deletions and translocations. Across species evolution, some transposases are tamed by their host and are made part of complex cellular systems. The proliferation of retroviruses is also dependent on transposase related enzymes termed integrases. Recombination‑activating gene protein (RAG)1 and metnase are just two examples of transposase domestication and together with retroviral integrases (INs), they belong to the DDE polynucleotidyl transferases superfamily. They share mechanistic and structural features linked to the RNase H‑like fold, harboring a DDE(D) metal dependent catalytic motif. Recent antiretroviral compounds target the catalytic domain of integrase, but they also have the potential of inhibiting other related enzymes. In this review, we report the activity of different classes of integrase inhibitors on various DDE transposases. Computational simulations are useful to predict the extent of off‑target activity and have been employed to study the interactions between RAG1 recombinase and compounds from three different pharmacologic classes. We demonstrate that strand‑transfer inhibitors display a higher affinity towards the RAG1 RNase H domain, as suggested by experimental data compared to allosteric inhibitors. While interference with RAG1 and 2 recombination is associated with a negative impact on immune function, the inhibition of metnase or HTLV‑1 integrase opens the way for the development of novel therapies for refractory cancers.
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Affiliation(s)
- Mihaela Georgiana Mușat
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - George Mihai Nițulescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Marius Surleac
- National Institute for Infectious Diseases ‘Matei Bals’, 021105 Bucharest, Romania
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Toxicology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Denisa Margină
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
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Affram Y, Zapata JC, Gholizadeh Z, Tolbert WD, Zhou W, Iglesias-Ussel MD, Pazgier M, Ray K, Latinovic OS, Romerio F. The HIV-1 Antisense Protein ASP Is a Transmembrane Protein of the Cell Surface and an Integral Protein of the Viral Envelope. J Virol 2019; 93:e00574-19. [PMID: 31434734 PMCID: PMC6803264 DOI: 10.1128/jvi.00574-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
The negative strand of HIV-1 encodes a highly hydrophobic antisense protein (ASP) with no known homologs. The presence of humoral and cellular immune responses to ASP in HIV-1 patients indicates that ASP is expressed in vivo, but its role in HIV-1 replication remains unknown. We investigated ASP expression in multiple chronically infected myeloid and lymphoid cell lines using an anti-ASP monoclonal antibody (324.6) in combination with flow cytometry and microscopy approaches. At baseline and in the absence of stimuli, ASP shows polarized subnuclear distribution, preferentially in areas with low content of suppressive epigenetic marks. However, following treatment with phorbol 12-myristate 13-acetate (PMA), ASP translocates to the cytoplasm and is detectable on the cell surface, even in the absence of membrane permeabilization, indicating that 324.6 recognizes an ASP epitope that is exposed extracellularly. Further, surface staining with 324.6 and anti-gp120 antibodies showed that ASP and gp120 colocalize, suggesting that ASP might become incorporated in the membranes of budding virions. Indeed, fluorescence correlation spectroscopy studies showed binding of 324.6 to cell-free HIV-1 particles. Moreover, 324.6 was able to capture and retain HIV-1 virions with efficiency similar to that of the anti-gp120 antibody VRC01. Our studies indicate that ASP is an integral protein of the plasma membranes of chronically infected cells stimulated with PMA, and upon viral budding, ASP becomes a structural protein of the HIV-1 envelope. These results may provide leads to investigate the possible role of ASP in the virus replication cycle and suggest that ASP may represent a new therapeutic or vaccine target.IMPORTANCE The HIV-1 genome contains a gene expressed in the opposite, or antisense, direction to all other genes. The protein product of this antisense gene, called ASP, is poorly characterized, and its role in viral replication remains unknown. We provide evidence that the antisense protein, ASP, of HIV-1 is found within the cell nucleus in unstimulated cells. In addition, we show that after PMA treatment, ASP exits the nucleus and localizes on the cell membrane. Moreover, we demonstrate that ASP is present on the surfaces of viral particles. Altogether, our studies identify ASP as a new structural component of HIV-1 and show that ASP is an accessory protein that promotes viral replication. The presence of ASP on the surfaces of both infected cells and viral particles might be exploited therapeutically.
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Affiliation(s)
- Yvonne Affram
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Juan C Zapata
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Zahra Gholizadeh
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - William D Tolbert
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Wei Zhou
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Maria D Iglesias-Ussel
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marzena Pazgier
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Olga S Latinovic
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Fabio Romerio
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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49
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Gavegnano C, Savarino A, Owanikoko T, Marconi VC. Crossroads of Cancer and HIV-1: Pathways to a Cure for HIV. Front Immunol 2019; 10:2267. [PMID: 31636630 PMCID: PMC6788429 DOI: 10.3389/fimmu.2019.02267] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/09/2019] [Indexed: 12/12/2022] Open
Abstract
Recently, a second individual (the “London patient”) with HIV-1 infection and concomitant leukemia was cured of both diseases by a conditioning myeloablative regimen followed by transplantation of stem cells bearing the homozygous CCR5 Δ32 mutation. The substantial risks and cost associated with this procedure render it unfeasible on a large scale. This strategy also indicates that a common pathway toward a cure for both HIV and cancer may exist. Successful approaches to curing both diseases should ideally possess three components, i.e., (1) direct targeting of pathological cells (neoplastic cells in cancer and the HIV-infected reservoir cells), (2) subsequent impediment to reconstitution of the pool of pathological cells and (3) sustained, immunologic control of the disease (both diseases are characterized by detrimental immune hyper-activation that hinders successful establishment of immunity). In this review, we explore medications that are either investigational or FDA-approved anticancer treatments that may be employed to achieve the goal of curing HIV-1. These include: thioredoxin reductase inhibitors (phases 1–3), immune checkpoint inhibitors (phases 1, 3), Jak inhibitors (FDA approved for arthritis and multiple cancer indications, summarized in Table 1). Of note, some of these medications such as arsenic trioxide and Jak inhibitors may also reversibly down regulate CCR5 expression on CD4+ T-cells, thus escaping the ethical issues of inducing or transferring mutations in CCR5 that are presently the subject of interest as it relates to HIV-1 cure strategies.
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Affiliation(s)
- Christina Gavegnano
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | | | - Taofeek Owanikoko
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, United States
| | - Vincent C Marconi
- Emory Vaccine Center, Rollins School of Public Health, Emory University School of Medicine, Atlanta, GA, United States.,Atlanta Veterans Affairs Medical Center, Atlanta, GA, United States
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50
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Verdikt R, Darcis G, Ait-Ammar A, Van Lint C. Applications of CRISPR/Cas9 tools in deciphering the mechanisms of HIV-1 persistence. Curr Opin Virol 2019; 38:63-69. [PMID: 31509794 DOI: 10.1016/j.coviro.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022]
Abstract
HIV-1 infection can be controlled but not cured by combination antiretroviral therapy. Indeed, the virus persists in treated individuals in viral reservoirs, the best described of which consisting in latently infected central memory CD4+ T cells. However, other cell types in other body compartments than in the peripheral blood contribute to HIV-1 persistence. Addressing the molecular mechanisms of HIV-1 persistence and their cell-specific and tissue-specific variations is thus crucial to develop HIV-1 curative strategies. CRISPR/Cas9 editing technologies have revolutionized genetic engineering by their high specificity and their versatility. Multiple applications now allow to investigate the molecular mechanisms of HIV-1 persistence. Here, we review recent advances in CRISPR-based technologies in deciphering HIV-1 gene expression regulation during persistence.
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Affiliation(s)
- Roxane Verdikt
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, 4000 Liège, Belgium
| | - Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium.
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