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D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
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Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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2
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Wilhelm E, Poirier M, Da Rocha M, Bédard M, McDonald PP, Lavigne P, Hunter CL, Bell B. Mitotic deacetylase complex (MiDAC) recognizes the HIV-1 core promoter to control activated viral gene expression. PLoS Pathog 2024; 20:e1011821. [PMID: 38781120 PMCID: PMC11115230 DOI: 10.1371/journal.ppat.1011821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
The human immunodeficiency virus (HIV) integrates into the host genome forming latent cellular reservoirs that are an obstacle for cure or remission strategies. Viral transcription is the first step in the control of latency and depends upon the hijacking of the host cell RNA polymerase II (Pol II) machinery by the 5' HIV LTR. Consequently, "block and lock" or "shock and kill" strategies for an HIV cure depend upon a full understanding of HIV transcriptional control. The HIV trans-activating protein, Tat, controls HIV latency as part of a positive feed-forward loop that strongly activates HIV transcription. The recognition of the TATA box and adjacent sequences of HIV essential for Tat trans-activation (TASHET) of the core promoter by host cell pre-initiation complexes of HIV (PICH) has been shown to be necessary for Tat trans-activation, yet the protein composition of PICH has remained obscure. Here, DNA-affinity chromatography was employed to identify the mitotic deacetylase complex (MiDAC) as selectively recognizing TASHET. Using biophysical techniques, we show that the MiDAC subunit DNTTIP1 binds directly to TASHET, in part via its CTGC DNA motifs. Using co-immunoprecipitation assays, we show that DNTTIP1 interacts with MiDAC subunits MIDEAS and HDAC1/2. The Tat-interacting protein, NAT10, is also present in HIV-bound MiDAC. Gene silencing revealed a functional role for DNTTIP1, MIDEAS, and NAT10 in HIV expression in cellulo. Furthermore, point mutations in TASHET that prevent DNTTIP1 binding block the reactivation of HIV by latency reversing agents (LRA) that act via the P-TEFb/7SK axis. Our data reveal a key role for MiDAC subunits DNTTIP1, MIDEAS, as well as NAT10, in Tat-activated HIV transcription and latency. DNTTIP1, MIDEAS and NAT10 emerge as cell cycle-regulated host cell transcription factors that can control activated HIV gene expression, and as new drug targets for HIV cure strategies.
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Affiliation(s)
| | | | - Morgane Da Rocha
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Mikaël Bédard
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Patrick P. McDonald
- Pulmonary Division, Medicine Faculty, Université de Sherbrooke; and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Pierre Lavigne
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | | | - Brendan Bell
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
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3
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Duggan NN, Dragic T, Chanda SK, Pache L. Breaking the Silence: Regulation of HIV Transcription and Latency on the Road to a Cure. Viruses 2023; 15:2435. [PMID: 38140676 PMCID: PMC10747579 DOI: 10.3390/v15122435] [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: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Antiretroviral therapy (ART) has brought the HIV/AIDS epidemic under control, but a curative strategy for viral eradication is still needed. The cessation of ART results in rapid viral rebound from latently infected CD4+ T cells, showing that control of viral replication alone does not fully restore immune function, nor does it eradicate viral reservoirs. With a better understanding of factors and mechanisms that promote viral latency, current approaches are primarily focused on the permanent silencing of latently infected cells ("block and lock") or reactivating HIV-1 gene expression in latently infected cells, in combination with immune restoration strategies to eliminate HIV infected cells from the host ("shock and kill"). In this review, we provide a summary of the current, most promising approaches for HIV-1 cure strategies, including an analysis of both latency-promoting agents (LPA) and latency-reversing agents (LRA) that have shown promise in vitro, ex vivo, and in human clinical trials to reduce the HIV-1 reservoir.
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Affiliation(s)
- Natasha N. Duggan
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Tatjana Dragic
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Sumit K. Chanda
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Lars Pache
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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Shin YH, Kim DE, Yu KL, Park CM, Kim HG, Kim KC, Bae S, Yoon CH. A Novel Time-Resolved Fluorescence Resonance Energy Transfer Assay for the Discovery of Small-Molecule Inhibitors of HIV-1 Tat-Regulated Transcription. Int J Mol Sci 2023; 24:ijms24119139. [PMID: 37298089 DOI: 10.3390/ijms24119139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) transactivator (Tat)-mediated transcription is essential for HIV-1 replication. It is determined by the interaction between Tat and transactivation response (TAR) RNA, a highly conserved process representing a prominent therapeutic target against HIV-1 replication. However, owing to the limitations of current high-throughput screening (HTS) assays, no drug that disrupts the Tat-TAR RNA interaction has been uncovered yet. We designed a homogenous (mix-and-read) time-resolved fluorescence resonance energy transfer (TR-FRET) assay using europium cryptate as a fluorescence donor. It was optimized by evaluating different probing systems for Tat-derived peptides or TAR RNA. The specificity of the optimal assay was validated by mutants of the Tat-derived peptides and TAR RNA fragment, individually and by competitive inhibition with known TAR RNA-binding peptides. The assay generated a constant Tat-TAR RNA interaction signal, discriminating the compounds that disrupted the interaction. Combined with a functional assay, the TR-FRET assay identified two small molecules (460-G06 and 463-H08) capable of inhibiting Tat activity and HIV-1 infection from a large-scale compound library. The simplicity, ease of operation, and rapidity of our assay render it suitable for HTS to identify Tat-TAR RNA interaction inhibitors. The identified compounds may also act as potent molecular scaffolds for developing a new HIV-1 drug class.
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Affiliation(s)
- Young Hyun Shin
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Dong-Eun Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Kyung Lee Yu
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Chul Min Park
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Hong Gi Kim
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Kyung-Chang Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Songmee Bae
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
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Whelan M, Pelchat M. Role of RNA Polymerase II Promoter-Proximal Pausing in Viral Transcription. Viruses 2022; 14:v14092029. [PMID: 36146833 PMCID: PMC9503719 DOI: 10.3390/v14092029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
The promoter-proximal pause induced by the binding of the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) to RNAP II is a key step in the regulation of metazoan gene expression. It helps maintain a permissive chromatin landscape and ensures a quick transcriptional response from stimulus-responsive pathways such as the innate immune response. It is also involved in the biology of several RNA viruses such as the human immunodeficiency virus (HIV), the influenza A virus (IAV) and the hepatitis delta virus (HDV). HIV uses the pause as one of its mechanisms to enter and maintain latency, leading to the creation of viral reservoirs resistant to antiretrovirals. IAV, on the other hand, uses the pause to acquire the capped primers necessary to initiate viral transcription through cap-snatching. Finally, the HDV RNA genome is transcribed directly by RNAP II and requires the small hepatitis delta antigen to displace NELF from the polymerase and overcome the transcriptional block caused by RNAP II promoter-proximal pausing. In this review, we will discuss the RNAP II promoter-proximal pause and the roles it plays in the life cycle of RNA viruses such as HIV, IAV and HDV.
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Verdikt R, Bendoumou M, Bouchat S, Nestola L, Pasternak AO, Darcis G, Avettand-Fenoel V, Vanhulle C, Aït-Ammar A, Santangelo M, Plant E, Douce VL, Delacourt N, Cicilionytė A, Necsoi C, Corazza F, Passaes CPB, Schwartz C, Bizet M, Fuks F, Sáez-Cirión A, Rouzioux C, De Wit S, Berkhout B, Gautier V, Rohr O, Van Lint C. Novel role of UHRF1 in the epigenetic repression of the latent HIV-1. EBioMedicine 2022; 79:103985. [PMID: 35429693 PMCID: PMC9038550 DOI: 10.1016/j.ebiom.2022.103985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The multiplicity, heterogeneity, and dynamic nature of human immunodeficiency virus type-1 (HIV-1) latency mechanisms are reflected in the current lack of functional cure for HIV-1. Accordingly, all classes of latency-reversing agents (LRAs) have been reported to present variable ex vivo potencies. Here, we investigated the molecular mechanisms underlying the potency variability of one LRA: the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC). METHODS We employed epigenetic interrogation methods (electrophoretic mobility shift assays, chromatin immunoprecipitation, Infinium array) in complementary HIV-1 infection models (latently-infected T-cell line models, primary CD4+ T-cell models and ex vivo cultures of PBMCs from HIV+ individuals). Extracellular staining of cell surface receptors and intracellular metabolic activity were measured in drug-treated cells. HIV-1 expression in reactivation studies was explored by combining the measures of capsid p24Gag protein, green fluorescence protein signal, intracellular and extracellular viral RNA and viral DNA. FINDINGS We uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) to the HIV-1 promoter. We showed that UHRF1 redundantly binds to the HIV-1 promoter with different binding modalities where DNA methylation was either non-essential, essential or enhancing UHRF1 binding. We further demonstrated the role of UHRF1 in the epigenetic repression of the latent viral promoter by a concerted control of DNA and histone methylations. INTERPRETATION A better understanding of the molecular mechanisms of HIV-1 latency allows for the development of innovative antiviral strategies. As a proof-of-concept, we showed that pharmacological inhibition of UHRF1 in ex vivo HIV+ patient cell cultures resulted in potent viral reactivation from latency. Together, we identify UHRF1 as a novel actor in HIV-1 epigenetic silencing and highlight that it constitutes a new molecular target for HIV-1 cure strategies. FUNDING Funding was provided by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium), the « Fondation Roi Baudouin », the NEAT (European AIDS Treatment Network) program, the Internationale Brachet Stiftung, ViiV Healthcare, the Télévie, the Walloon Region (« Fonds de Maturation »), « Les Amis des Instituts Pasteur à Bruxelles, asbl », the University of Brussels (Action de Recherche Concertée ULB grant), the Marie Skodowska Curie COFUND action, the European Union's Horizon 2020 research and innovation program under grant agreement No 691119-EU4HIVCURE-H2020-MSCA-RISE-2015, the French Agency for Research on AIDS and Viral Hepatitis (ANRS), the Sidaction and the "Alsace contre le Cancer" Foundation. This work is supported by 1UM1AI164562-01, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Roxane Verdikt
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Maryam Bendoumou
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Sophie Bouchat
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Lorena Nestola
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Alexander O Pasternak
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam 1105 AZ, the Netherland
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, Liège 4000, Belgium
| | - Véronique Avettand-Fenoel
- AP-HP, Hôpital Necker-Enfants-Malades, Service de Microbiologie clinique, Paris 75015, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France; INSERM, U1016, Institut Cochin, Paris, 75014, France; CNRS, UMR8104, Paris 75014, France
| | - Caroline Vanhulle
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Amina Aït-Ammar
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Marion Santangelo
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Valentin Le Douce
- Centre for Research in Infectious Diseases, University College Dublin, Dublin 4, Ireland
| | - Nadège Delacourt
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Aurelija Cicilionytė
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam 1105 AZ, the Netherland
| | - Coca Necsoi
- Service des Maladies Infectieuses, CHU St-Pierre, Université Libre de Bruxelles (ULB), Brussels 1000, Belgium
| | - Francis Corazza
- Laboratory of Immunology, IRISLab, CHU Brugmann, Université Libre de Bruxelles (ULB), Brussels 1020, Belgium
| | | | - Christian Schwartz
- Laboratoire DHPI EA7292, Université de Strasbourg, Schiltigheim, 67300, France; IUT Louis Pasteur, Université de Strasbourg, Schiltigheim, 67300, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels 1070, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels 1070, Belgium
| | - Asier Sáez-Cirión
- Départements de Virologie et Immunologie, Institut Pasteur, Unité HIV, Inflammation et Persistance, Paris 75015, France
| | - Christine Rouzioux
- AP-HP, Hôpital Necker-Enfants-Malades, Service de Microbiologie clinique, Paris 75015, France
| | - Stéphane De Wit
- Service des Maladies Infectieuses, CHU St-Pierre, Université Libre de Bruxelles (ULB), Brussels 1000, Belgium
| | - Ben Berkhout
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam 1105 AZ, the Netherland
| | - Virginie Gautier
- Centre for Research in Infectious Diseases, University College Dublin, Dublin 4, Ireland
| | - Olivier Rohr
- Laboratoire DHPI EA7292, Université de Strasbourg, Schiltigheim, 67300, France; IUT Louis Pasteur, Université de Strasbourg, Schiltigheim, 67300, France
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium.
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Buttler CA, Chuong EB. Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev 2022; 305:165-178. [PMID: 34816452 PMCID: PMC8766910 DOI: 10.1111/imr.13042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023]
Abstract
In recent years, there has been significant progress toward understanding the transcriptional networks underlying mammalian immune responses, fueled by advances in regulatory genomic technologies. Epigenomic studies profiling immune cells have generated detailed genome-wide maps of regulatory elements that will be key to deciphering the regulatory networks underlying cellular immune responses and autoimmune disorders. Unbiased analyses of these genomic maps have uncovered endogenous retroviruses as an unexpected ally in the regulation of human immune systems. Despite their parasitic origins, studies are finding an increasing number of examples of retroviral sequences having been co-opted for beneficial immune function and regulation by the host cell. Here, we review how endogenous retroviruses have given rise to numerous regulatory elements that shape the epigenetic landscape of host immune responses. We will discuss the implications of these elements on the function, dysfunction, and evolution of innate immunity.
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8
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A functional screen identifies transcriptional networks that regulate HIV-1 and HIV-2. Proc Natl Acad Sci U S A 2021; 118:2012835118. [PMID: 33836568 DOI: 10.1073/pnas.2012835118] [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] [Indexed: 12/13/2022] Open
Abstract
The molecular networks involved in the regulation of HIV replication, transcription, and latency remain incompletely defined. To expand our understanding of these networks, we performed an unbiased high-throughput yeast one-hybrid screen, which identified 42 human transcription factors and 85 total protein-DNA interactions with HIV-1 and HIV-2 long terminal repeats. We investigated a subset of these transcription factors for transcriptional activity in cell-based models of infection. KLF2 and KLF3 repressed HIV-1 and HIV-2 transcription in CD4+ T cells, whereas PLAGL1 activated transcription of HIV-2 through direct protein-DNA interactions. Using computational modeling with interacting proteins, we leveraged the results from our screen to identify putative pathways that define intrinsic transcriptional networks. Overall, we used a high-throughput functional screen, computational modeling, and biochemical assays to identify and confirm several candidate transcription factors and biochemical processes that influence HIV-1 and HIV-2 transcription and latency.
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9
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Bruce JW, Bracken M, Evans E, Sherer N, Ahlquist P. ZBTB2 represses HIV-1 transcription and is regulated by HIV-1 Vpr and cellular DNA damage responses. PLoS Pathog 2021; 17:e1009364. [PMID: 33635925 PMCID: PMC7946322 DOI: 10.1371/journal.ppat.1009364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 03/10/2021] [Accepted: 02/08/2021] [Indexed: 11/19/2022] Open
Abstract
Previously, we reported that cellular transcription factor ZASC1 facilitates DNA-dependent/RNA-independent recruitment of HIV-1 TAT and the cellular elongation factor P-TEFb to the HIV-1 promoter and is a critical factor in regulating HIV-1 transcriptional elongation (PLoS Path e1003712). Here we report that cellular transcription factor ZBTB2 is a novel repressor of HIV-1 gene expression. ZBTB2 strongly co-immunoprecipitated with ZASC1 and was dramatically relocalized by ZASC1 from the cytoplasm to the nucleus. Mutations abolishing ZASC1/ZBTB2 interaction prevented ZBTB2 nuclear relocalization. We show that ZBTB2-induced repression depends on interaction of cellular histone deacetylases (HDACs) with the ZBTB2 POZ domain. Further, ZASC1 interaction specifically recruited ZBTB2 to the HIV-1 promoter, resulting in histone deacetylation and transcription repression. Depleting ZBTB2 by siRNA knockdown or CRISPR/CAS9 knockout in T cell lines enhanced transcription from HIV-1 vectors lacking Vpr, but not from these vectors expressing Vpr. Since HIV-1 Vpr activates the viral LTR by inducing the ATR kinase/DNA damage response pathway, we investigated ZBTB2 response to Vpr and DNA damaging agents. Expressing Vpr or stimulating the ATR pathway with DNA damaging agents impaired ZASC1’s ability to localize ZBTB2 to the nucleus. Moreover, the effects of DNA damaging agents and Vpr on ZBTB2 localization could be blocked by ATR kinase inhibitors. Critically, Vpr and DNA damaging agents decreased ZBTB2 binding to the HIV-1 promoter and increased promoter histone acetylation. Thus, ZBTB2 is recruited to the HIV-1 promoter by ZASC1 and represses transcription, but ATR pathway activation leads to ZBTB2 removal from the promoter, cytoplasmic sequestration and activation of viral transcription. Together, our data show that ZASC1/ZBTB2 integrate the functions of TAT and Vpr to maximize HIV-1 gene expression. The Human immunodeficiency virus 1 (HIV-1) TAT and VPR proteins, in combination with cellular transcription factors, regulate the switch between transcriptionally active productive infection and the transcriptionally inactive latent state. Previously we reported that ZASC1, a cellular transcription factor linked to multiple squamous cell carcinomas and inherited ataxias, contributes to an RNA-independent, DNA-dependent step in recruiting the TAT/P-TEFb complex that is critical for HIV-1 transcription elongation to the HIV-1 promoter. Here we show ZASC1 interacts with ZBTB2, another cellular transcription factor with strong links to cancer. ZASC1 interaction relocalizes ZBTB2 from the cytoplasm to the HIV-1 promoter in the nucleus where ZBTB2 interacts with cellular HDACs, increases HIV-1 promoter histone deacetylation and represses viral transcription. We show that Vpr-mediated activation of the ATR/DNA damage pathway regulates ZBTB2 relocalization by ZASC1. Thus, the cellular transcription factors ZASC1 and ZBTB2 regulate the transcription elongation activities of HIV-1 TAT and the Vpr activation of the cellular DNA damage response pathway to determine the transcriptional fate of the HIV-1 provirus. These results also have strong implications for the role of ZASC1/ZBTB2 and the DNA damage response in cancer and inherited ataxias.
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Affiliation(s)
- James W. Bruce
- Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Megan Bracken
- Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Edward Evans
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Nathan Sherer
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Paul Ahlquist
- Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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10
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Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions. Methods 2020; 189:22-33. [PMID: 33096239 DOI: 10.1016/j.ymeth.2020.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/29/2020] [Accepted: 10/18/2020] [Indexed: 02/01/2023] Open
Abstract
Identifying genes and non-coding genetic variants that are genetically associated with complex diseases and the underlying mechanisms is one of the most important questions in functional genomics. Due to the limited statistical power and the lack of mechanistic modeling, traditional genome-wide association studies (GWAS) is restricted to fully address this question. Based on multi-omics data integration, cell-type specific regulatory networks can be built to improve GWAS analysis. In this study, we developed a new computational infrastructure, APRIL, to incorporate 3D chromatin interactions into regulatory network construction, which can extend the networks to include long-range cis-regulatory links between non-coding GWAS SNPs and target genes. Combinatorial transcription factors that co-regulate groups of genes are also inferred to further expand the networks with trans-regulation. A suite of machine learning predictions and statistical tests are incorporated in APRIL to predict novel disease-associated genes based on the expanded regulatory networks. Important features of non-coding regulatory elements and genetic variants are prioritized in network-based predictions, providing systems-level insights on the mechanisms of transcriptional dysregulation associated with complex diseases.
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Bisht I, Ambasta RK, Kumar P. An integrated approach to unravel a putative crosstalk network in Alzheimer's disease and Parkinson's disease. Neuropeptides 2020; 83:102078. [PMID: 32807513 DOI: 10.1016/j.npep.2020.102078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 12/31/2022]
Abstract
Integration of multiple profiling data and construction of functional regulatory networks provide a powerful approach to uncover functional relationships and significant molecular entities from transcriptomic data, highlighting the molecular mechanisms of complex diseases. Despite having an overlap in the neuropathologies of AD and PD, the molecular entities overlapped and mechanisms behind them are less known. Here we used an integrated strategy to analyze miRNA and gene transcriptomic data to understand the role of miRNAs and genes in regulatory activities taking place in cells, and find transcriptomic signatures linking AD and PD. We preprocessed and analyzed publicly available microarray datasets and identified 97 DEGs and 21 DEmiRs that may be involved in the overlapped mechanisms between these two disorders. Among the DEGs, we found HSPA9, PGK1, SDHC, FH, DLD, YWHAZ and ACLY as the major protein-coding genes involved in the crosstalk for AD-PD pathogenesis. Further we integrated these DEGs and DEmiRs with regulatory TFs to construct an overlapped dysregulated network of AD and PD. In the network, miR-27a-3p, miR-148a-3p and miR-15a-5p were found to be the most relevant with maximum interactions, describing their significance in the potential crosstalk. We also looked into the dysregulated biological processes and pathways overlapped in AD and PD. In conclusion, we highlighted the DEGs, DEmiRs, their interactions and related pathways overlapped in AD and PD pathogenesis, also describing a potential crosstalk at molecular level. Besides, our findings can further be used for molecular studies to reveal an assured AD-PD crosstalk.
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Affiliation(s)
- Indu Bisht
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India.
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12
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Langer S, Yin X, Diaz A, Portillo AJ, Gordon DE, Rogers UH, Marlett JM, Krogan NJ, Young JAT, Pache L, Chanda SK. The E3 Ubiquitin-Protein Ligase Cullin 3 Regulates HIV-1 Transcription. Cells 2020; 9:E2010. [PMID: 32882949 PMCID: PMC7564853 DOI: 10.3390/cells9092010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022] Open
Abstract
The infectious life cycle of the human immunodeficiency virus type 1 (HIV-1) is characterized by an ongoing battle between a compendium of cellular proteins that either promote or oppose viral replication. On the one hand, HIV-1 utilizes dependency factors to support and sustain infection and complete the viral life cycle. On the other hand, both inducible and constitutively expressed host factors mediate efficient and functionally diverse antiviral processes that counteract an infection. To shed light into the complex interplay between HIV-1 and cellular proteins, we previously performed a targeted siRNA screen to identify and characterize novel regulators of viral replication and identified Cullin 3 (Cul3) as a previously undescribed factor that negatively regulates HIV-1 replication. Cul3 is a component of E3-ubiquitin ligase complexes that target substrates for ubiquitin-dependent proteasomal degradation. In the present study, we show that Cul3 is expressed in HIV-1 target cells, such as CD4+ T cells, monocytes, and macrophages and depletion of Cul3 using siRNA or CRISPR/Cas9 increases HIV-1 infection in immortalized cells and primary CD4+ T cells. Conversely, overexpression of Cul3 reduces HIV-1 infection in single replication cycle assays. Importantly, the antiviral effect of Cul3 was mapped to the transcriptional stage of the viral life cycle, an effect which is independent of its role in regulating the G1/S cell cycle transition. Using isogenic viruses that only differ in their promotor region, we find that the NF-κB/NFAT transcription factor binding sites in the LTR are essential for Cul3-dependent regulation of viral gene expression. Although Cul3 effectively suppresses viral gene expression, HIV-1 does not appear to antagonize the antiviral function of Cul3 by targeting it for degradation. Taken together, these results indicate that Cul3 is a negative regulator of HIV-1 transcription which governs productive viral replication in infected cells.
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Affiliation(s)
- Simon Langer
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (S.L.); (X.Y.); (A.J.P.); (U.H.R.)
- Boehringer Ingelheim Pharma GmbH & Co. KG, 55216 Ingelheim am Rhein, Germany
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (S.L.); (X.Y.); (A.J.P.); (U.H.R.)
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, CA 92515, USA;
- The Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA;
| | - Alex J. Portillo
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (S.L.); (X.Y.); (A.J.P.); (U.H.R.)
- Atara Biotherapeutics, Inc., Thousand Oaks, CA 91320, USA
| | - David E. Gordon
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA 94143, USA; (D.E.G.); (N.J.K.)
- Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA
| | - Umu H. Rogers
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (S.L.); (X.Y.); (A.J.P.); (U.H.R.)
- UC San Diego School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - John M. Marlett
- The Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA;
| | - Nevan J. Krogan
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA 94143, USA; (D.E.G.); (N.J.K.)
- Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA
| | - John A. T. Young
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland;
| | - Lars Pache
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (S.L.); (X.Y.); (A.J.P.); (U.H.R.)
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (S.L.); (X.Y.); (A.J.P.); (U.H.R.)
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13
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Mantini G, Vallés AM, Le Large TYS, Capula M, Funel N, Pham TV, Piersma SR, Kazemier G, Bijlsma MF, Giovannetti E, Jimenez CR. Co-expression analysis of pancreatic cancer proteome reveals biology and prognostic biomarkers. Cell Oncol (Dordr) 2020; 43:1147-1159. [PMID: 32860207 PMCID: PMC7716908 DOI: 10.1007/s13402-020-00548-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 01/02/2023] Open
Abstract
Purpose Despite extensive biological and clinical studies, including comprehensive genomic and transcriptomic profiling efforts, pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease, with a poor survival and limited therapeutic options. The goal of this study was to assess co-expressed PDAC proteins and their associations with biological pathways and clinical parameters. Methods Correlation network analysis is emerging as a powerful approach to infer tumor biology from omics data and to prioritize candidate genes as biomarkers or drug targets. In this study, we applied a weighted gene co-expression network analysis (WGCNA) to the proteome of 20 surgically resected PDAC specimens (PXD015744) and confirmed its clinical value in 82 independent primary cases. Results Using WGCNA, we obtained twelve co-expressed clusters with a distinct biology. Notably, we found that one module enriched for metabolic processes and epithelial-mesenchymal-transition (EMT) was significantly associated with overall survival (p = 0.01) and disease-free survival (p = 0.03). The prognostic value of three proteins (SPTBN1, KHSRP and PYGL) belonging to this module was confirmed using immunohistochemistry in a cohort of 82 independent resected patients. Risk score evaluation of the prognostic signature confirmed its association with overall survival in multivariate analyses. Finally, immunofluorescence analysis confirmed co-expression of SPTBN1 and KHSRP in Hs766t PDAC cells. Conclusions Our WGCNA analysis revealed a PDAC module enriched for metabolic and EMT-associated processes. In addition, we found that three of the proteins involved were associated with PDAC survival. Electronic supplementary material The online version of this article (10.1007/s13402-020-00548-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- G Mantini
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Fondazione Pisana Per La Scienza, Pisa, Italy
| | - A M Vallés
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - T Y S Le Large
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, Univ of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands.,Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Amsterdam, The Netherlands
| | - M Capula
- Fondazione Pisana Per La Scienza, Pisa, Italy
| | - N Funel
- U.O. Anatomia ed Istologia Patologica II Azienda Ospedaliero Universitaria Pisana , Pisa, Italy
| | - T V Pham
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - S R Piersma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - G Kazemier
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Amsterdam, The Netherlands
| | - M F Bijlsma
- U.O. Anatomia ed Istologia Patologica II Azienda Ospedaliero Universitaria Pisana , Pisa, Italy.,Oncode Institute, Amsterdam, The Netherlands
| | - E Giovannetti
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands. .,Fondazione Pisana Per La Scienza, Pisa, Italy.
| | - C R Jimenez
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands.
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14
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Chung CH, Allen AG, Atkins AJ, Sullivan NT, Homan G, Costello R, Madrid R, Nonnemacher MR, Dampier W, Wigdahl B. Safe CRISPR-Cas9 Inhibition of HIV-1 with High Specificity and Broad-Spectrum Activity by Targeting LTR NF-κB Binding Sites. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:965-982. [PMID: 32818921 PMCID: PMC7452136 DOI: 10.1016/j.omtn.2020.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/26/2022]
Abstract
Viral latency of human immunodeficiency virus type 1 (HIV-1) has become a major hurdle to a cure in the highly effective antiretroviral therapy (ART) era. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has successfully been demonstrated to excise or inactivate integrated HIV-1 provirus from infected cells by targeting the long terminal repeat (LTR) region. However, the guide RNAs (gRNAs) have classically avoided transcription factor binding sites (TFBSs) that are readily observed and known to be important in human promoters. Although conventionally thought unfavorable due to potential impact on human promoters, our computational pipeline identified gRNA sequences that were predicted to inactivate HIV-1 transcription by targeting the nuclear factor κB (NF-κB) binding sites (gNFKB0, gNFKB1) with a high safety profile (lack of predicted or observed human edits) and broad-spectrum activity (predicted coverage of known viral sequences). Genome-wide, unbiased identification of double strand breaks (DSBs) enabled by sequencing (GUIDE-seq) showed that the gRNAs targeting NF-κB binding sites had no detectable CRISPR-induced off-target edits in HeLa cells. 5′ LTR-driven HIV-1 transcription was significantly reduced in three HIV-1 reporter cell lines. These results demonstrate a working model to specifically target well-known TFBSs in the HIV-1 LTR that are readily observed in human promoters to reduce HIV-1 transcription with a high-level safety profile and broad-spectrum activity.
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Affiliation(s)
- Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Alexander G Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Andrew J Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Neil T Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Greg Homan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Robert Costello
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Rebekah Madrid
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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15
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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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16
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Key Players in HIV-1 Transcriptional Regulation: Targets for a Functional Cure. Viruses 2020; 12:v12050529. [PMID: 32403278 PMCID: PMC7291152 DOI: 10.3390/v12050529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 establishes a life-long infection when proviral DNA integrates into the host genome. The provirus can then either actively transcribe RNA or enter a latent state, without viral production. The switch between these two states is governed in great part by the viral protein, Tat, which promotes RNA transcript elongation. Latency is also influenced by the availability of host transcription factors, integration site, and the surrounding chromatin environment. The latent reservoir is established in the first few days of infection and serves as the source of viral rebound upon treatment interruption. Despite effective suppression of HIV-1 replication by antiretroviral therapy (ART), to below the detection limit, ART is ineffective at reducing the latent reservoir size. Elimination of this reservoir has become a major goal of the HIV-1 cure field. However, aside from the ideal total HIV-1 eradication from the host genome, an HIV-1 remission or functional cure is probably more realistic. The “block-and-lock” approach aims at the transcriptional silencing of the viral reservoir, to render suppressed HIV-1 promoters extremely difficult to reactivate from latency. There are unfortunately no clinically available HIV-1 specific transcriptional inhibitors. Understanding the mechanisms that regulate latency is expected to provide novel targets to be explored in cure approaches.
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17
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Nchioua R, Bosso M, Kmiec D, Kirchhoff F. Cellular Factors Targeting HIV-1 Transcription and Viral RNA Transcripts. Viruses 2020; 12:v12050495. [PMID: 32365692 PMCID: PMC7290996 DOI: 10.3390/v12050495] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Restriction factors are structurally and functionally diverse cellular proteins that constitute a first line of defense against viral pathogens. Exceptions exist, but typically these proteins are upregulated by interferons (IFNs), target viral components, and are rapidly evolving due to the continuous virus–host arms race. Restriction factors may target HIV replication at essentially each step of the retroviral replication cycle, and the suppression of viral transcription and the degradation of viral RNA transcripts are emerging as major innate immune defense mechanisms. Recent data show that some antiviral factors, such as the tripartite motif-containing protein 22 (TRIM22) and the γ-IFN-inducible protein 16 (IFI16), do not target HIV-1 itself but limit the availability of the cellular transcription factor specificity protein 1 (Sp1), which is critical for effective viral gene expression. In addition, several RNA-interacting cellular factors including RNAse L, the NEDD4-binding protein 1 (N4BP1), and the zinc finger antiviral protein (ZAP) have been identified as important immune effectors against HIV-1 that may be involved in the maintenance of the latent viral reservoirs, representing the major obstacle against viral elimination and cure. Here, we review recent findings on specific cellular antiviral factors targeting HIV-1 transcription or viral RNA transcripts and discuss their potential role in viral latency.
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Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
| | - Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
| | - Dorota Kmiec
- Department of Infectious Diseases, King’s College London, Guy’s Hospital, London SE1 9RT, UK;
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
- Correspondence: ; Tel.: +49-731-5006-5150
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18
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Le Hingrat Q, Visseaux B, Bertine M, Chauveau L, Schwartz O, Collin F, Damond F, Matheron S, Descamps D, Charpentier C. Genetic Variability of Long Terminal Repeat Region between HIV-2 Groups Impacts Transcriptional Activity. J Virol 2020; 94:e01504-19. [PMID: 31915276 PMCID: PMC7081896 DOI: 10.1128/jvi.01504-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/13/2019] [Indexed: 11/20/2022] Open
Abstract
The HIV-2 long terminal repeat (LTR) region contains several transcription factor (TF) binding sites. Efficient LTR transactivation by cellular TF and viral proteins is crucial for HIV-2 reactivation and viral production. Proviral LTRs from 66 antiretroviral-naive HIV-2-infected patients included in the French ANRS HIV-2 CO5 Cohort were sequenced. High genetic variability within the HIV-2 LTR was observed, notably in the U3 subregion, the subregion encompassing most known TF binding sites. Genetic variability was significantly higher in HIV-2 group B than in group A viruses. Notably, all group B viruses lacked the peri-ETS binding site, and 4 group B sequences (11%) also presented a complete deletion of the first Sp1 binding site. The lack of a peri-ETS binding site was responsible for lower transcriptional activity in activated T lymphocytes, while deletion of the first Sp1 binding site lowered basal or Tat-mediated transcriptional activities, depending on the cell line. Interestingly, the HIV-2 cellular reservoir was less frequently quantifiable in patients infected by group B viruses and, when quantifiable, the reservoirs were significantly smaller than in patients infected by group A viruses. Our findings suggest that mutations observed in vivo in HIV-2 LTR sequences are associated with differences in transcriptional activity and may explain the small cellular reservoirs in patients infected by HIV-2 group B, providing new insight into the reduced pathogenicity of HIV-2 infection.IMPORTANCE Over 1 million patients are infected with HIV-2, which is often described as an attenuated retroviral infection. Patients frequently have undetectable viremia and evolve at more slowly toward AIDS than HIV-1-infected patients. Several studies have reported a smaller viral reservoir in peripheral blood mononuclear cells in HIV-2-infected patients than in HIV-1-infected patients, while others have found similar sizes of reservoirs but a reduced amount of cell-associated RNA, suggesting a block in HIV-2 transcription. Recent studies have found associations between mutations within the HIV-1 LTR and reduced transcriptional activities. Until now, mutations within the HIV-2 LTR region have scarcely been studied. We conducted this research to discover if such mutations exist in the HIV-2 LTR and their potential association with the viral reservoir and transcriptional activity. Our study indicates that transcription of HIV-2 group B proviruses may be impaired, which might explain the small viral reservoir observed in patients.
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Affiliation(s)
- Quentin Le Hingrat
- Université de Paris, IAME, UMR 1137, IINSERM, Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat, Paris, France
| | - Benoit Visseaux
- Université de Paris, IAME, UMR 1137, IINSERM, Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat, Paris, France
| | - Mélanie Bertine
- Université de Paris, IAME, UMR 1137, IINSERM, Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat, Paris, France
| | - Lise Chauveau
- Institut Pasteur, Unité Virus et Immunité, Paris, France
| | | | - Fidéline Collin
- ISPED, UMR 897, INSERM, Université Bordeaux, Epidémiologie-Biostatistique, Bordeaux, France
| | - Florence Damond
- Université de Paris, IAME, UMR 1137, IINSERM, Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat, Paris, France
| | - Sophie Matheron
- Université de Paris, IAME, UMR 1137, IINSERM, Paris, France
- Service de Maladies Infectieuses et Tropicales, AP-HP, Hôpital Bichat, Paris, France
| | - Diane Descamps
- Université de Paris, IAME, UMR 1137, IINSERM, Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat, Paris, France
| | - Charlotte Charpentier
- Université de Paris, IAME, UMR 1137, IINSERM, Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat, Paris, France
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19
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Moar P, Sushmita K, Kateriya S, Tandon R. Transcriptional profiling indicates cAMP-driven reversal of HIV latency in monocytes occurs via transcription factor SP-1. Virology 2020; 542:40-53. [PMID: 32056667 DOI: 10.1016/j.virol.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/11/2020] [Accepted: 01/14/2020] [Indexed: 01/16/2023]
Abstract
Latent HIV reservoir is a major barrier to absolute HIV cure. Studies on latency reversal agents (LRA) have by far focused mainly on CD4+ T-lymphocytes, while myeloid reservoirs remain under-represented despite their persistence and key contribution to HIV pathogenesis. cAMP has been shown to increase HIV-1 transcription in latently-infected monocytes/macrophages. In this communication, we explored the potential of commercially available pharmacological drugs and phosphodiesterase inhibitors to reactivate HIV in latently-infected monocytic cell-line, U1. We showed that increased levels of intracellular cAMP reverse HIV latency in vitro, which is specific to cells of the myeloid lineage. High throughput RNA-seq analysis revealed that cAMP modulates transcriptional profile of latently HIV-infected cells and provides favourable cellular environment for HIV to produce viral proteins. This reactivation of latent HIV was inhibited by Mithramycin A, a selective Sp1 inhibitor, indicating that the reversal of HIV latency in monocytes is driven by transcription factor Sp1.
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Affiliation(s)
- Preeti Moar
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Kumari Sushmita
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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20
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Donahue PS, Draut JW, Muldoon JJ, Edelstein HI, Bagheri N, Leonard JN. The COMET toolkit for composing customizable genetic programs in mammalian cells. Nat Commun 2020; 11:779. [PMID: 32034124 PMCID: PMC7005830 DOI: 10.1038/s41467-019-14147-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
Engineering mammalian cells to carry out sophisticated and customizable genetic programs requires a toolkit of multiple orthogonal and well-characterized transcription factors (TFs). To address this need, we develop the COmposable Mammalian Elements of Transcription (COMET)-an ensemble of TFs and promoters that enable the design and tuning of gene expression to an extent not, to the best of our knowledge, previously possible. COMET currently comprises 44 activating and 12 inhibitory zinc-finger TFs and 83 cognate promoters, combined in a framework that readily accommodates new parts. This system can tune gene expression over three orders of magnitude, provides chemically inducible control of TF activity, and enables single-layer Boolean logic. We also develop a mathematical model that provides mechanistic insights into COMET performance characteristics. Altogether, COMET enables the design and construction of customizable genetic programs in mammalian cells.
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Affiliation(s)
- Patrick S Donahue
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Joseph W Draut
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Joseph J Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Hailey I Edelstein
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA
- Biology and Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA.
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21
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Khan SZ, Gasperino S, Zeichner SL. Nuclear Transit and HIV LTR Binding of NF-κB Subunits Held by IκB Proteins: Implications for HIV-1 Activation. Viruses 2019; 11:v11121162. [PMID: 31888181 PMCID: PMC6949894 DOI: 10.3390/v11121162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
No effective therapy to eliminate the HIV latently infected cell reservoir has been developed. One approach, “shock and kill”, employs agents that activate HIV, subsequently killing the activated infected cells and/or virus. Shock and kill requires agents that safely and effectively activate HIV. One class of activation agents works through classical NF-κB pathways, but global NF-κB activators are non-specific and toxic. There exist two major IκBs: IκBα, and IκBε, which hold activating NF-κB subunits in the cytoplasm, releasing them for nuclear transit upon cell stimulation. IκBα was considered the main IκB responsible for gene expression regulation, including HIV activation. IκBε is expressed in cells constituting much of the latent HIV reservoir, and IκBε knockout mice have a minimal phenotype, suggesting that IκBε could be a valuable target for HIV activation and reservoir depletion. We previously showed that targeting IκBε yields substantial increases in HIV expression. Here, we show that IκBε holds c-Rel and p65 activating NF-κB subunits in the cytoplasm, and that targeting IκBε with siRNA produces a strong increase in HIV expression associated with enhanced c-Rel and p65 transit to the nucleus and binding to the HIV LTR of the activating NF-κBs, demonstrating a mechanism through which targeting IκBε increases HIV expression. The findings suggest that it may be helpful to develop HIV activation approaches, acting specifically to target IκBε and its interactions with the NF-κBs.
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Affiliation(s)
- Sohrab Z. Khan
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
| | - Sofia Gasperino
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
| | - Steven L. Zeichner
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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Vpr and Its Cellular Interaction Partners: R We There Yet? Cells 2019; 8:cells8111310. [PMID: 31652959 PMCID: PMC6912716 DOI: 10.3390/cells8111310] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Vpr is a lentiviral accessory protein that is expressed late during the infection cycle and is packaged in significant quantities into virus particles through a specific interaction with the P6 domain of the viral Gag precursor. Characterization of the physiologically relevant function(s) of Vpr has been hampered by the fact that in many cell lines, deletion of Vpr does not significantly affect viral fitness. However, Vpr is critical for virus replication in primary macrophages and for viral pathogenesis in vivo. It is generally accepted that Vpr does not have a specific enzymatic activity but functions as a molecular adapter to modulate viral or cellular processes for the benefit of the virus. Indeed, many Vpr interacting factors have been described by now, and the goal of this review is to summarize our current knowledge of cellular proteins targeted by Vpr.
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23
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Hotter D, Bosso M, Jønsson KL, Krapp C, Stürzel CM, Das A, Littwitz-Salomon E, Berkhout B, Russ A, Wittmann S, Gramberg T, Zheng Y, Martins LJ, Planelles V, Jakobsen MR, Hahn BH, Dittmer U, Sauter D, Kirchhoff F. IFI16 Targets the Transcription Factor Sp1 to Suppress HIV-1 Transcription and Latency Reactivation. Cell Host Microbe 2019; 25:858-872.e13. [PMID: 31175045 PMCID: PMC6681451 DOI: 10.1016/j.chom.2019.05.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/28/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
Abstract
The interferon γ-inducible protein 16 (IFI16) is known as immune sensor of retroviral DNA intermediates. We show that IFI16 restricts HIV-1 independently of immune sensing by binding and inhibiting the host transcription factor Sp1 that drives viral gene expression. This antiretroviral activity and ability to bind Sp1 require the N-terminal pyrin domain and nuclear localization of IFI16, but not the HIN domains involved in DNA binding. Highly prevalent clade C HIV-1 strains are more resistant to IFI16 and less dependent on Sp1 than other HIV-1 subtypes. Furthermore, inhibition of Sp1 by IFI16 or pharmacologically by Mithramycin A suppresses reactivation of latent HIV-1 in CD4+ T cells. Finally, IFI16 also inhibits retrotransposition of LINE-1, known to engage Sp1, and murine IFI16 homologs restrict Friend retrovirus replication in mice. Thus, IFI16 restricts retroviruses and retrotransposons by interfering with Sp1-dependent gene expression, and evasion from this restriction may facilitate spread of HIV-1 subtype C.
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Affiliation(s)
- Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Kasper L Jønsson
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Christian Krapp
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Atze Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, University of Amsterdam, 1105 Amsterdam, the Netherlands
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, University of Amsterdam, 1105 Amsterdam, the Netherlands
| | - Alina Russ
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sabine Wittmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Yue Zheng
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Laura J Martins
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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Mediouni S, Kessing CF, Jablonski JA, Thenin-Houssier S, Clementz M, Kovach MD, Mousseau G, de Vera IMS, Li C, Kojetin DJ, Evans DT, Valente ST. The Tat inhibitor didehydro-cortistatin A suppresses SIV replication and reactivation. FASEB J 2019; 33:8280-8293. [PMID: 31021670 DOI: 10.1096/fj.201801165r] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The HIV-1 transactivation protein (Tat) binds the HIV mRNA transactivation responsive element (TAR), regulating transcription and reactivation from latency. Drugs against Tat are unfortunately not clinically available. We reported that didehydro-cortistatin A (dCA) inhibits HIV-1 Tat activity. In human CD4+ T cells isolated from aviremic individuals and in the humanized mouse model of latency, combining dCA with antiretroviral therapy accelerates HIV-1 suppression and delays viral rebound upon treatment interruption. This drug class is amenable to block-and-lock functional cure approaches, aimed at a durable state of latency. Simian immunodeficiency virus (SIV) infection of rhesus macaques (RhMs) is the best-characterized model for AIDS research. Here, we demonstrate, using in vitro and cell-based assays, that dCA directly binds to SIV Tat's basic domain. dCA specifically inhibits SIV Tat binding to TAR, but not a Tat-Rev fusion protein, which activates transcription when Rev binds to its cognate RNA binding site replacing the apical region of TAR. Tat-TAR inhibition results in loss of RNA polymerase II recruitment to the SIV promoter. Importantly, dCA potently inhibits SIV reactivation from latently infected Hut78 cells and from primary CD4+ T cells explanted from SIVmac239-infected RhMs. In sum, dCA's remarkable breadth of activity encourages SIV-infected RhM use for dCA preclinical evaluation.-Mediouni, S., Kessing, C. F., Jablonski, J. A., Thenin-Houssier, S., Clementz, M., Kovach, M. D., Mousseau, G., de Vera, I.M.S., Li, C., Kojetin, D. J., Evans, D. T., Valente, S. T. The Tat inhibitor didehydro-cortistatin A suppresses SIV replication and reactivation.
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Affiliation(s)
- Sonia Mediouni
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Cari F Kessing
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Joseph A Jablonski
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Suzie Thenin-Houssier
- Institute of Human Genetics (IGH), CNRS-University of Montpelier, Montpelier, France
| | - Mark Clementz
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Melia D Kovach
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Guillaume Mousseau
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Ian Mitchelle S de Vera
- Department of Pharmacology and Physiology, St. Louis University School of Medicine, St. Louis, Missouri, USA
| | - Chuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, USA
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
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Cat and Mouse: HIV Transcription in Latency, Immune Evasion and Cure/Remission Strategies. Viruses 2019; 11:v11030269. [PMID: 30889861 PMCID: PMC6466452 DOI: 10.3390/v11030269] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
There is broad scientific and societal consensus that finding a cure for HIV infection must be pursued. The major barrier to achieving a cure for HIV/AIDS is the capacity of the HIV virus to avoid both immune surveillance and current antiretroviral therapy (ART) by rapidly establishing latently infected cell populations, termed latent reservoirs. Here, we provide an overview of the rapidly evolving field of HIV cure/remission research, highlighting recent progress and ongoing challenges in the understanding of HIV reservoirs, the role of HIV transcription in latency and immune evasion. We review the major approaches towards a cure that are currently being explored and further argue that small molecules that inhibit HIV transcription, and therefore uncouple HIV gene expression from signals sent by the host immune response, might be a particularly promising approach to attain a cure or remission. We emphasize that a better understanding of the game of "cat and mouse" between the host immune system and the HIV virus is a crucial knowledge gap to be filled in both cure and vaccine research.
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26
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Chen L, Keppler OT, Schölz C. Post-translational Modification-Based Regulation of HIV Replication. Front Microbiol 2018; 9:2131. [PMID: 30254620 PMCID: PMC6141784 DOI: 10.3389/fmicb.2018.02131] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) relies heavily on the host cellular machinery for production of viral progeny. To exploit cellular proteins for replication and to overcome host factors with antiviral activity, HIV has evolved a set of regulatory and accessory proteins to shape an optimized environment for its replication and to facilitate evasion from the immune system. Several cellular pathways are hijacked by the virus to modulate critical steps during the viral life cycle. Thereby, post-translational modifications (PTMs) of viral and cellular proteins gain increasingly attention as modifying enzymes regulate virtually every step of the viral replication cycle. This review summarizes the current knowledge of HIV-host interactions influenced by PTMs with a special focus on acetylation, ubiquitination, and phosphorylation of proteins linked to cellular signaling and viral replication. Insights into these interactions are surmised to aid development of new intervention strategies.
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Affiliation(s)
- Lin Chen
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christian Schölz
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
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27
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Castro-Gonzalez S, Colomer-Lluch M, Serra-Moreno R. Barriers for HIV Cure: The Latent Reservoir. AIDS Res Hum Retroviruses 2018; 34:739-759. [PMID: 30056745 PMCID: PMC6152859 DOI: 10.1089/aid.2018.0118] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Thirty-five years after the identification of HIV-1 as the causative agent of AIDS, we are still in search of vaccines and treatments to eradicate this devastating infectious disease. Progress has been made in understanding the molecular pathogenesis of this infection, which has been crucial for the development of the current therapy regimens. However, despite their efficacy at limiting active viral replication, these drugs are unable to purge the latent reservoir: a pool of cells that harbor transcriptionally inactive, but replication-competent HIV-1 proviruses, and that represent the main barrier to eradicate HIV-1 from affected individuals. In this review, we discuss advances in the field that have allowed a better understanding of HIV-1 latency, including the diverse cell types that constitute the latent reservoir, factors influencing latency, tools to study HIV-1 latency, as well as current and prospective therapeutic approaches to target these latently infected cells, so a functional cure for HIV/AIDS can become a reality.
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Affiliation(s)
- Sergio Castro-Gonzalez
- Department of Biological Sciences, College of Arts and Sciences, Texas Tech University, Lubbock, Texas
| | - Marta Colomer-Lluch
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Ruth Serra-Moreno
- Department of Biological Sciences, College of Arts and Sciences, Texas Tech University, Lubbock, Texas
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28
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Asamitsu K, Fujinaga K, Okamoto T. HIV Tat/P-TEFb Interaction: A Potential Target for Novel Anti-HIV Therapies. Molecules 2018; 23:E933. [PMID: 29673219 PMCID: PMC6017356 DOI: 10.3390/molecules23040933] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 11/16/2022] Open
Abstract
Transcription is a crucial step in the life cycle of the human immunodeficiency virus type 1 (HIV 1) and is primarily involved in the maintenance of viral latency. Both viral and cellular transcription factors, including transcriptional activators, suppressor proteins and epigenetic factors, are involved in HIV transcription from the proviral DNA integrated within the host cell genome. Among them, the virus-encoded transcriptional activator Tat is the master regulator of HIV transcription. Interestingly, unlike other known transcriptional activators, Tat primarily activates transcriptional elongation and initiation by interacting with the cellular positive transcriptional elongation factor b (P-TEFb). In this review, we describe the molecular mechanism underlying how Tat activates viral transcription through interaction with P-TEFb. We propose a novel therapeutic strategy against HIV replication through blocking Tat action.
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan.
| | - Koh Fujinaga
- Department of Medicine, Microbiology and Immunology, University of California, San Francisco, CA 94143-0703, USA.
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan.
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29
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Mbondji-wonje C, Dong M, Wang X, Zhao J, Ragupathy V, Sanchez AM, Denny TN, Hewlett I. Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains. PLoS One 2018; 13:e0195661. [PMID: 29664930 PMCID: PMC5903597 DOI: 10.1371/journal.pone.0195661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Functional mapping of the 5’LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by extensive variability, here we aimed to describe mutations in the U3R from various HIV-1 clades and CRFs in order to highlight strain specific differences that may impact the biological properties of diverse HIV-1 strains. To achieve our purpose, the U3R sequence of plasma derived virus belonging to different clades (A1, B, C, D, F2) and recombinants (CRF02_AG, CRF01_AE and CRF22_01A1) was obtained using Illumina technology. Overall, the R region was very well conserved among and across different strains, while in the U3 region the average inter-strains nucleotide dissimilarity was up to 25%. The TAR hairpin displayed a strain-distinctive cluster of mutations affecting the bulge and the loop, but mostly the stem. Like in previous studies we found a TATAA motif in U3 promoter region from the majority of HIV-1 strains and a TAAAA motif in CRF01_AE; but also in LTRs from CRF22_01A1 isolates. Although LTRs from CRF22_01A1 specimens were assigned CRF01_AE, they contained two NF-kB sites instead of the single TFBS described in CRF01_AE. Also, as previously describe in clade C isolates, we found no C/EBP binding site directly upstream of the enhancer region in CRF22_01A1 specimens. In our study, one-third of CRF02_AG LTRs displayed three NF-kB sites which have been mainly described in clade C isolates. Overall, the number, location and binding patterns of potential regulatory elements found along the U3R might be specific to some HIV-1 strains such as clade F2, CRF02_AG, CRF01_AE and CRF22_01A1. These features may be worth consideration as they may be involved in distinctive regulation of HIV-1 transcription and replication by different and diverse infecting strains.
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Affiliation(s)
- Christelle Mbondji-wonje
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- Department of Molecular Biology, Faculty of Medicine, Pharmacy and Biomedical sciences, University of Douala, Douala, Cameroon
- * E-mail: (CM); (IH)
| | - Ming Dong
- U.S. Military HIV Research Program, Silver Spring, Maryland United States of America
| | - Xue Wang
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Viswanath Ragupathy
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ana M. Sanchez
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Thomas N. Denny
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Indira Hewlett
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (CM); (IH)
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Vicenzi E, Poli G. The interferon-stimulated gene TRIM22: A double-edged sword in HIV-1 infection. Cytokine Growth Factor Rev 2018; 40:40-47. [PMID: 29650252 DOI: 10.1016/j.cytogfr.2018.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/07/2018] [Indexed: 12/17/2022]
Abstract
Infection of target cells by the human immunodeficiency virus type-1 (HIV-1) is hampered by constitutively expressed host cell proteins preventing or curtailing virus replication and therefore defined as "restriction factors". Among them, members of the tripartite motif (TRIM) family have emerged as important players endowed with both antiviral effects and modulatory capacity of the innate immune response. TRIM5α and TRIM19 (i.e. promyelocytic leukemia, PML) are among the best-characterized family members; however, in this review we will focus on the potential role of another family member, i.e. TRIM22, a factor strongly induced by interferon stimulation, in HIV infection in vivo and in vitro in the context of its broader antiviral effects. We will also focus on the potential role of TRIM22 in HIV-1-infected individuals speculating on its dual role in controlling virus replication and more complex role in chronic infection. At the molecular levels, we will review the evidence in favor of a relevant role of TRIM22 as epigenetic inhibitor of HIV-1 transcription acting by preventing the binding of the host cell transcription factor Sp1 to the viral promoter. These evidences suggest that TRIM22 should be considered a potential new player in either the establishment or maintenance of HIV-1 reservoirs of latently infected cells unaffected by combination antiretroviral therapy.
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Affiliation(s)
- Elisa Vicenzi
- Viral Pathogens and Biosafety Unit, P2-P3 Laboratories, DIBIT, Via Olgettina n. 58, 20132, Milano, Italy.
| | - Guido Poli
- AIDS Immunopathogenesis Unit, San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, School of Medicine, Milan, Italy
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31
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Harwig A, Landick R, Berkhout B. The Battle of RNA Synthesis: Virus versus Host. Viruses 2017; 9:v9100309. [PMID: 29065472 PMCID: PMC5691660 DOI: 10.3390/v9100309] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022] Open
Abstract
Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage.
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Affiliation(s)
- Alex Harwig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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Shin Y, Choi BS, Kim KC, Kang C, Kim K, Yoon CH. Development of a dual reporter screening assay for distinguishing the inhibition of HIV Tat-mediated transcription from off-target effects. J Virol Methods 2017; 249:1-9. [PMID: 28807730 DOI: 10.1016/j.jviromet.2017.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 12/29/2022]
Abstract
Human immunodeficiency virus (HIV) encodes a transcription trans-activator (Tat) with an essential role in the transcriptional elongation of viral RNA based on the viral promoter long terminal repeat (LTR). Tat-mediated transcription is conserved and can be distinguished from host transcription, so it is a therapeutic target for combating HIV replication. Traditional screening assays for Tat-mediated transcriptional inhibitors are based on the biochemical properties of Tat and transactivation-responsive RNA. We developed an inducible system based on two lentiviral expression cassettes for doxycycline (Dox)-inducible Tat and Renilla luciferase (R-Luc) using TZM-bl cells harboring LTR-driven firefly luciferase (F-Luc). The cells simultaneously expressed both Tat-induced F-Luc and R-Luc, so it was possible to recognize off-target effects in the presence of Dox. The system was validated with known inhibitors: CYC202 obtained high sensitivity and specificity, whereas 6Bio and DRB had off-target effects. The MTT-based cytotoxicity test indicated the resistance of the system even at concentrations with off-target effects. The specificity of the system was confirmed using antiretroviral drugs. Our dual reporter system can simply detect Tat inhibitory effects, as well as precisely discriminate between the inhibitory and off-target effects of inhibitors, and may be useful for the development of a therapeutic anti-HIV drug.
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Affiliation(s)
- YoungHyun Shin
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Byeong-Sun Choi
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Kyung-Chang Kim
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Chun Kang
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Diseases, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Kisoon Kim
- Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
| | - Cheol-Hee Yoon
- Division of AIDS, Korea National Institute of Health, Chungbuk, Republic of Korea; Division of Viral Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
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Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses. Sci Rep 2017; 7:2018. [PMID: 28515481 PMCID: PMC5435695 DOI: 10.1038/s41598-017-02291-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/03/2017] [Indexed: 12/25/2022] Open
Abstract
G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5′-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NFκB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5′-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place.
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Romani B, Allahbakhshi E. Underlying mechanisms of HIV-1 latency. Virus Genes 2017; 53:329-339. [PMID: 28258391 DOI: 10.1007/s11262-017-1443-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 02/27/2017] [Indexed: 02/07/2023]
Abstract
Similarly to other retroviruses, HIV-1 integrates its genome into the cellular chromosome. Expression of viral genes from the integrated viral DNA could then be regulated by the host genome. If the infected cell suppresses viral gene expression, the virus will undergo latency. The latently infected cells cannot be detected or cleared by the immune system since they do not express viral antigens. These cells remain undetected for several years, even under antiretroviral treatments. The silenced HIV-1 DNA could be reactivated under certain conditions. Despite the efficient use of antiretroviral drugs, HIV-1 latently infected cells remain the major obstacles to a permanent cure. In this review, we discuss the cellular and molecular mechanisms through which HIV-1 establishes latency.
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Affiliation(s)
- Bizhan Romani
- Cellular and Molecular Research Center (CMRC), Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences (AJUMS), 61357-15794, Ahvaz, Iran.,Department of Biology, Faculty of Science, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Elham Allahbakhshi
- Cellular and Molecular Research Center (CMRC), Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences (AJUMS), 61357-15794, Ahvaz, Iran.
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Gray LR, Cowley D, Welsh C, Lu HK, Brew BJ, Lewin SR, Wesselingh SL, Gorry PR, Churchill MJ. CNS-specific regulatory elements in brain-derived HIV-1 strains affect responses to latency-reversing agents with implications for cure strategies. Mol Psychiatry 2016; 21:574-84. [PMID: 26303660 PMCID: PMC4804184 DOI: 10.1038/mp.2015.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/18/2015] [Accepted: 06/25/2015] [Indexed: 12/19/2022]
Abstract
Latency-reversing agents (LRAs), including histone deacetylase inhibitors (HDACi), are being investigated as a strategy to eliminate latency in HIV-infected patients on suppressive antiretroviral therapy. The effectiveness of LRAs in activating latent infection in HIV strains derived from the central nervous system (CNS) is unknown. Here we show that CNS-derived HIV-1 strains possess polymorphisms within and surrounding the Sp transcription factor motifs in the long terminal repeat (LTR). These polymorphisms result in decreased ability of the transcription factor specificity protein 1 to bind CNS-derived LTRs, reducing the transcriptional activity of CNS-derived viruses. These mutations result in CNS-derived viruses being less responsive to activation by the HDACi panobinostat and romidepsin compared with lymphoid-derived viruses from the same subjects. Our findings suggest that HIV-1 strains residing in the CNS have unique transcriptional regulatory mechanisms, which impact the regulation of latency, the consideration of which is essential for the development of HIV-1 eradication strategies.
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Affiliation(s)
- L R Gray
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia,Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - D Cowley
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - C Welsh
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - H K Lu
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia,Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - B J Brew
- Departments of Neurology, Immunology and Infectious Diseases and Peter Duncan Neurosciences Unit, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - S R Lewin
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia,Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia,Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia
| | - S L Wesselingh
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - P R Gorry
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia,Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia,School of Applied Sciences and Program in Metabolism, Exercise and Disease, Health Initiatives Research Institute, RMIT University, Melbourne, Victoria, Australia,Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - M J Churchill
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia,Department of Medicine, Monash University, Melbourne, Victoria, Australia,Department of Microbiology, Monash University, Melbourne, Victoria, Australia,Centre for Biomedical Research, Burnet Institute, 85 Commercial Road, Melbourne, Victoria 3004, Australia. E-mail:
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Ordemann JM, Austin RN. Lead neurotoxicity: exploring the potential impact of lead substitution in zinc-finger proteins on mental health. Metallomics 2016; 8:579-88. [DOI: 10.1039/c5mt00300h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This critical review focuses on one possible link between the cellular biology of lead and its neurotoxic effects: the link between Pb2+substitution for Zn2+in zinc-finger proteins and mental illness in adulthood.
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Turrini F, Marelli S, Kajaste-Rudnitski A, Lusic M, Van Lint C, Das AT, Harwig A, Berkhout B, Vicenzi E. HIV-1 transcriptional silencing caused by TRIM22 inhibition of Sp1 binding to the viral promoter. Retrovirology 2015; 12:104. [PMID: 26683615 PMCID: PMC4683785 DOI: 10.1186/s12977-015-0230-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 12/01/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Intracellular defense proteins, also referred to as restriction factors, are capable of interfering with different steps of the viral life cycle. Among these, we have shown that Tripartite motif 22 (TRIM22) suppresses basal as well as phorbol ester-induced HIV-1 long terminal repeat (LTR)-mediated transcription, independently of its E3 ubiquitin ligase activity, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) binding to the U3 region and Tat interaction with the TAR region of the HIV-1 LTR. As basal HIV-1 transcription is driven by the transcription factor specificity protein 1 (Sp1), we have investigated whether TRIM22 could interfere with Sp1-driven transcriptional activation of the HIV-1 LTR. FINDINGS 293T cells, devoid of endogenous TRIM22 expression, were transfected with a TRIM22-expressing plasmid together with reporter plasmids driven by the HIV-1 LTR promoter either containing or lacking Sp1 binding sites or with reporter plasmids driven by non-viral promoter sequences either containing or lacking the three Sp1 binding sites from the HIV-1 LTR. These reporter assays showed that TRIM22 efficiently inhibited Sp1-driven transcription. Knocking down TRIM22 expression in the CD4(+) SupT1 T cell line increased the replication of Sp1-dependent HIV-1 variants. TRIM22 did not interact with Sp1, but prevented binding of Sp1 to the HIV-1 promoter, as demonstrated in protein-DNA pull down and chromatin immunoprecipitation assays. CONCLUSION TRIM22 acts as a suppressor of basal HIV-1 LTR-driven transcription by preventing Sp1 binding to the HIV-1 promoter.
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Affiliation(s)
- Filippo Turrini
- Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, P2-P3 Laboratories, DIBIT, Via Olgettina n.58, 20132, Milan, Italy.
| | - Sara Marelli
- Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, P2-P3 Laboratories, DIBIT, Via Olgettina n.58, 20132, Milan, Italy. .,Viral Oncology Unit, UCL Cancer Institute, London, UK.
| | - Anna Kajaste-Rudnitski
- Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, P2-P3 Laboratories, DIBIT, Via Olgettina n.58, 20132, Milan, Italy. .,San Raffaele Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, 20132, Milan, Italy.
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg and German Center for Infection Research, Heidelberg, Germany.
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Elisa Vicenzi
- Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, P2-P3 Laboratories, DIBIT, Via Olgettina n.58, 20132, Milan, Italy.
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Tyagi M, Weber J, Bukrinsky M, Simon GL. The effects of cocaine on HIV transcription. J Neurovirol 2015; 22:261-74. [PMID: 26572787 DOI: 10.1007/s13365-015-0398-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/01/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
Illicit drug users are a high-risk population for infection with the human immunodeficiency virus (HIV). A strong correlation exists between prohibited drug use and an increased rate of HIV transmission. Cocaine stands out as one of the most frequently abused illicit drugs, and its use is correlated with HIV infection and disease progression. The central nervous system (CNS) is a common target for both drugs of abuse and HIV, and cocaine intake further accelerates neuronal injury in HIV patients. Although the high incidence of HIV infection in illicit drug abusers is primarily due to high-risk activities such as needle sharing and unprotected sex, several studies have demonstrated that cocaine enhances the rate of HIV gene expression and replication by activating various signal transduction pathways and downstream transcription factors. In order to generate mature HIV genomic transcript, HIV gene expression has to pass through both the initiation and elongation phases of transcription, which requires discrete transcription factors. In this review, we will provide a detailed analysis of the molecular mechanisms that regulate HIV transcription and discuss how cocaine modulates those mechanisms to upregulate HIV transcription and eventually HIV replication.
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Affiliation(s)
- Mudit Tyagi
- Division of Infectious Diseases, Department of Medicine, The George Washington University, 2300 Eye Street, N.W., Washington, DC, 20037, USA. .,Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, 20037, USA.
| | - Jaime Weber
- Division of Infectious Diseases, Department of Medicine, The George Washington University, 2300 Eye Street, N.W., Washington, DC, 20037, USA
| | - Michael Bukrinsky
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, 20037, USA
| | - Gary L Simon
- Division of Infectious Diseases, Department of Medicine, The George Washington University, 2300 Eye Street, N.W., Washington, DC, 20037, USA
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40
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Bose D, Gagnon J, Chebloune Y. Comparative Analysis of Tat-Dependent and Tat-Deficient Natural Lentiviruses. Vet Sci 2015; 2:293-348. [PMID: 29061947 PMCID: PMC5644649 DOI: 10.3390/vetsci2040293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023] Open
Abstract
The emergence of human immunodeficiency virus (HIV) causing acquired immunodeficiency syndrome (AIDS) in infected humans has resulted in a global pandemic that has killed millions. HIV-1 and HIV-2 belong to the lentivirus genus of the Retroviridae family. This genus also includes viruses that infect other vertebrate animals, among them caprine arthritis-encephalitis virus (CAEV) and Maedi-Visna virus (MVV), the prototypes of a heterogeneous group of viruses known as small ruminant lentiviruses (SRLVs), affecting both goat and sheep worldwide. Despite their long host-SRLV natural history, SRLVs were never found to be responsible for immunodeficiency in contrast to primate lentiviruses. SRLVs only replicate productively in monocytes/macrophages in infected animals but not in CD4+ T cells. The focus of this review is to examine and compare the biological and pathological properties of SRLVs as prototypic Tat-independent lentiviruses with HIV-1 as prototypic Tat-dependent lentiviruses. Results from this analysis will help to improve the understanding of why and how these two prototypic lentiviruses evolved in opposite directions in term of virulence and pathogenicity. Results may also help develop new strategies based on the attenuation of SRLVs to control the highly pathogenic HIV-1 in humans.
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Affiliation(s)
- Deepanwita Bose
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Jean Gagnon
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Yahia Chebloune
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
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41
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Jin L, Datta PK. Oncogenic STRAP functions as a novel negative regulator of E-cadherin and p21(Cip1) by modulating the transcription factor Sp1. Cell Cycle 2015; 13:3909-20. [PMID: 25483064 DOI: 10.4161/15384101.2014.973310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have previously reported the identification of a novel WD-domain protein, STRAP that plays a role in maintenance of mesenchymal morphology by regulating E-cadherin and that enhances tumorigenicity partly by downregulating CDK inhibitor p21(Cip1). However, the functional mechanism of regulation of E-cadherin and p21(Cip1) by STRAP is unknown. Here, we have employed STRAP knock out and knockdown cell models (mouse embryonic fibroblast, human cancer cell lines) to show how STRAP downregulates E-cadherin and p21(Cip1) by abrogating the binding of Sp1 to its consensus binding sites. Moreover, ChIP assays suggest that STRAP recruits HDAC1 to Sp1 binding sites in p21(Cip1) promoter. Interestingly, loss of STRAP can stabilize Sp1 by repressing its ubiquitination in G1 phase, resulting in an enhanced expression of p21(Cip1) by >4.5-fold and cell cycle arrest. Using Bioinformatics and Microarray analyses, we have observed that 87% mouse genes downregulated by STRAP have conserved Sp1 binding sites. In NSCLC, the expression levels of STRAP inversely correlated with that of Sp1 (60%). These results suggest a novel mechanism of regulation of E-cadherin and p21(Cip1) by STRAP by modulating Sp1-dependent transcription, and higher expression of STRAP in lung cancer may contribute to downregulation of E-cadherin and p21(Cip1) and to tumor progression.
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Key Words
- CDK2, cyclin-dependent kinase 2
- CDK4, cyclin-dependent kinase 4
- HDAC1, histone deacetylase 1
- HDAC2, histone deacetylase 2
- HDAC3, histone deacetylase 3
- HNF4, hepatocyte nuclear factor 4
- MEF, mouse embryonic fibroblast
- NF-YA, nuclear transcription factor Y subunit alpha
- PARP, poly (ADP-ribose) polymerase
- RNase, A ribonuclease A
- RhoA, Ras homolog gene family, member A
- STRAP
- STRAP, serine threonine kinase receptor-associated protein
- SWI/SNF, SWItch/Sucrose nonfermentable
- Sp/KLF, specificity protein/Krüppel-like factor
- Sp1
- Sp1, specificity protein 1
- TSA, trichostatin A
- TSS, transcription start site
- TβR I, II, TGF-β receptor I, II
- cell cycle
- p300/CBP, p300/ CREB-binding protein
- transcription factor
- ubiquitination
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Affiliation(s)
- Lin Jin
- a Division of Hematology and Oncology; Department of Medicine; UAB Comprehensive Cancer Center; University of Alabama at Birmingham ; Birmingham , AL USA
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Takahashi M, Burnett JC, Rossi JJ. Aptamer–siRNA Chimeras for HIV. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 848:211-34. [DOI: 10.1007/978-1-4939-2432-5_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Kim HY, Choi BS, Kim SS, Roh TY, Park J, Yoon CH. NUCKS1, a novel Tat coactivator, plays a crucial role in HIV-1 replication by increasing Tat-mediated viral transcription on the HIV-1 LTR promoter. Retrovirology 2014; 11:67. [PMID: 25116364 PMCID: PMC4181878 DOI: 10.1186/s12977-014-0067-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 07/28/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus-1 (HIV-1) Tat protein plays an essential role in HIV gene transcription from the HIV-1 long terminal repeat (LTR) and replication. Transcriptional activity of Tat is modulated by several host factors, but the mechanism responsible for Tat regulation by host factors is not understood fully. RESULTS Using a yeast two-hybrid screening system, we identified Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 (NUCKS1) as a novel Tat-interacting partner. Here, we report its function as a positive regulator of Tat. In a coimmunoprecipitation assay, HIV-1 Tat interacted sufficiently with both endogenous and ectopically expressed NUCKS1. In a reporter assay, ectopic expression of NUCKS1 significantly increased Tat-mediated transcription of the HIV-1 LTR, whereas knockdown of NUCKS1 by small interfering RNA diminished Tat-mediated transcription of the HIV-1 LTR. We also investigated which mechanism contributes to NUCKS1-mediated Tat activation. In a chromatin immunoprecipitation assay (ChIP), knockdown of NUCKS1 interrupted the accumulation of Tat in the transactivation-responsive (TAR) region on the LTR, which then led to suppression of viral replication. However, NUCKS1 expression did not increase Tat nuclear localization and interaction with Cyclin T1. Interestingly, the NUCKS1 expression level was lower in latently HIV-1-infected cells than in uninfected parent cells. Besides, expression level of NUCKS1 was markedly induced, which then facilitated HIV-1 reactivation in latently infected cells. CONCLUSION Taken together, our data demonstrate clearly that NUCKS1 is a novel Tat coactivator that is required for Tat-mediated HIV-1 transcription and replication, and that it may contribute to HIV-1 reactivation in latently HIV-1 infected cells.
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Affiliation(s)
- Hye-Young Kim
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
| | - Byeong-Sun Choi
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
| | - Sung Soon Kim
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
| | - Tae-Young Roh
- />Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 790-784 Republic of Korea
| | - Jihwan Park
- />Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 790-784 Republic of Korea
| | - Cheol-Hee Yoon
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
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Churchill MJ, Cowley DJ, Wesselingh SL, Gorry PR, Gray LR. HIV-1 transcriptional regulation in the central nervous system and implications for HIV cure research. J Neurovirol 2014; 21:290-300. [PMID: 25060300 DOI: 10.1007/s13365-014-0271-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/25/2014] [Accepted: 06/27/2014] [Indexed: 12/15/2022]
Abstract
Human immunodeficiency virus type-1 (HIV-1) invades the central nervous system (CNS) during acute infection which can result in HIV-associated neurocognitive disorders in up to 50% of patients, even in the presence of combination antiretroviral therapy (cART). Within the CNS, productive HIV-1 infection occurs in the perivascular macrophages and microglia. Astrocytes also become infected, although their infection is restricted and does not give rise to new viral particles. The major barrier to the elimination of HIV-1 is the establishment of viral reservoirs in different anatomical sites throughout the body and viral persistence during long-term treatment with cART. While the predominant viral reservoir is believed to be resting CD4(+) T cells in the blood, other anatomical compartments including the CNS, gut-associated lymphoid tissue, bone marrow, and genital tract can also harbour persistently infected cellular reservoirs of HIV-1. Viral latency is predominantly responsible for HIV-1 persistence and is most likely governed at the transcriptional level. Current clinical trials are testing transcriptional activators, in the background of cART, in an attempt to purge these viral reservoirs and reverse viral latency. These strategies aim to activate viral transcription in cells constituting the viral reservoir, so they can be recognised and cleared by the immune system, while new rounds of infection are blocked by co-administration of cART. The CNS has several unique characteristics that may result in differences in viral transcription and in the way latency is established. These include CNS-specific cell types, different transcription factors, altered immune surveillance, and reduced antiretroviral drug bioavailability. A comprehensive understanding of viral transcription and latency in the CNS is required in order to determine treatment outcomes when using transcriptional activators within the CNS.
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Affiliation(s)
- Melissa J Churchill
- Center for Biomedical Research, Burnet Institute, 85 Commercial Rd, Melbourne, 3004, Victoria, Australia,
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Zhang Y, Fan M, Geng G, Liu B, Huang Z, Luo H, Zhou J, Guo X, Cai W, Zhang H. A novel HIV-1-encoded microRNA enhances its viral replication by targeting the TATA box region. Retrovirology 2014; 11:23. [PMID: 24620741 PMCID: PMC4007588 DOI: 10.1186/1742-4690-11-23] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/18/2014] [Indexed: 01/12/2023] Open
Abstract
Background A lot of microRNAs (miRNAs) derived from viral genomes have been identified. Many of them play various important roles in virus replication and virus-host interaction. Cellular miRNAs have been shown to participate in the regulation of HIV-1 viral replication, while the role of viral-encoded miRNAs in this process is largely unknown. Results In this report, through a strategy combining computational prediction and deep sequencing, we identified a novel HIV-1-encoded miRNA, miR-H3. MiR-H3 locates in the mRNA region encoding the active center of reverse transcriptase (RT) and exhibits high sequence conservation among different subtypes of HIV-1 viruses. Overexpression of miR-H3 increases viral production and the mutations in miR-H3 sequence significantly impair the viral replication of wildtype HIV-1 viruses, suggesting that it is a replication-enhancing miRNA. MiR-H3 upregulates HIV-1 RNA transcription and protein expression. A serial deletion assay suggests that miR-H3 targets HIV-1 5′ LTR and upregulates the promoter activity. It interacts with the TATA box in HIV-1 5′ LTR and sequence-specifically activates the viral transcription. In addition, chemically-synthesized small RNAs targeting HIV-1 TATA box activate HIV-1 production from resting CD4+ T cells isolated from HIV-1-infected patients on suppressive highly active antiretroviral therapy (HAART). Conclusions We have identified a novel HIV-1-encoded miRNA which specifically enhances viral production and provide a specific method to activate HIV-1 latency.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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Manic G, Maurin-Marlin A, Laurent F, Vitale I, Thierry S, Delelis O, Dessen P, Vincendeau M, Leib-Mösch C, Hazan U, Mouscadet JF, Bury-Moné S. Impact of the Ku complex on HIV-1 expression and latency. PLoS One 2013; 8:e69691. [PMID: 23922776 PMCID: PMC3726783 DOI: 10.1371/journal.pone.0069691] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 06/17/2013] [Indexed: 01/20/2023] Open
Abstract
Ku, a cellular complex required for human cell survival and involved in double strand break DNA repair and multiple other cellular processes, may modulate retroviral multiplication, although the precise mechanism through which it acts is still controversial. Recently, Ku was identified as a possible anti-human immunodeficiency virus type 1 (HIV-1) target in human cells, in two global approaches. Here we investigated the role of Ku on the HIV-1 replication cycle by analyzing the expression level of a panel of non-replicative lentiviral vectors expressing the green fluorescent protein in human colorectal carcinoma HCT 116 cells, stably or transiently depleted of Ku. We found that in this cellular model the depletion of Ku did not affect the efficiency of (pre-)integrative steps but decreased the early HIV-1 expression by acting at the transcriptional level. This negative effect was specific of the HIV-1 promoter, required the obligatory step of viral DNA integration and was reversed by transient depletion of p53. We also provided evidence on a direct binding of Ku to HIV-1 LTR in transduced cells. Ku not only promotes the early transcription from the HIV-1 promoter, but also limits the constitution of viral latency. Moreover, in the presence of a normal level of Ku, HIV-1 expression was gradually lost over time, likely due to the counter-selection of HIV-1-expressing cells. On the contrary, the reactivation of transgene expression from HIV-1 by means of trichostatin A- or tumor necrosis factor α-administration was enhanced under condition of Ku haplodepletion, suggesting a phenomenon of provirus latency. These observations plead in favor of the hypothesis that Ku has an impact on HIV-1 expression and latency at early- and mid-time after integration.
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Affiliation(s)
- Gwenola Manic
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Aurélie Maurin-Marlin
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Fanny Laurent
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Ilio Vitale
- Regina Elena National Cancer Institute, Rome, Italy
- National Institute of Health, Rome, Italy
| | - Sylvain Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Philippe Dessen
- Institut Gustave Roussy, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale-U985, Villejuif, France
| | - Michelle Vincendeau
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christine Leib-Mösch
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Hematology and Oncology, Mannheim Medical Center, University of Heidelberg, Mannheim, Germany
| | - Uriel Hazan
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Jean-François Mouscadet
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Stéphanie Bury-Moné
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre national de la recherche scientifique-UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
- * E-mail:
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47
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Doyle SL, Shirey KA, McGettrick AF, Kenny EF, Carpenter S, Caffrey BE, Gargan S, Quinn SR, Caamaño JH, Moynagh P, Vogel SN, O'Neill LA. Nuclear factor κB2 p52 protein has a role in antiviral immunity through IκB kinase epsilon-dependent induction of Sp1 protein and interleukin 15. J Biol Chem 2013; 288:25066-25075. [PMID: 23873932 DOI: 10.1074/jbc.m113.469122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study we describe a previously unreported function for NFκB2, an NFκB family transcription factor, in antiviral immunity. NFκB2 is induced in response to poly(I:C), a mimic of viral dsRNA. Poly(I:C), acting via TLR3, induces p52-dependent transactivation of a reporter gene in a manner that requires the kinase activity of IκB kinase ε (IKKε) and the transactivating potential of RelA/p65. We identify a novel NFκB2 binding site in the promoter of the transcription factor Sp1 that is required for Sp1 gene transcription activated by poly(I:C). We show that Sp1 is required for IL-15 induction by both poly(I:C) and respiratory syncytial virus, a response that also requires NFκB2 and IKKε. Our study identifies NFκB2 as a target for IKKε in antiviral immunity and describes, for the first time, a role for NFκB2 in the regulation of gene expression in response to viral infection.
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Affiliation(s)
- Sarah L Doyle
- From the Immunology Research Centre, Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland,.
| | - Kari Ann Shirey
- the Department of Microbiology and Immunology, University of Maryland, Baltimore, School of Medicine, Baltimore, Maryland 21201
| | - Anne F McGettrick
- From the Immunology Research Centre, Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Elaine F Kenny
- From the Immunology Research Centre, Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Susan Carpenter
- From the Immunology Research Centre, Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Brian E Caffrey
- the Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Siobhan Gargan
- the Institute of Immunology, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland, and
| | - Susan R Quinn
- From the Immunology Research Centre, Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Jorge H Caamaño
- the Institute for BioMedical Research-Medical Research Council (IBR-MRC) Centre for Immune Regulation, College of Medicine and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Paul Moynagh
- the Institute of Immunology, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland, and
| | - Stefanie N Vogel
- the Department of Microbiology and Immunology, University of Maryland, Baltimore, School of Medicine, Baltimore, Maryland 21201
| | - Luke A O'Neill
- From the Immunology Research Centre, Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
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48
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Miller-Jensen K, Skupsky R, Shah PS, Arkin AP, Schaffer DV. Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression. PLoS Comput Biol 2013; 9:e1003135. [PMID: 23874178 PMCID: PMC3708878 DOI: 10.1371/journal.pcbi.1003135] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/16/2013] [Indexed: 12/13/2022] Open
Abstract
The sequence of a promoter within a genome does not uniquely determine gene expression levels and their variability; rather, promoter sequence can additionally interact with its location in the genome, or genomic context, to shape eukaryotic gene expression. Retroviruses, such as human immunodeficiency virus-1 (HIV), integrate their genomes into those of their host and thereby provide a biomedically-relevant model system to quantitatively explore the relationship between promoter sequence, genomic context, and noise-driven variability on viral gene expression. Using an in vitro model of the HIV Tat-mediated positive-feedback loop, we previously demonstrated that fluctuations in viral Tat-transactivating protein levels generate integration-site-dependent, stochastically-driven phenotypes, in which infected cells randomly ‘switch’ between high and low expressing states in a manner that may be related to viral latency. Here we extended this model and designed a forward genetic screen to systematically identify genetic elements in the HIV LTR promoter that modulate the fraction of genomic integrations that specify ‘Switching’ phenotypes. Our screen identified mutations in core promoter regions, including Sp1 and TATA transcription factor binding sites, which increased the Switching fraction several fold. By integrating single-cell experiments with computational modeling, we further investigated the mechanism of Switching-fraction enhancement for a selected Sp1 mutation. Our experimental observations demonstrated that the Sp1 mutation both impaired Tat-transactivated expression and also altered basal expression in the absence of Tat. Computational analysis demonstrated that the observed change in basal expression could contribute significantly to the observed increase in viral integrations that specify a Switching phenotype, provided that the selected mutation affected Tat-mediated noise amplification differentially across genomic contexts. Our study thus demonstrates a methodology to identify and characterize promoter elements that affect the distribution of stochastic phenotypes over genomic contexts, and advances our understanding of how promoter mutations may control the frequency of latent HIV infection. The sequence of a gene within a cellular genome does not uniquely determine its expression level, even for a single type of cell under fixed conditions. Numerous other factors, including gene location on the chromosome and random gene-expression “noise,” can alter expression patterns and cause differences between otherwise identical cells. This poses new challenges for characterizing the genotype–phenotype relationship. Infection by the human immunodeficiency virus-1 (HIV-1) provides a biomedically important example in which transcriptional noise and viral genomic location impact the decision between viral replication and latency, a quiescent but reversible state that cannot be eliminated by anti-viral therapies. Here, we designed a forward genetic screen to systematically identify mutations in the HIV promoter that alter the fraction of genomic integrations that specify noisy/reactivating expression phenotypes. The mechanisms by which the selected mutations specify the observed phenotypic enrichments are investigated through a combination of single-cell experiments and computational modeling. Our study provides a framework for identifying genetic sequences that alter the distribution of stochastic expression phenotypes over genomic locations and for characterizing their mechanisms of regulation. Our results also may yield further insights into the mechanisms by which HIV sequence evolution can alter the propensity for latent infections.
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Affiliation(s)
- Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail: (KMJ); (DVS)
| | - Ron Skupsky
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Priya S. Shah
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - David V. Schaffer
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
- * E-mail: (KMJ); (DVS)
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49
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Groen JN, Morris KV. Chromatin, non-coding RNAs, and the expression of HIV. Viruses 2013; 5:1633-45. [PMID: 23812489 PMCID: PMC3738951 DOI: 10.3390/v5071633] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/21/2013] [Accepted: 06/21/2013] [Indexed: 12/20/2022] Open
Abstract
HIV is a chronic viral infection affecting an estimated 34 million people worldwide. Current therapies employ the use of a cocktail of antiretroviral medications to reduce the spread and effects of HIV, however complete eradication from an individual currently remains unattainable. Viral latency and regulation of gene expression is a key consideration when developing effective treatments. While our understanding of these processes remains incomplete new developments suggest that non-coding RNA (ncRNA) mediated regulation may provide an avenue to controlling both viral expression and latency. Here we discuss the importance of known regulatory mechanisms and suggest directions for further study, in particular the use ncRNAs in controlling HIV expression.
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Affiliation(s)
- Jessica N. Groen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia; E-Mail:
| | - Kevin V. Morris
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia; E-Mail:
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-2-9385-2019
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50
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Karn J, Stoltzfus CM. Transcriptional and posttranscriptional regulation of HIV-1 gene expression. Cold Spring Harb Perspect Med 2013; 2:a006916. [PMID: 22355797 DOI: 10.1101/cshperspect.a006916] [Citation(s) in RCA: 276] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Control of HIV-1 gene expression depends on two viral regulatory proteins, Tat and Rev. Tat stimulates transcription elongation by directing the cellular transcriptional elongation factor P-TEFb to nascent RNA polymerases. Rev is required for the transport from the nucleus to the cytoplasm of the unspliced and incompletely spliced mRNAs that encode the structural proteins of the virus. Molecular studies of both proteins have revealed how they interact with the cellular machinery to control transcription from the viral LTR and regulate the levels of spliced and unspliced mRNAs. The regulatory feedback mechanisms driven by HIV-1 Tat and Rev ensure that HIV-1 transcription proceeds through distinct phases. In cells that are not fully activated, limiting levels of Tat and Rev act as potent blocks to premature virus production.
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Affiliation(s)
- Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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