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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bellefroid M, Rodari A, Galais M, Krijger PHL, Tjalsma SJD, Nestola L, Plant E, Vos ESM, Cristinelli S, Van Driessche B, Vanhulle C, Ait-Ammar A, Burny A, Ciuffi A, de Laat W, Van Lint C. Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization. Nucleic Acids Res 2022; 50:3190-3202. [PMID: 35234910 PMCID: PMC8989512 DOI: 10.1093/nar/gkac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 01/12/2023] Open
Abstract
Bovine leukemia virus (BLV)-induced tumoral development is a multifactorial phenomenon that remains incompletely understood. Here, we highlight the critical role of the cellular CCCTC-binding factor (CTCF) both in the regulation of BLV transcriptional activities and in the deregulation of the three-dimensional (3D) chromatin architecture surrounding the BLV integration site. We demonstrated the in vivo recruitment of CTCF to three conserved CTCF binding motifs along the provirus. Next, we showed that CTCF localized to regions of transitions in the histone modifications profile along the BLV genome and that it is implicated in the repression of the 5′Long Terminal Repeat (LTR) promoter activity, thereby contributing to viral latency, while favoring the 3′LTR promoter activity. Finally, we demonstrated that BLV integration deregulated the host cellular 3D chromatin organization through the formation of viral/host chromatin loops. Altogether, our results highlight CTCF as a new critical effector of BLV transcriptional regulation and BLV-induced physiopathology.
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Affiliation(s)
- Maxime Bellefroid
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Anthony Rodari
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Mathilde Galais
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sjoerd J D Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Lorena Nestola
- 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
| | - Erica S M Vos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Benoit Van Driessche
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Caroline Vanhulle
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Arsène Burny
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
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