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Fombellida-Lopez C, Berkhout B, Darcis G, Pasternak AO. Persistent HIV-1 transcription during ART: time to reassess its significance? Curr Opin HIV AIDS 2024; 19:124-132. [PMID: 38502547 PMCID: PMC10990031 DOI: 10.1097/coh.0000000000000849] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), HIV-1 reservoirs persist and reignite viral replication if therapy is interrupted. Persistence of the viral reservoir in people with HIV-1 (PWH) is the main obstacle to an HIV-1 cure. The reservoirs are not transcriptionally silent, and viral transcripts can be detected in most ART-treated individuals. Here, we review the recent progress in the characterization of persistent HIV-1 transcription during ART. RECENT FINDINGS Evidence from several studies indicates that, although cell-associated unspliced (US) HIV-1 RNA is abundantly expressed in ART-treated PWH, intact full-length US transcripts are rare and most US RNA is derived from defective proviruses. The transcription- and translation-competent defective proviruses, previously considered irrelevant, are increasingly being linked to residual HIV-1 pathogenesis under suppressive ART. Recent data suggest a continuous crosstalk between the residual HIV-1 activity under ART and the immune system. Persistent HIV-1 transcription on ART, despite being mostly derived from defective proviruses, predicts viral rebound upon therapy interruption, suggesting its role as an indicator of the strength of the host antiviral immune response that is shaping the viral rebound. SUMMARY In light of the recent findings, the significance of persistent HIV-1 transcription during ART for the long-term health of PWH and the cure research should be reassessed.
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Affiliation(s)
- Céline Fombellida-Lopez
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gilles Darcis
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège
- Department of General Internal Medicine and Infectious Diseases, University Hospital of Liège, Liège, Belgium
| | - Alexander O. Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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2
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Liu Y, Binda CS, Berkhout B, Das AT. CRISPR-Cas attack of HIV-1 proviral DNA can cause unintended deletion of surrounding cellular DNA. J Virol 2023; 97:e0133423. [PMID: 37982648 PMCID: PMC10734527 DOI: 10.1128/jvi.01334-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Although HIV replication can be effectively inhibited by antiretroviral therapy, this does not result in a cure as the available drugs do not inactivate the integrated HIV-1 DNA in infected cells. Consequently, HIV-infected individuals need lifelong therapy to prevent viral rebound. Several preclinical studies indicate that CRISPR-Cas gene-editing systems can be used to achieve permanent inactivation of the viral DNA. It was previously shown that this inactivation was due to small inactivating mutations at the targeted sites in the HIV genome and to excision or inversion of the viral DNA fragment between two target sites. We, here, demonstrate that CRISPR-Cas treatment also causes large unintended deletions, which can include surrounding chromosomal sequences. As the loss of chromosomal sequences may cause oncogenic transformation of the cell, such unintended large deletions form a potential safety risk in clinical application of this antiviral application and possibly all CRISPR-Cas gene-editing approaches.
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Affiliation(s)
- Ye Liu
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Caroline S. Binda
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Atze T. Das
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
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3
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Theuerkauf SA, Herrera-Carrillo E, John F, Zinser LJ, Molina MA, Riechert V, Thalheimer FB, Börner K, Grimm D, Chlanda P, Berkhout B, Buchholz CJ. AAV vectors displaying bispecific DARPins enable dual-control targeted gene delivery. Biomaterials 2023; 303:122399. [PMID: 37992599 PMCID: PMC10721713 DOI: 10.1016/j.biomaterials.2023.122399] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
Precise delivery of genes to therapy-relevant cells is crucial for in vivo gene therapy. Receptor-targeting as prime strategy for this purpose is limited to cell types defined by a single cell-surface marker. Many target cells are characterized by combinations of more than one marker, such as the HIV reservoir cells. Here, we explored the tropism of adeno-associated viral vectors (AAV2) displaying designed ankyrin repeat proteins (DARPins) mono- and bispecific for CD4 and CD32a. Cryo-electron tomography revealed an unaltered capsid structure in the presence of DARPins. Surprisingly, bispecific AAVs transduced CD4/CD32a double-positive cells at much higher efficiencies than single-positive cells, even if present in low amounts in cell mixtures or human blood. This preference was confirmed when vector particles were systemically administered into mice. Cell trafficking studies revealed an increased cell entry rate for bispecific over monospecific AAVs. When equipped with an HIV genome-targeting CRISPR/Cas cassette, the vectors prevented HIV replication in T cell cultures. The data provide proof-of-concept for high-precision gene delivery through tandem-binding regions on AAV. Reminiscent of biological products following Boolean logic AND gating, the data suggest a new option for receptor-targeted vectors to improve the specificity and safety of in vivo gene therapy.
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Affiliation(s)
- Samuel A Theuerkauf
- Gene Therapy and Molecular Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | | | - Fabian John
- Gene Therapy and Molecular Biotechnology, Paul-Ehrlich-Institut, Langen, Germany; Frankfurt Cancer Institute, Goethe University, Frankfurt, Germany
| | - Luca J Zinser
- Gene Therapy and Molecular Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | | | - Vanessa Riechert
- Gene Therapy and Molecular Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Frederic B Thalheimer
- Gene Therapy and Molecular Biotechnology, Paul-Ehrlich-Institut, Langen, Germany; Frankfurt Cancer Institute, Goethe University, Frankfurt, Germany
| | - Kathleen Börner
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany; BioQuant, Heidelberg University, Heidelberg, Germany; German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Dirk Grimm
- BioQuant, Heidelberg University, Heidelberg, Germany; German Center for Infection Research (DZIF), Heidelberg, Germany; Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Heidelberg University Hospital, Heidelberg, Germany; German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Petr Chlanda
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany; BioQuant, Heidelberg University, Heidelberg, Germany; Schaller Research Groups, Heidelberg University, Heidelberg, Germany
| | | | - Christian J Buchholz
- Gene Therapy and Molecular Biotechnology, Paul-Ehrlich-Institut, Langen, Germany; Frankfurt Cancer Institute, Goethe University, Frankfurt, Germany.
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Molina MA, Vink M, Berkhout B, Herrera-Carrillo E. In-house ELISA protocols for capsid p24 detection of diverse HIV isolates. Virol J 2023; 20:269. [PMID: 37978551 PMCID: PMC10656996 DOI: 10.1186/s12985-023-02242-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The capsid p24 (CA-p24) antigen is a component of the viral capsid of human immunodeficiency virus (HIV) that has been commonly used for clinical diagnosis and monitoring of HIV infections in Enzyme-linked Immunosorbent Assays (ELISAs). Commercial CA-p24 ELISAs are widely used in research settings, but these kits are costly and have limited breadth for detecting diverse HIV isolates. METHODS Commercial CA-p24 antibodies were used as capture and detection antibodies. Specific CA-p24 ELISAs were established with these antibodies and tested for the detection of HIV-1 isolates with the aim of developing in-house protocols to recognize HIV-1 infections in vitro for research purposes. RESULTS Here we present four protocols for in-house ELISAs to detect HIV CA-p24 using commercial antibodies. The assays were able to detect the CA-p24 antigen of different HIV-1 isolates tested. Comparison between the protocols showed that these in-house ELISAs exhibit high specificity, sensitivity, and reproducibility for CA-p24 quantitation but their reactivity varied per HIV-1 isolate and subtype. CONCLUSIONS These optimized ELISA protocols represent valuable tools to investigate HIV-1 infections in research facilities at a lower price than commercial CA-p24 kits.
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Affiliation(s)
- Mariano A Molina
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam UMC, AMC Location, University of Amsterdam, Amsterdam, The Netherlands
| | - Monique Vink
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam UMC, AMC Location, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam UMC, AMC Location, University of Amsterdam, Amsterdam, The Netherlands
| | - Elena Herrera-Carrillo
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam UMC, AMC Location, University of Amsterdam, Amsterdam, The Netherlands.
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Pasternak AO, Tsukamoto T, Berkhout B. 'Zombie' proviruses in the spotlight: exploring the dark side of HIV persistence. AIDS 2023; 37:2239-2241. [PMID: 37877277 DOI: 10.1097/qad.0000000000003721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tetsuo Tsukamoto
- Department of Health Informatics, Niigata University of Health and Welfare, Niigata, Japan
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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6
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Galy A, Berkhout B, Breckpot K, Pichon C, Bloom K, Kiem HP, Mühlebach MD, McCune JM. Recent Advances Using Genetic Therapies Against Infectious Diseases and for Vaccination. Hum Gene Ther 2023; 34:896-904. [PMID: 37639360 DOI: 10.1089/hum.2023.123] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
The development of prophylatic or therapeutic medicines for infectious diseases is one of the priorities for health organizations worldwide. Innovative solutions are required to achieve effective, safe, and accessible treatments for most if not all infectious diseases, particularly those that are chronic in nature or that emerge unexpectedly over time. Genetic technologies offer versatile possibilities to design therapies against pathogens. Recent developments such as mRNA vaccines, CRISPR gene editing, and immunotherapies provide unprecedented hope to achieve significant results in the field of infectious diseases. This review will focus on advances in this domain, showcasing the cross-fertilization with other fields (e.g., oncology), and addressing some of the logistical and economic concerns important to consider when making these advances accessible to diverse populations around the world.
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Affiliation(s)
- Anne Galy
- ART-TG, Inserm, Corbeil-Essonnes, France
| | - Ben Berkhout
- Department of Medical Microbiology Laboratory of Experimental Virology Amsterdam UMC, AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Karine Breckpot
- Department of Biomedical Sciences, Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS, ART-ARNm, Inserm, Orléans
- Institut Universitaire de France, Paris, France
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Infectious Diseases and Oncology Research Institute (IDORI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hans-Peter Kiem
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | | | - Joseph M McCune
- HIV Frontiers, Global Health Accelerator, Bill and Melinda Gates Foundation, Seattle, Washington, USA
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7
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Fan M, Bao Y, Berkhout B, Herrera-Carrillo E. CRISPR-Cas12b enables a highly efficient attack on HIV proviral DNA in T cell cultures. Biomed Pharmacother 2023; 165:115046. [PMID: 37379644 DOI: 10.1016/j.biopha.2023.115046] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND The novel endonuclease Cas12b was engineered for targeted genome editing in mammalian cells and is a promising tool for certain applications because of its small size, high sequence specificity and ability to generate relatively large deletions. We previously reported inhibition of the human immunodeficiency virus (HIV) in cell culture infections upon attack of the integrated viral DNA genome by spCas9 and Cas12a. METHODS We now tested the ability of the Cas12b endonuclease to suppress a spreading HIV infection in cell culture with anti-HIV gRNAs. Virus inhibition was tested in long-term HIV replication studies, which allowed us to test for viral escape and the potential for reaching a CURE of the infected T cells. FINDINGS We demonstrate that Cas12b can achieve complete HIV inactivation with only a single gRNA, a result for which Cas9 required two gRNAs. When the Cas12b system is programmed with two antiviral gRNAs, the overall anti-HIV potency is improved and more grossly mutated HIV proviruses are generated as a result of multiple cut-repair actions. Such "hypermutated" HIV proviruses are more likely to be defective due to mutation of multiple essential parts of the HIV genome. We report that the mutational profiles of the Cas9, Cas12a and Cas12b endonucleases differ significantly, which may have an impact on the level of virus inactivation. These combined results make Cas12b the preferred editing system for HIV-inactivation. INTERPRETATION These results provide in vitro "proof of concept' for CRISPR-Cas12b mediated HIV-1 inactivation.
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Affiliation(s)
- Minghui Fan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Yuanling Bao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
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8
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Dekker JG, Klaver B, Berkhout B, Das AT. HIV-1 3'-Polypurine Tract Mutations Confer Dolutegravir Resistance by Switching to an Integration-Independent Replication Mechanism via 1-LTR Circles. J Virol 2023; 97:e0036123. [PMID: 37125907 PMCID: PMC10231180 DOI: 10.1128/jvi.00361-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/07/2023] [Indexed: 05/02/2023] Open
Abstract
Several recent studies indicate that mutations in the human immunodeficiency virus type 1 (HIV-1) 3'polypurine tract (3'PPT) motif can reduce sensitivity to the integrase inhibitor dolutegravir (DTG). Using an in vivo systematic evolution of ligands by exponential enrichment (SELEX) approach, we discovered that multiple different mutations in this viral RNA element can confer DTG resistance, suggesting that the inactivation of this critical reverse transcription element causes resistance. An analysis of the viral DNA products formed upon infection by these 3'PPT mutants revealed that they replicate without integration into the host cell genome, concomitant with an increased production of 1-LTR circles. As the replication of these virus variants is activated by the human T-lymphotropic virus 1 (HTLV-1) Tax protein, a factor that reverses epigenetic silencing of episomal HIV DNA, these data indicate that the 3'PPT-mutated viruses escape from the integrase inhibitor DTG by switching to an integration-independent replication mechanism. IMPORTANCE The integrase inhibitor DTG is a potent inhibitor of HIV replication and is currently recommended in drug regimens for people living with HIV. Whereas HIV normally escapes from antiviral drugs by the acquisition of specific mutations in the gene that encodes the targeted enzyme, mutational inactivation of the viral 3'PPT sequence, an RNA element that has a crucial role in the viral reverse transcription process, was found to allow HIV replication in the presence of DTG in cell culture experiments. While the integration of the viral DNA into the cellular genome is considered one of the hallmarks of retroviruses, including HIV, 3'PPT inactivation caused integration-independent replication, which can explain the reduced DTG sensitivity. Whether this exotic escape route can also contribute to viral escape in HIV-infected persons remains to be determined, but our results indicate that screening for 3'PPT mutations in patients that fail on DTG therapy should be considered.
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Affiliation(s)
- José G. Dekker
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Bep Klaver
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Atze T. Das
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
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Riechert V, Hein S, Visser M, Zimmermann M, Wesche J, Adams PA, Theuerkauf SA, Jamali A, Wangorsch A, Reuter A, Pasternak A, Hartmann J, Greinacher A, Herrera-Carrillo E, Berkhout B, Cichutek K, Buchholz CJ. FcγRIIA-specific DARPins as novel tools in blood cell analysis and platelet aggregation. J Biol Chem 2023; 299:104743. [PMID: 37100283 DOI: 10.1016/j.jbc.2023.104743] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
Fc receptors are involved in a variety of physiologically and disease relevant responses. Among them, FcγRIIA (CD32a) is known for its activating functions in pathogen recognition and platelet biology, and, as potential marker of T lymphocytes latently infected with HIV-1. The latter has not been without controversy due to technical challenges complicated by T-B cell conjugates and trogocytosis as well as a lack of antibodies distinguishing between the closely related isoforms of FcγRII. To generate high-affinity binders specific for FcγRIIA, libraries of designed ankyrin repeat proteins (DARPins) were screened for binding to its extracellular domains by ribosomal display. Counter-selection against FcγRIIB eliminated binders cross-reacting with both isoforms. The identified DARPins bound FcγRIIA with no detectable binding for FcγRIIB. Their affinities for FcγRIIA were in the low nanomolar range and could be enhanced by cleavage of the His-tag and dimerization. Interestingly, complex formation between DARPin and FcγRIIA followed a two-state reaction model and discrimination from FcγRIIB was based on a single amino acid residue. In flow cytometry, DARPin F11 detected FcγRIIA+ cells even when they made up less than 1% of the cell population. Image stream analysis of primary human blood cells confirmed that F11 caused dim but reliable cell surface staining of a small subpopulation of T lymphocytes. When incubated with platelets, F11 inhibited their aggregation equally efficient as antibodies unable to discriminate between both FcγRII isoforms. The selected DARPins are unique novel tools for platelet aggregation studies as well as the role of FcγRIIA for the latent HIV-1 reservoir.
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Affiliation(s)
- Vanessa Riechert
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Sascha Hein
- Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Mayken Visser
- Haematology and Transfusion Medicine, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Mathias Zimmermann
- Institute for Transfusion Medicine, University Medicine Greifswald, Germany
| | - Jan Wesche
- Institute for Transfusion Medicine, University Medicine Greifswald, Germany
| | - Philipp A Adams
- Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
| | - Samuel A Theuerkauf
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Arezoo Jamali
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Andrea Wangorsch
- Molecular Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Andreas Reuter
- Division of Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Alexander Pasternak
- Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
| | - Jessica Hartmann
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Andreas Greinacher
- Institute for Transfusion Medicine, University Medicine Greifswald, Germany
| | - Elena Herrera-Carrillo
- Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
| | - Ben Berkhout
- Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
| | - Klaus Cichutek
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Christian J Buchholz
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany.
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10
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Pasternak AO, Berkhout B. HIV persistence: silence or resistance? Curr Opin Virol 2023; 59:101301. [PMID: 36805974 DOI: 10.1016/j.coviro.2023.101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 02/19/2023]
Abstract
Despite decades of suppressive antiretroviral therapy, human immunodeficiency virus (HIV) reservoirs in infected individuals persist and fuel viral rebound once therapy is interrupted. The persistence of viral reservoirs is the main obstacle to achieving HIV eradication or a long-term remission. The last decade has seen a profound change in our understanding of the mechanisms behind HIV persistence, which appears to be much more complex than originally assumed. In addition to the persistence of transcriptionally silent proviruses in a stable latent reservoir that is invisible to the immune system, HIV is increasingly recognized to persist by resistance to the immune clearance, which appears to play a surprisingly prominent role in shaping the reservoir. In this review, we discuss some emerging insights into the mechanisms of HIV persistence, as well as their implications for the development of strategies towards an HIV cure.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
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11
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Hussein M, Andrade dos Ramos Z, Vink MA, Kroon P, Yu Z, Enjuanes L, Zuñiga S, Berkhout B, Herrera-Carrillo E. Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2. Viruses 2023; 15:v15030686. [PMID: 36992394 PMCID: PMC10051389 DOI: 10.3390/v15030686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
The current SARS-CoV-2 pandemic forms a major global health burden. Although protective vaccines are available, concerns remain as new virus variants continue to appear. CRISPR-based gene-editing approaches offer an attractive therapeutic strategy as the CRISPR-RNA (crRNA) can be adjusted rapidly to accommodate a new viral genome sequence. This study aimed at using the RNA-targeting CRISPR-Cas13d system to attack highly conserved sequences in the viral RNA genome, thereby preparing for future zoonotic outbreaks of other coronaviruses. We designed 29 crRNAs targeting highly conserved sequences along the complete SARS-CoV-2 genome. Several crRNAs demonstrated efficient silencing of a reporter with the matching viral target sequence and efficient inhibition of a SARS-CoV-2 replicon. The crRNAs that suppress SARS-CoV-2 were also able to suppress SARS-CoV, thus demonstrating the breadth of this antiviral strategy. Strikingly, we observed that only crRNAs directed against the plus-genomic RNA demonstrated antiviral activity in the replicon assay, in contrast to those that bind the minus-genomic RNA, the replication intermediate. These results point to a major difference in the vulnerability and biology of the +RNA versus −RNA strands of the SARS-CoV-2 genome and provide important insights for the design of RNA-targeting antivirals.
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Affiliation(s)
- Mouraya Hussein
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Zaria Andrade dos Ramos
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Monique A. Vink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Pascal Kroon
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Zhenghao Yu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Correspondence:
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Namer LS, Harwig A, Heynen SP, Das AT, Berkhout B, Kaempfer R. HIV co-opts a cellular antiviral mechanism, activation of stress kinase PKR by its RNA, to enable splicing of rev/tat mRNA. Cell Biosci 2023; 13:28. [PMID: 36774495 PMCID: PMC9922466 DOI: 10.1186/s13578-023-00972-1] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/24/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Activation of RNA-dependent stress kinase PKR, especially by viral double-stranded RNA, induces eukaryotic initiation factor 2 α-chain (eIF2α) phosphorylation, attenuating thereby translation. We report that this RNA-mediated negative control mechanism, considered a cornerstone of the cell's antiviral response, positively regulates splicing of a viral mRNA. RESULTS Excision of the large human immunodeficiency virus (HIV) rev/tat intron depends strictly on activation of PKR by the viral RNA and on eIF2α phosphorylation. Rev/tat mRNA splicing was blocked by viral PKR antagonists Vaccinia E3L and Ebola VP35, as well as by a trans-dominant negative mutant of PKR, yet enhanced by overexpressing PKR. Expression of non-phosphorylatable mutant eIF2αS51A, but not of wild type eIF2α, abrogated efficient splicing of rev/tat mRNA. By contrast, expression of eIF2αS51D, a phosphomimetic mutant of eIF2α, left rev/tat mRNA splicing intact. Unlike eIF2αS51A, eIF2αS51D does not inhibit eIF2α phosphorylation by activated PKR. All HIV mRNA species contain terminal trans-activation response (TAR) stem-loop sequences that potentially could activate PKR, yet even upon TAR deletion, HIV mRNA production remained sensitive to inhibitors of PKR activation. Bioinformatic and mutational analyses revealed a compact RNA pseudoknot upstream of 3'-terminal TAR that promotes splicing by activating PKR. Supporting its essential role in control of splicing, this pseudoknot is conserved among diverse HIV and nonhuman primate SIVcpz isolates. The pseudoknot and 3'-terminal TAR collaborate in mediating PKR-regulated splicing of rev/tat intron, the pseudoknot being dominant. CONCLUSIONS Our results on HIV provide the first example of a virus co-opting activation of PKR by its RNA, a cellular antiviral mechanism, to promote splicing. They raise the question whether other viruses may use local activation of host kinase PKR through RNA elements within their genome to achieve efficient splicing of their mRNA. Our experiments reveal an indispensable role for eIF2α phosphorylation in HIV rev/tat mRNA splicing that accounts for the need for PKR activation.
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Affiliation(s)
- Lise Sarah Namer
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102 Jerusalem, Israel
| | - Alex Harwig
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Stephan P. Heynen
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Atze T. Das
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Ben Berkhout
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel.
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Adams P, Berkhout B, Pasternak AO. Towards a molecular profile of antiretroviral therapy-free HIV remission. Curr Opin HIV AIDS 2022; 17:301-307. [PMID: 35938464 DOI: 10.1097/coh.0000000000000749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW To summarize the current status and highlight recent findings on predictive biomarkers for posttreatment HIV control (PTC) and virological remission. While historically, many studies focused on virological markers, there is an increasing tendency to enter immune and metabolic factors into the equation. RECENT FINDINGS On the virological side, several groups reported that cell-associated HIV RNA could predict time to viral rebound. Recent data hints at the possible importance of the genic location and chromatin context of the integrated provirus, although these factors still need to be assessed in relation to PTC and virological remission. Evidence from immunological studies highlighted innate and humoral immunity as important factors for prolonged HIV remission. Interestingly, novel metabolic markers have emerged, which offer additional angles to our understanding of latency and viral rebound. SUMMARY Facilitating PTC and virological remission remain top priorities for the HIV cure research. We advocate for clear and precise definitions for both phenomena in order to avoid misconceptions and to strengthen the conclusions that can be drawn. As no one-size-fits-all marker has emerged yet, more biomarkers are on the horizon, and viral rebound is a complex and heterogeneous process, it is likely that a combination of various biomarkers in cohesion will be necessary for a more accurate prediction of antiretroviral therapy-free HIV remission.
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Affiliation(s)
- Philipp Adams
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Berkhout B, van Hemert FJ. Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure. Virus Evol 2022; 8:veac072. [PMID: 36533144 PMCID: PMC9752802 DOI: 10.1093/ve/veac072] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/13/2022] [Accepted: 08/04/2022] [Indexed: 07/30/2023] Open
Abstract
There is a strong evolutionary tendency of the human immunodeficiency virus (HIV) to accumulate A nucleotides in its RNA genome, resulting in a mere 40 per cent A count. This A bias is especially dominant for the so-called silent codon positions where any nucleotide can be present without changing the encoded protein. However, particular silent codon positions in HIV RNA refrain from becoming A, which became apparent upon genome analysis of many virus isolates. We analyzed these 'noA' genome positions to reveal the underlying reason for their inability to facilitate the A nucleotide. We propose that local RNA structure requirements can explain the absence of A at these sites. Thus, noA sites may be prominently involved in the correct folding of the viral RNA. Turning things around, the presence of multiple clustered noA sites may reveal the presence of important sequence and/or structural elements in the HIV RNA genome.
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Affiliation(s)
| | - Formijn J van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
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Abstract
CRISPR-Cas12a is an alternative class 2 gene editing tool that may cause less off-target effects than the original Cas9 system. We have previously demonstrated that Cas12a attack with a single CRISPR RNA (crRNA) can neutralize all infectious HIV in an infected T cell line in cell culture. However, we demonstrated that HIV escapes from most crRNAs by acquisition of a mutation in the crRNA target sequence, thus providing resistance against Cas12a attack. Here, we tested the antiviral activity of seven dual crRNA combinations and analyzed the HIV proviral genomes for mutations at the target sites. We demonstrated that dual crRNA combinations exhibit more robust antiviral activity than a single crRNA attack and, more important, that the dual-crRNA therapy can prevent virus escape in long-term cultures. We confirmed the absence of any replication-competent virus in these apparently cured cultures. Surprisingly, we did not detect excision of the HIV sequences located between two Cas12a cleavage sites. Instead, we observed almost exclusively HIV inactivation by “hypermutation,” that is, the introduction of indel mutations at both target sites due to the error-prone cellular DNA repair machinery.
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Affiliation(s)
- Minghui Fan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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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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Eggink D, Bontjer I, de Taeye SW, Langedijk JP, Berkhout B, Sanders RW. Correction: HIV-1 anchor inhibitors and membrane fusion inhibitors target distinct but overlapping steps in virus entry. J Biol Chem 2022; 298:101811. [PMID: 35290891 PMCID: PMC8918835 DOI: 10.1016/j.jbc.2022.101811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Ferretti L. Phylogenetic Estimation of the Viral Fitness Landscape of HIV-1 Set-Point Viral Load. Virus Evol 2022; 8:veac022. [PMID: 35402002 PMCID: PMC8986633 DOI: 10.1093/ve/veac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/11/2021] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 104 and 105 copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 105 copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.
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Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | | | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd, Cambridge, UK
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands
- Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Hussein M, Andrade dos Ramos Z, Berkhout B, Herrera-Carrillo E. In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack. Viruses 2022; 14:v14020385. [PMID: 35215977 PMCID: PMC8880226 DOI: 10.3390/v14020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.
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Affiliation(s)
| | | | - Ben Berkhout
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
| | - Elena Herrera-Carrillo
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
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20
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Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Pijnappel FJJ, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Smalhout SY, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Weijsenfeld AM, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Jurriaans S, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Back NKT, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Zaaijer HL, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Berkhout B, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Cornelissen MTE, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Schinkel CJ, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet N, Rey D, Cheneau C, Partisani M, Priester M, Bernard-Henry C, Batard ML, Fischer P, Berger JL, Kmiec I, Robineau O, Huleux T, Ajana F, Alcaraz I, Allienne C, Baclet V, Meybeck A, Valette M, Viget N, Aissi E, Biekre R, Cornavin P, Merrien D, Seghezzi JC, Machado M, Diab G, Raffi F, Bonnet B, Allavena C, Grossi O, Reliquet V, Billaud E, Brunet C, Bouchez S, Morineau-Le Houssine P, Sauser F, Boutoille D, Besnier M, Hue H, Hall N, Brosseau D, Souala F, Michelet C, Tattevin P, Arvieux C, Revest M, Leroy H, Chapplain JM, Dupont M, Fily F, Patra-Delo S, Lefeuvre C, Bernard L, Bastides F, Nau P, Verdon R, de la Blanchardiere A, Martin A, Feret P, Geffray L, Daniel C, Rohan J, Fialaire P, Chennebault JM, Rabier V, Abgueguen P, Rehaiem S, Luycx O, Niault M, Moreau P, Poinsignon Y, Goussef M, Mouton-Rioux V, Houlbert D, Alvarez-Huve S, Barbe F, Haret S, Perre P, Leantez-Nainville S, Esnault JL, Guimard T, Suaud I, Girard JJ, Simonet V, Debab Y, Schmit JL, Jacomet C, Weinberck P, Genet C, Pinet P, Ducroix S, Durox H, Denes É, Abraham B, Gourdon F, Antoniotti O, Molina JM, Ferret S, Lascoux-Combe C, Lafaurie M, Colin de Verdiere N, Ponscarme D, De Castro N, Aslan A, Rozenbaum W, Pintado C, Clavel F, Taulera O, Gatey C, Munier AL, Gazaigne S, Penot P, Conort G, Lerolle N, Leplatois A, Balausine S, Delgado J, Timsit J, Tabet M, Gerard L, Girard PM, Picard O, Tredup J, Bollens D, Valin N, Campa P, Bottero J, Lefebvre B, Tourneur M, Fonquernie L, Wemmert C, Lagneau JL, Yazdanpanah Y, Phung B, Pinto A, Vallois D, Cabras O, Louni F, Pialoux G, Lyavanc T, Berrebi V, Chas J, Lenagat S, Rami A, Diemer M, Parrinello M, Depond A, Salmon D, Guillevin L, Tahi T, Belarbi L, Loulergue P, Zak Dit Zbar O, Launay O, Silbermann B, Leport C, Alagna L, Pietri MP, Simon A, Bonmarchand M, Amirat N, Pichon F, Kirstetter M, Katlama C, Valantin MA, Tubiana R, Caby F, Schneider L, Ktorza N, Calin R, Merlet A, Ben Abdallah S, Weiss L, Buisson M, Batisse D, Karmochine M, Pavie J, Minozzi C, Jayle D, Castel P, Derouineau J, Kousignan P, Eliazevitch M, Pierre I, Collias L, Viard JP, Gilquin J, Sobel A, Slama L, Ghosn J, Hadacek B, Thu-Huyn N, Nait-Ighil L, Cros A, Maignan A, Duvivier C, Consigny PH, Lanternier F, Shoai-Tehrani M, Touam F, Jerbi S, Bodard L, Jung C, Goujard C, Quertainmont Y, Duracinsky M, Segeral O, Blanc A, Peretti D, Cheret A, Chantalat C, Dulucq MJ, Levy Y, Lelievre JD, Lascaux AS, Dumont C, Boue F, Chambrin V, Abgrall S, Kansau I, Raho-Moussa M, De Truchis P, Dinh A, Davido B, Marigot D, Berthe H, Devidas A, Chevojon P, Chabrol A, Agher N, Lemercier Y, Chaix F, Turpault I, Bouchaud O, Honore P, Rouveix E, Reimann E, Belan AG, Godin Collet C, Souak S, Mortier E, Bloch M, Simonpoli AM, Manceron V, Cahitte I, Hiraux E, Lafon E, Cordonnier F, Zeng AF, Zucman D, Majerholc C, Bornarel D, Uludag A, Gellen-Dautremer J, Lefort A, Bazin C, Daneluzzi V, Gerbe J, Jeantils V, Coupard M, Patey O, Bantsimba J, Delllion S, Paz PC, Cazenave B, Richier L, Garrait V, Delacroix I, Elharrar B, Vittecoq D, Bolliot C, Lepretre A, Genet P, Masse V, Perrone V, Boussard JL, Chardon P, Froguel E, Simon P, Tassi S, Avettand Fenoel V, Barin F, Bourgeois C, Cardon F, Chaix ML, Delfraissy JF, Essat A, Fischer H, Lecuroux C, Meyer L, Petrov-Sanchez V, Rouzioux C, Saez-Cirion A, Seng R, Kuldanek K, Mullaney S, Young C, Zucchetti A, Bevan MA, McKernan S, Wandolo E, Richardson C, Youssef E, Green P, Faulkner S, Faville R, Herman S, Care C, Blackman H, Bellenger K, Fairbrother K, Phillips A, Babiker A, Delpech V, Fidler S, Clarke M, Fox J, Gilson R, Goldberg D, Hawkins D, Johnson A, Johnson M, McLean K, Nastouli E, Post F, Kennedy N, Pritchard J, Andrady U, Rajda N, Donnelly C, McKernan S, Drake S, Gilleran G, White D, Ross J, Harding J, Faville R, Sweeney J, Flegg P, Toomer S, Wilding H, Woodward R, Dean G, Richardson C, Perry N, Gompels M, Jennings L, Bansaal D, Browing M, Connolly L, Stanley B, Estreich S, Magdy A, O'Mahony C, Fraser P, Jebakumar SPR, David L, Mette R, Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022; 375:540-545. [PMID: 35113714 DOI: 10.1126/science.abk1688] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
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Affiliation(s)
- Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,IAME, UMR 1137, INSERM, Université de Paris, Paris, France
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | - Matti Ristola
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd., Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands.,Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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21
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Grandi N, Tramontano E, Berkhout B. Integration of SARS-CoV-2 RNA in infected human cells by retrotransposons: an unlikely hypothesis and old viral relationships. Retrovirology 2021; 18:34. [PMID: 34715873 PMCID: PMC8554740 DOI: 10.1186/s12977-021-00578-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Zhang et al. (Proc Natl Acad Sci 118:e2105968118, 2021) recently reported that SARS-CoV-2 RNA can be retrotranscribed and integrated into the DNA of human cells by the L1 retrotransposon machinery. This phenomenon could cause persistence of viral sequences in patients and may explain the prolonged PCR-positivity of SARS-CoV-2 infected patients, even long after the phase of active virus replication has ended. This commentary does critically review the available data on this topic and discusses them in the context of findings made for other exogenous viruses and ancestral endogenous retroviral elements.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari - Cittadella Universitaria di Monserrato, SS554, Monserrato (Cagliari), Italy.
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari - Cittadella Universitaria di Monserrato, SS554, Monserrato (Cagliari), Italy.,Istituto di Ricerca Genetica e Biomedica (IRGB), CNR - SS554, Monserrato (Cagliari), Italy
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam Medical Centers, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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22
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Espíndola ODM, Siteur-van Rijnstra E, Frankin E, Weijer K, van der Velden YU, Berkhout B, Blom B, Villaudy J. Early Effects of HTLV-1 Infection on the Activation, Exhaustion, and Differentiation of T-Cells in Humanized NSG Mice. Cells 2021; 10:cells10102514. [PMID: 34685494 PMCID: PMC8534134 DOI: 10.3390/cells10102514] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022] Open
Abstract
Adult T-cell leukemia/lymphoma (ATLL) is an aggressive malignancy of CD4+ T-cells associated with HTLV-1 infection. In this study, we used the model of immunodeficient NSG mice reconstituted with a functional human immune system (HIS) to investigate early events in HTLV-1 pathogenesis. Upon infection, human T-cells rapidly increased in the blood and lymphoid tissues, particularly CD4+CD25+ T-cells. Proliferation of CD4+ T-cells in the spleen and mesenteric lymph nodes (MLN) correlated with HTLV-1 proviral load and CD25 expression. In addition, splenomegaly, a common feature of ATLL in humans, was also observed. CD4+ and CD8+ T-cells predominantly displayed an effector memory phenotype (CD45RA−CCR7−) and expressed CXCR3 and CCR5 chemokine receptors, suggesting the polarization into a Th1 phenotype. Activated CD8+ T-cells expressed granzyme B and perforin; however, the interferon-γ response by these cells was limited, possibly due to elevated PD-1 expression and increased frequency of CD4+FoxP3+ regulatory T-cells in MLN. Thus, HTLV-1-infected HIS-NSG mice reproduced several characteristics of infection in humans, and it may be helpful to investigate ATLL-related events and to perform preclinical studies. Moreover, aspects of chronic infection were already present at early stages in this experimental model. Collectively, we suggest that HTLV-1 infection modulates host immune responses to favor viral persistence.
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Affiliation(s)
- Otávio de Melo Espíndola
- Laboratory for Clinical Research in Neuroinfections, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.S.-v.R.); (E.F.); (K.W.); (B.B.)
- Correspondence:
| | - Esther Siteur-van Rijnstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.S.-v.R.); (E.F.); (K.W.); (B.B.)
| | - Esmay Frankin
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.S.-v.R.); (E.F.); (K.W.); (B.B.)
| | - Kees Weijer
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.S.-v.R.); (E.F.); (K.W.); (B.B.)
| | - Yme Ubeles van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (Y.U.v.d.V.); (B.B.); (J.V.)
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (Y.U.v.d.V.); (B.B.); (J.V.)
| | - Bianca Blom
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.S.-v.R.); (E.F.); (K.W.); (B.B.)
| | - Julien Villaudy
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (Y.U.v.d.V.); (B.B.); (J.V.)
- J&S Preclinical Solutions, 5345 RR Oss, The Netherlands
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23
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Pasternak AO, Berkhout B. The Splice of Life: Does RNA Processing Have a Role in HIV-1 Persistence? Viruses 2021; 13:v13091751. [PMID: 34578332 PMCID: PMC8471011 DOI: 10.3390/v13091751] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 12/28/2022] Open
Abstract
Antiretroviral therapy (ART) suppresses HIV-1 replication but does not eradicate the virus. Persistence of HIV-1 latent reservoirs in ART-treated individuals is considered the main obstacle to achieving an HIV-1 cure. However, these HIV-1 reservoirs are not transcriptionally silent, and viral transcripts can be detected in most ART-treated individuals. HIV-1 latency is regulated at the transcriptional and at multiple post-transcriptional levels. Here, we review recent insights into the possible contribution of viral RNA processing to the persistence of HIV-1 reservoirs, and discuss the clinical implications of persistence of viral RNA species in ART-treated individuals.
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24
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Pasternak AO, Vroom J, Kootstra NA, Wit FW, de Bruin M, De Francesco D, Bakker M, Sabin CA, Winston A, Prins JM, Reiss P, Berkhout B. Non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy is associated with lower cell-associated HIV RNA and DNA levels as compared with therapy based on protease inhibitors. eLife 2021; 10:68174. [PMID: 34387543 PMCID: PMC8460250 DOI: 10.7554/elife.68174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/07/2021] [Indexed: 11/28/2022] Open
Abstract
Background: It remains unclear whether combination antiretroviral therapy (ART) regimens differ in their ability to fully suppress human immunodeficiency virus (HIV) replication. Here, we report the results of two cross-sectional studies that compared levels of cell-associated (CA) HIV markers between individuals receiving suppressive ART containing either a non-nucleoside reverse transcriptase inhibitor (NNRTI) or a protease inhibitor (PI). Methods: CA HIV unspliced RNA and total HIV DNA were quantified in two cohorts (n = 100, n = 124) of individuals treated with triple ART regimens consisting of two nucleoside reverse transcriptase inhibitors (NRTIs) plus either an NNRTI or a PI. To compare CA HIV RNA and DNA levels between the regimens, we built multivariable models adjusting for age, gender, current and nadir CD4+ count, plasma viral load zenith, duration of virological suppression, NRTI backbone composition, low-level plasma HIV RNA detectability, and electronically measured adherence to ART. Results: In both cohorts, levels of CA HIV RNA and DNA strongly correlated (rho = 0.70 and rho = 0.54) and both markers were lower in NNRTI-treated than in PI-treated individuals. In the multivariable analysis, CA RNA in both cohorts remained significantly reduced in NNRTI-treated individuals (padj = 0.02 in both cohorts), with a similar but weaker association between the ART regimen and total HIV DNA (padj = 0.048 and padj = 0.10). No differences in CA HIV RNA or DNA levels were observed between individual NNRTIs or individual PIs, but CA HIV RNA was lower in individuals treated with either nevirapine or efavirenz, compared to PI-treated individuals. Conclusions: All current classes of antiretroviral drugs only prevent infection of new cells but do not inhibit HIV RNA transcription in long-lived reservoir cells. Therefore, these differences in CA HIV RNA and DNA levels by treatment regimen suggest that NNRTIs are more potent in suppressing HIV residual replication than PIs, which may result in a smaller viral reservoir size. Funding: This work was supported by ZonMw (09120011910035) and FP7 Health (305522).
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Affiliation(s)
- Alexander O Pasternak
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jelmer Vroom
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ferdinand Wnm Wit
- Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marijn de Bruin
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Davide De Francesco
- Institute for Global Health, University College London, London, United Kingdom
| | - Margreet Bakker
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, United Kingdom
| | - Alan Winston
- Medicine, Imperial College London, London, United Kingdom
| | - Jan M Prins
- Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, New Caledonia
| | - Peter Reiss
- Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Berkhout
- Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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25
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Herrera-Carrillo E, Gao Z, Berkhout B. CRISPR therapy towards an HIV cure. Brief Funct Genomics 2021; 19:201-208. [PMID: 31711197 DOI: 10.1093/bfgp/elz021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022] Open
Abstract
Tools based on RNA interference (RNAi) and the recently developed clustered regularly short palindromic repeats (CRISPR) system enable the selective modification of gene expression, which also makes them attractive therapeutic reagents for combating HIV infection and other infectious diseases. Several parallels can be drawn between the RNAi and CRISPR-Cas9 platforms. An ideal RNAi or CRISPR-Cas9 therapeutic strategy for treating infectious or genetic diseases should exhibit potency, high specificity and safety. However, therapeutic applications of RNAi and CRISPR-Cas9 have been challenged by several major limitations, some of which can be overcome by optimal design of the therapy or the design of improved reagents. In this review, we will discuss some advantages and limitations of anti-HIV strategies based on RNAi and CRISPR-Cas9 with a focus on the efficiency, specificity, off-target effects and delivery methods.
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Affiliation(s)
- Elena Herrera-Carrillo
- Department of Medical Microbiology Laboratory of Experimental Virology Amsterdam UMC, AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Zongliang Gao
- Department of Medical Microbiology Laboratory of Experimental Virology Amsterdam UMC, AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology Laboratory of Experimental Virology Amsterdam UMC, AMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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26
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Darcis G, Kootstra NA, Hooibrink B, van Montfort T, Maurer I, Groen K, Jurriaans S, Bakker M, van Lint C, Berkhout B, Pasternak AO. CD32 +CD4 + T Cells Are Highly Enriched for HIV DNA and Can Support Transcriptional Latency. Cell Rep 2021; 30:2284-2296.e3. [PMID: 32075737 PMCID: PMC7050565 DOI: 10.1016/j.celrep.2020.01.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 02/07/2023] Open
Abstract
The HIV latent reservoir forms the major hurdle to an HIV cure. The discovery of CD32 as marker of this reservoir has aroused much interest, but subsequent reports have challenged this finding. Here, we observe a positive correlation between the percentages of CD32+ cells among CD4+ T cells of aviremic cART-treated, HIV-infected individuals and their HIV DNA loads in peripheral blood. Moreover, optimization of the CD32+CD4+ T cell purification protocol reveals prominent enrichment for HIV DNA (mean, 292-fold) in these cells. However, no enrichment for HIV RNA is observed in CD32+CD4+ cells, yielding significantly reduced HIV RNA/DNA ratios. Furthermore, HIV proviruses in CD32+CD4+ cells can be reactivated ex vivo to produce virus, strongly suggesting that these cells support HIV transcriptional latency. Our results underscore the importance of isolating pure, bona fide CD32+CD4+ T cells for future studies and indicate that CD32 remains a promising candidate marker of the HIV reservoir.
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Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Infectious Diseases Department, Liège University Hospital, Liège, Belgium.
| | - Neeltje A Kootstra
- Laboratory of Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Berend Hooibrink
- Department of Cell Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Thijs van Montfort
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Irma Maurer
- Laboratory of Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Kevin Groen
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Suzanne Jurriaans
- Laboratory of Clinical Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Carine van Lint
- Service of Molecular Virology, Département de Biologie Moléculaire (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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27
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Pasternak AO, Psomas CK, Berkhout B. Predicting Post-treatment HIV Remission: Does Size of the Viral Reservoir Matter? Front Microbiol 2021; 12:648434. [PMID: 33717047 PMCID: PMC7952863 DOI: 10.3389/fmicb.2021.648434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
Combination antiretroviral therapy (ART) suppresses human immunodeficiency virus (HIV) replication and improves immune function. However, due to the persistence of long-lived HIV reservoirs, therapy interruption almost inevitably leads to a fast viral rebound. A small percentage of individuals who are able to control HIV replication for extended periods after therapy interruption are of particular interest because they may represent a model of long-term HIV remission without ART. These individuals are characterized by a limited viral reservoir and low reservoir measures can predict post-treatment HIV remission. However, most individuals with a low reservoir still experience fast viral rebound. In this Perspective, we discuss the possible reasons behind this and propose to develop an integral profile, composed of viral and host biomarkers, that could allow the accurate prediction of post-treatment HIV remission. We also propose to incorporate information on the chromatin context of the proviral integration sites into the characterization of the HIV reservoir, as this likely influences the reactivation capacity of latent proviruses and, together with the actual number of intact proviruses, contributes to the replication competence of the reservoir.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Christina K Psomas
- Department of Infectious Diseases and Internal Medicine, European Hospital, Marseille, France
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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28
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Berkhout B, Gao Z, Herrera-Carrillo E. Design and Evaluation of Guide RNA Transcripts with a 3'-Terminal HDV Ribozyme to Enhance CRISPR-Based Gene Inactivation. Methods Mol Biol 2021; 2167:205-224. [PMID: 32712922 PMCID: PMC7896425 DOI: 10.1007/978-1-0716-0716-9_12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
The recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 system, now reclassified as Cas12a, is a DNA-editing platform analogous to the widely used CRISPR-Cas9 system. The Cas12a system exhibits several distinct features over the CRISPR-Cas9 system, such as increased specificity and a smaller gene size to encode the nuclease and the matching CRISPR guide RNA (crRNA), which could mitigate off-target and delivery problems, respectively, described for the Cas9 system. However, the Cas12a system exhibits reduced gene editing efficiency compared to Cas9. A closer inspection of the crRNA sequence raised some uncertainty about the actual 5' and 3'-ends. RNA Polymerase (Pol) III promoters are generally used for the production of small RNAs with a precise 5' terminus, but the Pol III enzyme generates small RNAs with 3' U-tails of variable length. To optimize the CRISPR-Cas12a system, we describe the inclusion of a self-cleaving ribozyme in the vector design to facilitate accurate 3'-end processing of the crRNA transcript to produce precise molecules. This optimized design enhanced not only the gene editing efficiency, but also the activity of the catalytically inactive Cas12a-based CRISPR gene activation platform. We thus generated an improved CRISPR-Cas12a system for more efficient gene editing and gene regulation purposes.
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Affiliation(s)
- Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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29
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Gao Z, van der Velden YU, Fan M, van der Linden CA, Vink M, Herrera-Carrillo E, Berkhout B. Engineered miniature H1 promoters with dedicated RNA polymerase II or III activity. J Biol Chem 2021; 296:100026. [PMID: 33154168 PMCID: PMC7949045 DOI: 10.1074/jbc.ra120.015386] [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: 07/27/2020] [Revised: 10/19/2020] [Accepted: 11/05/2020] [Indexed: 11/24/2022] Open
Abstract
RNA polymerase III (Pol III) promoters, such as 7SK, U6, and H1, are widely used for the expression of small noncoding RNAs, including short hairpin RNAs for RNAi experiments and guide RNAs for CRISPR-mediated genome editing. We previously reported dual RNA polymerase activity (Pol II/III) for the human H1 promoter and demonstrated that this promiscuous RNA polymerase use can be exploited for the simultaneous expression of both a noncoding RNA and an mRNA. However, this combination is not a desired feature in other experimental and therapeutic settings. To overcome this limitation of the H1 promoter, we engineered a miniature H1/7SK hybrid promoter with minimal Pol II activity, thereby boosting Pol III activity to a level that is higher than that of either parental promoter. In parallel, we also engineered small Pol II-specific H1 promoter variants and explored their use as general Pol II promoters for protein expression. The newly engineered promoter variants form an attractive alternative to the commonly used H1 promoter in terms of not only activity and small promoter size but also concerning safety by exclusive expression of the desired therapeutic transcript (either pol II or pol III but not both).
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Affiliation(s)
- Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Yme Ubeles van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Minghui Fan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Cynthia Alyssa van der Linden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Monique Vink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
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Berkhout B, Herrera-Carrillo E. Design and Evaluation of AgoshRNAs with 3'-Terminal HDV Ribozymes to Enhance the Silencing Activity. Methods Mol Biol 2021; 2167:225-252. [PMID: 32712923 DOI: 10.1007/978-1-0716-0716-9_13] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Since the first application of RNA interference (RNAi) in mammalian cells, the expression of short hairpin RNA (shRNA) molecules for targeted gene silencing has become a benchmark technology. Plasmid and viral vector systems can be used to express shRNA precursor transcripts that are processed by the cellular RNAi pathway to trigger sequence-specific gene knockdown. Intensive RNAi investigations documented that only a small percentage of computationally predicted target sequences can be used for efficient gene silencing, in part because not all shRNA designs are active. Many factors influence the shRNA activity and guidelines for optimal shRNA design have been proposed. We recently described an alternatively processed shRNA molecule termed AgoshRNA with a ~18 base pairs (bp) stem and a 3-5 nucleotides (nt) loop. This molecule is alternatively processed by the Argonaute (Ago) protein into a single guide RNA strand that efficiently induces the RNAi mechanism. The design rules proposed for regular shRNAs do not apply to AgoshRNA molecules and therefore new rules had to be defined. We optimized the AgoshRNA design and managed to create a set of active AgoshRNAs targeted against the human immunodeficiency virus (HIV). In an attempt to enhance the silencing activity of the AgoshRNA molecules, we included the hepatitis delta virus (HDV) ribozyme at the 3' terminus, which generates a uniform 3' end instead of a 3' U-tail of variable length. We evaluated the impact of this 3'-end modification on AgoshRNA processing and its gene silencing activity and we demonstrate that this novel AgoshRNA-HDV design exhibits enhanced antiviral activity.
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Affiliation(s)
- Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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van der Velden YU, Villaudy J, Siteur-van Rijnstra E, van der Linden CA, Vink MA, Schermer EE, Weijer K, Berkhout B, Sanders RW, van Gils MJ. Diverse HIV-1 escape pathways from broadly neutralizing antibody PGDM1400 in humanized mice. MAbs 2020; 12:1845908. [PMID: 33218286 PMCID: PMC7755169 DOI: 10.1080/19420862.2020.1845908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Recent studies have shown the potential of broadly neutralizing antibodies (bnAbs) for HIV-1 treatment. One of the candidate antibodies moving into clinical trials is the bnAb PGDM1400. Here, we studied the therapeutic potency and escape pathways of bnAb PGDM1400 during monovalent therapy in human immune system (HIS) mice using the BG505, REJO, MJ4 and AMC008 virus isolates. PGDM1400 administered during chronic infection caused a modest decrease in viral load in the first week of administration in 7 out of 10 animals, which correlated with the in vitro neutralization sensitivity of the viruses to PGDM1400. As expected for monotherapy, viral loads rebounded after about a week and different viral escape pathways were observed, involving the deletion of glycans in the envelope glycoprotein at positions 130 or 160. (Pre)clinical trials should reveal whether PGDM1400 is a useful component of an antibody combination treatment or as part of a tri-specific antibody.
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Affiliation(s)
- Yme U van der Velden
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands
| | - Julien Villaudy
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands.,AIMM Therapeutics , Amsterdam, the Netherlands
| | | | - Cynthia A van der Linden
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands.,HIS mouse facility, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands
| | - Monique A Vink
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands
| | - Kees Weijer
- HIS mouse facility, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University , New York, NY, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam , Amsterdam, the Netherlands
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Gao Z, Fan M, Das AT, Herrera-Carrillo E, Berkhout B. Extinction of all infectious HIV in cell culture by the CRISPR-Cas12a system with only a single crRNA. Nucleic Acids Res 2020; 48:5527-5539. [PMID: 32282899 PMCID: PMC7261156 DOI: 10.1093/nar/gkaa226] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 02/13/2020] [Revised: 03/21/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
The CRISPR-Cas9 system has been used for genome editing of various organisms. We reported inhibition of the human immunodeficiency virus (HIV) in cell culture infections with a single guide RNA (gRNA) and subsequent viral escape, but complete inactivation of infectious HIV with certain combinations of two gRNAs. The new RNA-guided endonuclease system CRISPR-Cas12a (formerly Cpf1) may provide a more promising tool for genome engineering with increased activity and specificity. We compared Cas12a to the original Cas9 system for inactivation of the integrated HIV DNA genome. Superior antiviral activity is reported for Cas12a, which can achieve full HIV inactivation with only a single gRNA (called crRNA). We propose that the different architecture of Cas9 versus Cas12a endonuclease explains this effect. We also disclose that DNA cleavage by the Cas12a endonuclease and subsequent DNA repair causes mutations with a sequence profile that is distinct from that of Cas9. Both CRISPR systems can induce the typical small deletions around the site of DNA cleavage and subsequent repair, but Cas12a does not induce the pure DNA insertions that are routinely observed for Cas9. Although these typical signatures are apparent in many literature studies, this is the first report that documents these striking differences.
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Affiliation(s)
- Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Minghui Fan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Life and Environmental Sciences, University of Cagliari, Italy
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Liang C, Berkhout B. Editorial overview: Engineering cellular resistance towards the HIV cure. Curr Opin Virol 2020; 38:iii-v. [PMID: 31718776 DOI: 10.1016/j.coviro.2019.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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van der Kuyl AC, Berkhout B. Viruses in the reproductive tract: On their way to the germ line? Virus Res 2020; 286:198101. [PMID: 32710926 DOI: 10.1016/j.virusres.2020.198101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 01/13/2023]
Abstract
Studies of vertebrate genomes have indicated that all species contain in their chromosomes stretches of DNA with sequence similarity to viral genomes. How such 'endogenous' viral elements (EVEs) ended up in host genomes is usually explained in general terms such as 'they entered the germ line at some point during evolution'. This seems a correct statement, but is also rather imprecise. The vast number of endogenous viral sequences suggest that common routes to the 'germ line' may exist, as relying on chance alone may not easily explain the abundance of EVEs in modern mammalian genomes. An increasing number of virus types have been detected in human semen and a growing number of studies have reported on viral infections that cause male infertility or subfertility and on viral infections that threaten in vitro fertilisation practices. Thus, it is timely to survey the pathway(s) that viruses can use to gain access to the human germ line. Embryo transfer and semen quality studies in livestock form another source of relevant information because virus infection during reproduction is clearly unwanted, as is the case for the human situation. In this review, studies on viruses in the male and female reproductive tract and in the early embryo will be discussed to propose a plausible viral route to the mammalian germ line.
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Affiliation(s)
- Antoinette Cornelia van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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35
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Pasternak AO, Grijsen ML, Wit FW, Bakker M, Jurriaans S, Prins JM, Berkhout B. Cell-associated HIV-1 RNA predicts viral rebound and disease progression after discontinuation of temporary early ART. JCI Insight 2020; 5:134196. [PMID: 32097124 DOI: 10.1172/jci.insight.134196] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/19/2020] [Indexed: 11/17/2022] Open
Abstract
Plasma viral load (VL) and CD4+ T cell count are widely used as biomarkers of HIV type 1 (HIV-1) replication, pathogenesis, and response to antiretroviral therapy (ART). However, the clinical potential of cell-associated (CA) HIV-1 molecular markers is much less understood. Here, we measured CA HIV-1 RNA and DNA in HIV-infected individuals treated with temporary ART initiated during primary HIV-1 infection. We demonstrate substantial predictive value of CA RNA for (a) the virological and immunological response to early ART, (b) the magnitude and time to viral rebound after discontinuation of early ART, and (c) disease progression in the absence of treatment. Remarkably, when adjusted for CA RNA, plasma VL no longer appeared as an independent predictor of any clinical endpoint in this cohort. The potential of CA RNA as an HIV-1 clinical marker, in particular as a predictive biomarker of virological control after stopping ART, should be explored in the context of HIV-1 curative interventions.
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Affiliation(s)
| | - Marlous L Grijsen
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ferdinand W Wit
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Global Health program, Amsterdam Public Health research institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.,HIV Monitoring Foundation, Amsterdam, Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, and
| | - Suzanne Jurriaans
- Laboratory of Clinical Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jan M Prins
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, and
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36
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Binda CS, Klaver B, Berkhout B, Das AT. CRISPR-Cas9 Dual-gRNA Attack Causes Mutation, Excision and Inversion of the HIV-1 Proviral DNA. Viruses 2020; 12:E330. [PMID: 32197474 PMCID: PMC7150824 DOI: 10.3390/v12030330] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 02/20/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 01/01/2023] Open
Abstract
Although several studies demonstrated that the HIV proviral DNA can be effectively targeted and inactivated by the CRISPR-Cas9 system, the precise inactivation mechanism has not yet been analyzed. Whereas some studies suggested efficient proviral DNA excision upon dual-gRNA/Cas9 treatment, we previously demonstrated that hypermutation of the target sites correlated with permanent virus inactivation. To better understand the mechanism underlying HIV inactivation, we analyzed the proviral DNA upon Cas9 attack with gRNA pairs. We observed that dual-gRNA targeting resulted more frequently in target site mutation than fragment excision, while fragment inversion was rarely observed. The frequencies varied for different gRNA combinations without an obvious relationship with the distance between the target sites, indicating that other gRNA and target DNA characteristics influence the DNA cleavage and repair processes.
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Affiliation(s)
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands; (C.S.B.); (B.K.)
| | - Atze T. Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands; (C.S.B.); (B.K.)
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37
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Hentzschel F, Mitesser V, Fraschka SAK, Krzikalla D, Carrillo EH, Berkhout B, Bártfai R, Mueller AK, Grimm D. Gene knockdown in malaria parasites via non-canonical RNAi. Nucleic Acids Res 2020; 48:e2. [PMID: 31680162 PMCID: PMC7145648 DOI: 10.1093/nar/gkz927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/05/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
The lack of endogenous RNAi machinery in the malaria parasite Plasmodium hampers gene annotation and hence antimalarial drug and vaccine development. Here, we engineered rodent Plasmodium berghei to express a minimal, non-canonical RNAi machinery that solely requires Argonaute 2 (Ago2) and a modified short hairpin RNA, so-called AgoshRNA. Using this strategy, we achieved robust and specific gene knockdown throughout the entire parasite life cycle. We also successfully silenced the endogenous gene perforin-like protein 2, phenocopying a full gene knockout. Transcriptionally restricting Ago2 expression to the liver stage further enabled us to perform a stage-specific gene knockout. The RNAi-competent Plasmodium lines reported here will be a valuable resource for loss-of-function phenotyping of the many uncharacterized genes of Plasmodium in low or high throughput, without the need to engineer the target gene locus. Thereby, our new strategy and transgenic Plasmodium lines will ultimately benefit the discovery of urgently needed antimalarial drug and vaccine candidates. Generally, the ability to render RNAi-negative organisms RNAi-competent by mere introduction of two components, Ago2 and AgoshRNA, is a unique paradigm that should find broad applicability in other species.
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Affiliation(s)
- Franziska Hentzschel
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Vera Mitesser
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | | | - Daria Krzikalla
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Elena Herrera Carrillo
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Meibergdreef 15, K3-110, 1105 AZ Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Meibergdreef 15, K3-110, 1105 AZ Amsterdam, The Netherlands
| | - Richárd Bártfai
- Radboud University, Dept. of Molecular Biology, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Ann-Kristin Mueller
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg
| | - Dirk Grimm
- Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg.,German Center for Cardiovascular Research (DZHK), partner site Heidelberg
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38
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Boerekamps A, Newsum AM, Smit C, Arends JE, Richter C, Reiss P, Rijnders BJA, Brinkman K, van der Valk M, Godfried MH, Goorhuis A, Hovius JW, van der Meer JTM, Kuijpers TW, Nellen FJB, van der Poll DT, Prins JM, van Vugt HJM, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, van Hes AMH, Mutschelknauss M, Nobel HE, Pijnappel FJJ, Weijsenfeld AM, Jurriaans S, Back NKT, Zaaijer HL, Berkhout B, Cornelissen MTE, Schinkel CJ, Wolthers KC, van den Berge M, Stegeman A, Baas S, de Looff LH, Wintermans B, Veenemans J, Pronk MJH, Ammerlaan HSM, de Munnik ES, Jansz AR, Tjhie J, Wegdam MCA, Deiman B, Scharnhorst V, van Eeden A, v d V M, Brokking W, Groot M, Elsenburg LJM, Damen M, Kwa IS, van Kasteren MEE, Brouwer AE, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Pfaf S, van der Ven B, de Kruijf-van de Wiel BAFM, van der Ven B, Buiting AGM, Kabel PJ, Versteeg D, van der Ende ME, Bax HI, van Gorp ECM, Nouwen JL, Schurink CAM, Verbon A, de Vries-Sluijs TEMS, de Jong-Peltenburg NC, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, van den Berg-Cameron HJ, de Groot J, de Zeeuw-de Man M, Boucher CAB, Koopmans MPG, van Kampen JJA, Pas SD, Branger J, Rijkeboer-Mes A, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van IJperen JM, Geilings J, van der Hut G, van Burgel ND, Haag D, Leyten EMS, Gelinck LBS, van Hartingsveld AY, Meerkerk C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, van der Bliek GL, Bor PCJ, Bloembergen P, Wolfhagen MJHM, Ruijs GJHM, Kroon FP, de Boer MGJ, Scheper H, Jolink H, Vollaard AM, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, Pogany K, Roukens A, Kastelijns M, Smit JV, Smit E, Struik-Kalkman D, Tearno C, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, Mulder JW, Vrouenraets SME, Lauw FN, van Broekhuizen MC, Vlasblom DJ, Smits PHM, Weijer S, El Moussaoui R, Bosma AS, van Vonderen MGA, van Houte DPF, Kampschreur LM, Dijkstra K, Faber S, Weel J, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Heins H, Lucas E, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, IJzerman EP, Jansen R, Rozemeijer W, van der Reijden WA, van den Berk GEL, Blok WL, Frissen PHJ, Lettinga KD, Schouten WEM, Veenstra J, Brouwer CJ, Geerders GF, Hoeksema K, Kleene MJ, van der Meché IB, Spelbrink M, Toonen AJM, Wijnands S, Kwa D, Regez R, van Crevel R, Keuter M, van der Ven AJAM, ter Hofstede HJM, Dofferhoff ASM, Hoogerwerf J, Grintjes-Huisman KJT, de Haan M, Marneef M, Hairwassers A, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Stienstra Y, Wilting KR, Wouthuyzen-Bakker M, Boonstra A, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, Wassenberg MWM, van Zoelen MAD, Aarsman K, van Elst-Laurijssen DHM, de Kroon I, van Rooijen CSAM, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Peters EJG, van Agtmael MA, Bomers M, Heitmuller M, Laan LM, Ang CW, van Houdt R, Pettersson AM, Vandenbroucke-Grauls CMJE, Reiss P, Bezemer DO, van Sighem AI, Smit C, Wit FWMN, Boender TS, Zaheri S, Hillebregt M, de Jong A, Bergsma D, Grivell S, Jansen A, Raethke M, Meijering R, Rutkens T, de Groot L, van den Akker M, Bakker Y, Bezemer M, Claessen E, El Berkaoui A, Geerlinks J, Koops J, Kruijne E, Lodewijk C, van der Meer R, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Timmerman A, Tuijn E, Veenenberg L, van der Vliet S, Wisse A, de Witte EC, Woudstra T, Tuk B. High Treatment Uptake in Human Immunodeficiency Virus/Hepatitis C Virus-Coinfected Patients After Unrestricted Access to Direct-Acting Antivirals in the Netherlands. Clin Infect Dis 2019; 66:1352-1359. [PMID: 29186365 DOI: 10.1093/cid/cix1004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/20/2017] [Indexed: 12/24/2022] Open
Abstract
Background The Netherlands has provided unrestricted access to direct-acting antivirals (DAAs) since November 2015. We analyzed the nationwide hepatitis C virus (HCV) treatment uptake among patients coinfected with human immunodeficiency virus (HIV) and HCV. Methods Data were obtained from the ATHENA HIV observational cohort in which >98% of HIV-infected patients ever registered since 1998 are included. Patients were included if they ever had 1 positive HCV RNA result, did not have spontaneous clearance, and were known to still be in care. Treatment uptake and outcome were assessed. When patients were treated more than once, data were included from only the most recent treatment episode. Data were updated until February 2017. In addition, each treatment center was queried in April 2017 for a data update on DAA treatment and achieved sustained virological response. Results Of 23574 HIV-infected patients ever linked to care, 1471 HCV-coinfected patients (69% men who have sex with men, 15% persons who [formerly] injected drugs, and 15% with another HIV transmission route) fulfilled the inclusion criteria. Of these, 87% (1284 of 1471) had ever initiated HCV treatment between 2000 and 2017, 76% (1124 of 1471) had their HCV infection cured; DAA treatment results were pending in 6% (92 of 1471). Among men who have sex with men, 83% (844 of 1022) had their HCV infection cured, and DAA treatment results were pending in 6% (66 of 1022). Overall, 187 patients had never initiated treatment, DAAs had failed in 14, and a pegylated interferon-alfa-based regimen had failed in 54. Conclusions Fifteen months after unrestricted DAA availability the majority of HIV/HCV-coinfected patients in the Netherlands have their HCV infection cured (76%) or are awaiting DAA treatment results (6%). This rapid treatment scale-up may contribute to future HCV elimination among these patients.
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Affiliation(s)
- Anne Boerekamps
- Department of Internal Medicine and Infectious Diseases, Erasmus Medical Center, Rotterdam
| | - Astrid M Newsum
- Department of Infectious Diseases Research and Prevention, Public Health Service of Amsterdam.,Division of Infectious Diseases, Amsterdam Infection and Immunity Institute, Academic Medical Center
| | | | - Joop E Arends
- Department of Internal Medicine, Section Infectious Diseases, University Medical Center Utrecht
| | - Clemens Richter
- Department of Internal Medicine and Infectious Diseases, Rijnstate Hospital, Arnhem
| | - Peter Reiss
- Division of Infectious Diseases, Amsterdam Infection and Immunity Institute, Academic Medical Center.,Stichting HIV Monitoring, Amsterdam.,Department of Global Health, Academic Medical Center and Amsterdam Institute for Global Health and Development
| | - Bart J A Rijnders
- Department of Internal Medicine and Infectious Diseases, Erasmus Medical Center, Rotterdam
| | - Kees Brinkman
- Department of Internal Medicine and Infectious Diseases, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands
| | - Marc van der Valk
- Division of Infectious Diseases, Amsterdam Infection and Immunity Institute, Academic Medical Center
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Abstract
Combination antiretroviral therapy (ART) suppresses human immunodeficiency virus (HIV) replication and improves immune function, but is unable to eradicate the virus. Therefore, development of an HIV cure has become one of the main priorities of the HIV research field. The main obstacle for an HIV cure is the formation of latent viral reservoirs, where the virus is able to “hide” despite decades of therapy, just to reignite active replication once therapy is stopped. Revealing HIV hiding places is thus central to HIV cure research, but the absence of markers of these reservoir cells greatly complicates the search for a cure. Identification of one or several marker(s) of latently infected cells would represent a significant step forward toward a better description of the cell types involved and improved understanding of HIV latency. Moreover, it could provide a “handle” for selective therapeutic targeting of the reservoirs. A number of cellular markers of HIV reservoir have recently been proposed, including immune checkpoint molecules, CD2, and CD30. CD32a is perhaps the most promising of HIV reservoir markers as it is reported to be associated with a very prominent enrichment in HIV DNA, although this finding has been challenged. In this review, we provide an update on the current knowledge about HIV reservoir markers. We specifically highlight studies that characterized markers of persistently infected cells in the lymphoid tissues.
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Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Infectious Diseases Department, Liège University Hospital, Liège, Belgium
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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40
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Abstract
Antiretroviral therapy (ART) can effectively suppress ongoing HIV replication and block disease progression, but the infection is never cured due to the persistence of a small pool of latently infected cells hosting integrated replication-competent HIV proviruses. However, the vast majority of HIV proviruses in ART-treated patients are replication-incompetent due to a variety of genetic defects. Most defective proviruses (around 90%) contain large internal deletions or are G-to-A hypermutated, resulting in destruction of most if not all viral open reading frames, which is consistent with the idea that cytotoxic T cells (CTLs) effectively remove cells that produce viral antigens. An intriguing subclass of defective proviruses (around 10%) that are consistently detected in such patients carry a small deletion or a point mutation in a relatively precise and well conserved region near the 5ʹ end of the HIV genome, in the area that encodes the major splice donor (MSD) site and the packaging signal Ѱ in the viral RNA genome. Why this subclass of proviruses is defective has never been properly understood. We now propose a mechanistic scenario for how these MSD-Ѱ mutations can prevent viral protein expression. Based on ample results in literature, we argue that MSD inactivation triggers the activity of the 5ʹ-polyadenylation site, resulting in the production of ultra-short non-protein-coding HIV transcripts.
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Affiliation(s)
- Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands. .,Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
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41
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Pasternak A, Darcis G, Kootstra N, Hooibrink B, van Montfort T, Groen K, Jurriaans S, Bakker M, van Lint C, Berkhout B. CD32+CD4+ T cells are highly enriched in HIV DNA. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)31042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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42
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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: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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43
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Abstract
RNA interference (RNAi) can be triggered by synthetic small interfering RNAs (siRNAs) or transgene-expressed short hairpin RNAs (shRNAs). Recent evidence indicates that shRNA molecules, with a relatively short stem and small loop, are processed by Argonaute 2 protein (Ago2). We named these molecules AgoshRNA as Ago2 is involved in both the processing and the subsequent mRNA-silencing reaction. This alternative processing route yields only a single guide strand, which thus avoids potential off-target effects induced by the passenger strand of a regular shRNA. We recently described that the introduction of a 5ʹ-terminal purine (A or G) and a mismatch at the bottom of the hairpin enhances the AgoshRNA activity. The critical 5ʹ-terminal nucleotide (nt) represents the +1 position of the transcriptional promoter, which influences the transcriptional efficiency and initiation accuracy as demonstrated for the H1 RNA polymerase (Pol) III promoter. These findings highlight the necessity of considering Pol III requirements in the design of optimized AgoshRNA cassettes. In this study, we report the design and expression of potent AgoshRNAs by two other popular Pol III promoters: U6 and 7SK, which were recently reported to have a distinct transcription profile compared to the H1 promoter. We propose general rules for the design and expression of potent AgoshRNA molecules using Pol III cassettes, which should augment the application of novel AgoshRNA reagents for basic research and therapeutic purposes.
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Affiliation(s)
- Zongliang Gao
- a Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC , University of Amsterdam , Amsterdam , the Netherlands
| | - Ben Berkhout
- a Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC , University of Amsterdam , Amsterdam , the Netherlands
| | - Elena Herrera-Carrillo
- a Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC , University of Amsterdam , Amsterdam , the Netherlands
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44
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Steba GS, Koekkoek SM, Vanhommerig JW, Brinkman K, Kwa D, Van Der Meer JTM, Prins M, Berkhout B, Tanck M, Paxton WA, Molenkamp R, Schinkel J. DC-SIGN Polymorphisms Associate with Risk of Hepatitis C Virus Infection Among Men who Have Sex with Men but not Among Injecting Drug Users. J Infect Dis 2019; 217:353-357. [PMID: 29140443 PMCID: PMC5853896 DOI: 10.1093/infdis/jix587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/10/2017] [Indexed: 12/16/2022] Open
Abstract
We aimed to identify whether genetic polymorphisms within L-SIGN or DC-SIGN correlate with hepatitis C virus (HCV) susceptibility. A men who have sex with men (MSM) and an injecting drug users (IDU) cohort of HCV cases and multiple-exposed uninfected controls were genotyped for numerous L-SIGN and DC-SIGN polymorphisms. DC-SIGN single nucleotide polymorphisms (SNPs) -139, -871, and -939 correlated with HCV acquisition in the MSM cohort only. When the same SNPs were introduced into a transcription activity assay they demonstrated a reduction in expression with predicted alteration in binding of transcription factors. DC-SIGN promoter SNPs correlated with risk of HCV acquisition via sexual but not IDU exposure, likely through modulation of mRNA expression levels.
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Affiliation(s)
- Gaby S Steba
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Sylvie M Koekkoek
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Joost W Vanhommerig
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands.,Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Kees Brinkman
- Department of Internal Medicine, Amsterdam, The Netherlands
| | - David Kwa
- Department of Microbiology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands
| | - Jan T M Van Der Meer
- Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine, and AIDS, Center for Infection and Immunity Amsterdam, Amsterdam, The Netherlands
| | - Maria Prins
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands.,Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Michael Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - William A Paxton
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, UK
| | - Richard Molenkamp
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
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45
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Herrera-Carrillo E, Gao Z, Berkhout B. Influence of a 3' Terminal Ribozyme on AgoshRNA Biogenesis and Activity. Mol Ther Nucleic Acids 2019; 16:452-462. [PMID: 31048184 PMCID: PMC6488825 DOI: 10.1016/j.omtn.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022]
Abstract
Short hairpin RNAs (shRNAs) can induce gene silencing via the RNA interference (RNAi) mechanism. We designed an alternative shRNA molecule with a relatively short base-paired stem that bypasses Dicer and instead is processed by the Argonaute 2 (Ago2) protein into a single guide RNA strand that effectively induces RNAi. We called these molecules AgoshRNAs. Active anti-HIV AgoshRNAs were developed, but their RNAi activity was generally reduced compared with the matching shRNAs. In an attempt to further optimize the AgoshRNA design, we inserted several self-cleaving ribozymes at the 3′ terminus of the transcribed AgoshRNA and evaluated the impact on AgoshRNA processing and activity. The hepatitis delta virus (HDV) ribozyme is efficiently removed from the transcribed AgoshRNAs and generates a uniform 3′ overhang, which translates into the enhanced antiviral activity of these molecules.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands.
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46
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Darcis G, Binda CS, Klaver B, Herrera-Carrillo E, Berkhout B, Das AT. The Impact of HIV-1 Genetic Diversity on CRISPR-Cas9 Antiviral Activity and Viral Escape. Viruses 2019; 11:E255. [PMID: 30871200 PMCID: PMC6466431 DOI: 10.3390/v11030255] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system is widely explored for sequence-specific attack on HIV-1 proviral DNA. We recently identified dual-guide RNA (dual-gRNA) combinations that can block HIV-1 replication permanently in infected cell cultures and prevent viral escape. Although the gRNAs were designed to target highly conserved viral sequences, their efficacy may be challenged by high genetic variation in the HIV-1 genome. We therefore evaluated the breadth of these dual-gRNA combinations against distinct HIV-1 isolates, including several subtypes. Replication of nearly all virus isolates could be prevented by at least one gRNA combination, which caused inactivation of the proviral genomes and the gradual loss of replication-competent virus over time. The dual-gRNA efficacy was not affected by most single nucleotide (nt) mismatches between gRNA and the viral target. However, 1-nt mismatches at the Cas9 cleavage site and two mismatches anywhere in the viral target sequence significantly reduced the inhibitory effect. Accordingly, sequence analysis of viruses upon breakthrough replication revealed the acquisition of escape mutations in perfectly matching and most 1-nt mismatching targets, but not in targets with a mismatch at the Cas9 cleavage site or with two mismatches. These results demonstrate that combinatorial CRISPR-Cas9 treatment can cure T cells infected by distinct HIV-1 isolates, but even minor sequence variation in conserved viral target sites can affect the efficacy of this strategy. Successful cure attempts against isolates with divergent target sequences may therefore require adaptation of the gRNAs.
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Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands.
- Infectious Diseases Department, Liège University Hospital, 4000 Liège, Belgium.
| | - Caroline S Binda
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands.
| | - Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands.
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands.
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47
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Steba GS, Koekkoek SM, Tanck MWT, Vanhommerig JW, van der Meer JTM, Kwa D, Brinkman K, Prins M, Berkhout B, Pollakis G, Molenkamp R, Schinkel J, Paxton WA. SNP rs688 within the low-density lipoprotein receptor (LDL-R) gene associates with HCV susceptibility. Liver Int 2019; 39:463-469. [PMID: 30260075 PMCID: PMC6588020 DOI: 10.1111/liv.13978] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Despite high-risk behaviour, 10%-20% of HCV multiple exposed individuals remain uninfected (MEU), whilst the remainder become infected (MEI). We hypothesize that host factors play a role in HCV susceptibility. We aimed to identify polymorphisms in host genes that encode for proteins involved in viral entry: CD81, Scavenger receptor 1 (SR-1), Low-density lipoprotein receptor (LDL-R), Claudin-1 (CLDN1), Occludin (OCLN) and Niemann-Pick C1-like 1 (NPC1L1). METHODS Multiple exposed infected and MEU from two observational cohorts were selected. From the MSM study of acute infection with HCV (MOSAIC), HIV-1 infected MEU cases (n = 30) and HIV-1 infected MEI controls (n = 32) were selected based on reported high-risk behaviour. From the Amsterdam Cohorts Studies (ACS) injecting drug users (IDU) cohort, MEU cases (n = 40) and MEI controls (n = 22) were selected who injected drugs for ≥2 years, in the nineties, when HCV incidence was high. Selected single nucleotide polymorphisms (SNPs) were determined by sequencing or SNP assays. RESULTS No associations were found for SNPs within genes coding for CD81, SR-1, Claudin-1 or Occludin between the MEU and MEI individuals from either cohort. We did observe a significant association for rs688 within the LDL-R gene with HCV infection (OR: 0.41 P = 0.001), however, LDL cholesterol levels did not vary between individuals carrying the differential SNPs. Additionally, a marginal significant effect was found for rs217434 and rs2072183 (OR: 2.07 P = 0.032 and OR: 1.76 P = 0.039, respectively) within NPC1L1. CONCLUSIONS Our results demonstrate that the rs688 SNP within the LDL-R gene associates with HCV susceptibility through mucosal as well as intravenous exposure.
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Affiliation(s)
- Gaby S. Steba
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Sylvie M. Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Michael W. T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Joost W. Vanhommerig
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Infectious DiseasesPublic Health Service of AmsterdamAmsterdamThe Netherlands
| | - Jan T. M. van der Meer
- Division of Infectious Diseases, Tropical Medicine and AIDS, Department of Internal Medicine, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - David Kwa
- Department of MicrobiologyOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Kees Brinkman
- Department of Internal MedicineOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Maria Prins
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | - Richard Molenkamp
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - William A. Paxton
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
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48
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van Montfort T, van der Sluis R, Darcis G, Beaty D, Groen K, Pasternak AO, Pollakis G, Vink M, Westerhout EM, Hamdi M, Bakker M, van der Putten B, Jurriaans S, Prins JH, Jeeninga R, Thomas AAM, Speijer D, Berkhout B. Dendritic cells potently purge latent HIV-1 beyond TCR-stimulation, activating the PI3K-Akt-mTOR pathway. EBioMedicine 2019; 42:97-108. [PMID: 30824386 PMCID: PMC6491380 DOI: 10.1016/j.ebiom.2019.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background The latent HIV-1 reservoir in treated patients primarily consists of resting memory CD4+ T cells. Stimulating the T-cell receptor (TCR), which facilitates transition of resting into effector T cells, is the most effective strategy to purge these latently infected cells. Here we supply evidence that TCR-stimulated effector T cells still frequently harbor latent HIV-1. Methods Primary HIV-1 infected cells were used in a latency assay with or without dendritic cells (DCs) and reversion of HIV-1 latency was determined, in the presence or absence of specific pathway inhibitors. Findings Renewed TCR-stimulation or subsequent activation with latency reversing agents (LRAs) did not overcome latency. However, interaction of infected effector cells with DCs triggered further activation of latent HIV-1. When compared to TCR-stimulation only, CD4+ T cells from aviremic patients receiving TCR + DC-stimulation reversed latency more frequently. Such a “one-two punch” strategy seems ideal for purging the reservoir. We determined that DC contact activates the PI3K-Akt-mTOR pathway in CD4+ T cells. Interpretation This insight could facilitate the development of a novel class of potent LRAs that purge latent HIV beyond levels reached by T-cell activation.
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Affiliation(s)
- Thijs van Montfort
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands.
| | - Renée van der Sluis
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Gilles Darcis
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands; Department of Infectious Diseases, Liege University Hospital, Liege, Belgium
| | - Doyle Beaty
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Kevin Groen
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Alexander O Pasternak
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), University of Liverpool, Liverpool, 8 West Derby Street, United Kingdom
| | - Monique Vink
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Ellen M Westerhout
- Department of Oncogenomics, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Mohamed Hamdi
- Department of Oncogenomics, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Margreet Bakker
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Boas van der Putten
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Suzanne Jurriaans
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Jan H Prins
- Department of Internal Medicine, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Rienk Jeeninga
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Adri A M Thomas
- Department Developmental Biology, Faculty Beta-Science, Utrecht, Padualaan 8, 3584, CH, the Netherlands
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
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Tomonaga K, Suzuki N, Berkhout B. "Integration of viral sequences into eukaryotic host genomes: legacy of ancient infections". Virus Res 2019; 262:1. [PMID: 30732705 DOI: 10.1016/j.virusres.2018.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Keizo Tomonaga
- Department of Virus Research, Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Ben Berkhout
- Laboratory of Experimental Virology, Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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Eggink D, Bontjer I, de Taeye SW, Langedijk JPM, Berkhout B, Sanders RW. HIV-1 anchor inhibitors and membrane fusion inhibitors target distinct but overlapping steps in virus entry. J Biol Chem 2019; 294:5736-5746. [PMID: 30696772 PMCID: PMC6463712 DOI: 10.1074/jbc.ra119.007360] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/25/2019] [Indexed: 12/03/2022] Open
Abstract
HIV-1 entry into cells is mediated by the envelope glycoprotein (Env) and represents an attractive target for therapeutic intervention. Two drugs that inhibit HIV entry are approved for clinical use: the membrane fusion-inhibitor T20 (Fuzeon, enfuvirtide) and the C-C chemokine receptor type 5 (CCR5) blocker maraviroc (Selzentry). Another class of entry inhibitors supposedly target the fusion peptide (FP) and are termed anchor inhibitors. These include the VIRIP peptide and VIRIP derivatives such as VIR165, VIR353, and VIR576. Here, we investigated the mechanism of inhibition by VIR165. We show that substitutions within the FP modulate sensitivity to VIR165, consistent with the FP being the drug target. Our results also revealed that VIR165 acts during an intermediate post-CD4–binding entry step that is overlapping but not identical to the step inhibited by fusion inhibitors such as T20. We found that some but not all resistance mutations to heptad repeat 2 (HR2)-targeting fusion inhibitors can provide cross-resistance to VIR165. In contrast, resistance mutations in the HR1-binding site for the fusion inhibitors did not cause cross-resistance to VIR165. However, Env with mutations located outside this binding site and thought to affect fusion kinetics, exhibited decreased sensitivity to VIR165. Although we found a strong correlation between Env stability and resistance to HR2-based fusion inhibitors, such correlation was not observed for Env stability and VIR165 resistance. We conclude that VIRIP analogs target the FP during an intermediate, post-CD4–binding entry step that overlaps with but is distinct from the step(s) inhibited by HR2-based fusion inhibitors.
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Affiliation(s)
- Dirk Eggink
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC), Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Ilja Bontjer
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC), Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Steven W de Taeye
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC), Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | | | - Ben Berkhout
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC), Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Rogier W Sanders
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers (Amsterdam UMC), Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; the Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10065.
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