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Chen MJ, Gatignol A, Scarborough RJ. The discovery and development of RNA-based therapies for treatment of HIV-1 infection. Expert Opin Drug Discov 2023; 18:163-179. [PMID: 36004505 DOI: 10.1080/17460441.2022.2117296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Long-term control of HIV-1 infection can potentially be achieved using autologous stem cell transplants with gene-modified cells. Non-coding RNAs represent a diverse class of therapeutic agents including ribozymes, RNA aptamers and decoys, small interfering RNAs, short hairpin RNAs, and U1 interference RNAs that can be designed to inhibit HIV-1 replication. They have been engineered for delivery as drugs to complement current HIV-1 therapies and as gene therapies for a potential HIV-1 functional cure. AREAS COVERED This review surveys the past three decades of development of these RNA technologies with a focus on their efficacy and safety for treating HIV-1 infections. We describe the mechanisms of each RNA-based agent, targets they have been developed against, efforts to enhance their stability and efficacy, and we evaluate their performance in past and ongoing preclinical and clinical trials. EXPERT OPINION RNA-based technologies are among the top candidates for gene therapies where they can be stably expressed for long-term suppression of HIV-1. Advances in both gene and drug delivery strategies and improvements to non-coding RNA stability and antiviral properties will cooperatively drive forward progress in improving drug therapy and engineering HIV-1 resistant cells.
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Affiliation(s)
- Michelle J Chen
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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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: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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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Herrera-Carrillo E, Gao Z, Berkhout B. Influence of a 3' Terminal Ribozyme on AgoshRNA Biogenesis and Activity. MOLECULAR THERAPY-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] [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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Darcis G, Das AT, Berkhout B. Tackling HIV Persistence: Pharmacological versus CRISPR-Based Shock Strategies. Viruses 2018; 10:v10040157. [PMID: 29596334 PMCID: PMC5923451 DOI: 10.3390/v10040157] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 02/07/2023] Open
Abstract
Jan Svoboda studied aspects of viral latency, in particular with respect to disease induction by avian RNA tumor viruses, which were later renamed as part of the extended retrovirus family. The course of retroviral pathogenesis is intrinsically linked to their unique property of integrating the DNA copy of the retroviral genome into that of the host cell, thus forming the provirus. Retroviral latency has recently become of major clinical interest to allow a better understanding of why we can effectively block the human immunodeficiency virus type 1 (HIV-1) in infected individuals with antiviral drugs, yet never reach a cure. We will discuss HIV-1 latency and its direct consequence—the formation of long-lasting HIV-1 reservoirs. We next focus on one of the most explored strategies in tackling HIV-1 reservoirs—the “shock and kill” strategy—which describes the broadly explored pharmacological way of kicking the latent provirus, with subsequent killing of the virus-producing cell by the immune system. We furthermore present how the clustered regularly interspaced palindromic repeats (CRISPR) and associated protein (Cas) system can be harnessed to reach the same objective by reactivating HIV-1 gene expression from latency. We will review the benefits and drawbacks of these different cure strategies.
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Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
- Infectious Diseases Department, Liège University Hospital, 4000 Liege, Belgium.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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Herrera-Carrillo E, Harwig A, Berkhout B. Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity. RNA Biol 2017; 14:1559-1569. [PMID: 28569591 PMCID: PMC5785215 DOI: 10.1080/15476286.2017.1328349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are widely used for gene silencing by the RNA interference (RNAi) mechanism. The shRNA precursor is processed by the Dicer enzyme into active small interfering RNAs (siRNAs) that subsequently target a complementary mRNA for cleavage by the Argonaute 2 (Ago2) complex. Recent evidence indicates that shRNAs with a relatively short basepaired stem bypass Dicer and are instead processed by Ago2. We termed these molecules AgoshRNAs as both processing and silencing steps are mediated by Ago2 and proposed rules for the design of effective AgoshRNA molecules. Active and non-cytotoxic AgoshRNAs against HIV-1 RNA were generated, but their silencing activity was generally reduced compared with the matching shRNAs. Thus, further optimization of the AgoshRNA design is needed. In this study, we evaluated the importance of the single-stranded loop, in particular its size and nucleotide sequence, in AgoshRNA-mediated silencing. We document that the pyrimidine/purine content is important for AgoshRNA-mediated silencing activity.
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Affiliation(s)
- Elena Herrera-Carrillo
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Alex Harwig
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Ben Berkhout
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
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6
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Herrera-Carrillo E, Berkhout B. Dicer-independent processing of small RNA duplexes: mechanistic insights and applications. Nucleic Acids Res 2017; 45:10369-10379. [PMID: 28977573 PMCID: PMC5737282 DOI: 10.1093/nar/gkx779] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages. As an example, we will present the route towards development of a durable gene therapy against HIV-1.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
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Herrera-Carrillo E, Berkhout B. Novel AgoshRNA molecules for silencing of the CCR5 co-receptor for HIV-1 infection. PLoS One 2017; 12:e0177935. [PMID: 28542329 PMCID: PMC5443530 DOI: 10.1371/journal.pone.0177935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/05/2017] [Indexed: 12/20/2022] Open
Abstract
Allogeneic transplantation of blood stem cells from a CCR5-Δ32 homozygous donor to an HIV-infected individual, the "Berlin patient", led to a cure. Since then there has been a search for approaches that mimic this intervention in a gene therapy setting. RNA interference (RNAi) has evolved as a powerful tool to regulate gene expression in a sequence-specific manner and can be used to inactivate the CCR5 mRNA. Short hairpin RNA (shRNA) molecules can impair CCR5 expression, but these molecules may cause unintended side effects and they will not be processed in cells that lack Dicer, such as monocytes. Dicer-independent RNAi pathways have opened opportunities for new AgoshRNA designs that rely exclusively on Ago2 for maturation. Furthermore, AgoshRNA processing yields a single active guide RNA, thus reducing off-target effects. In this study, we tested different AgoshRNA designs against CCR5. We selected AgoshRNAs that potently downregulated CCR5 expression on human T cells and peripheral blood mononuclear cells (PBMC) and that had no apparent adverse effect on T cell development as assessed in a competitive cell growth assay. CCR5 knockdown significantly protected T cells from CCR5 tropic HIV-1 infection.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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8
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Xu X, Li Z, Zhao X, Keen L, Kong X. Calcium phosphate nanoparticles-based systems for siRNA delivery. Regen Biomater 2016; 3:187-95. [PMID: 27252888 PMCID: PMC4881614 DOI: 10.1093/rb/rbw010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 12/15/2022] Open
Abstract
Despite the enormous therapeutic potential of siRNA as a treatment strategy, the delivery is still a problem due to unfavorable biodistribution profiles and poor intracellular bioavailability. Calcium phosphate (CaP) co-precipitate has been used for nearly 40 years for in vitro transfection due to its non-toxic nature and simplicity of preparation. The surface charge of CaP will be tuned into positive by surface modification, which is important for siRNA loading and crossing cell membrane without enzymatic degradation. The new siRNA carrier system will also promote the siRNA escape from lysosome to achieve siRNA sustained delivery and high-efficiency silence. In this review, we focus on the current research activity in the development of CaP nanoparticles for siRNA delivery. These nanoparticles are mainly classified into lipid coated, polymer coated and various other types for discussion.
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Affiliation(s)
- Xiaochun Xu
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zehao Li
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xueqin Zhao
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Lawrence Keen
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiangdong Kong
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- College of Materials and Textiles, Zhejiang Sci-Tech University, Hangzhou 310018, China
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9
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Swamy MN, Wu H, Shankar P. Recent advances in RNAi-based strategies for therapy and prevention of HIV-1/AIDS. Adv Drug Deliv Rev 2016; 103:174-186. [PMID: 27013255 PMCID: PMC4935623 DOI: 10.1016/j.addr.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
RNA interference (RNAi) provides a powerful tool to silence specific gene expression and has been widely used to suppress host factors such as CCR5 and/or viral genes involved in HIV-1 replication. Newer nuclease-based gene-editing technologies, such as zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, also provide powerful tools to ablate specific genes. Because of differences in co-receptor usage and the high mutability of the HIV-1 genome, a combination of host factors and viral genes needs to be suppressed for effective prevention and treatment of HIV-1 infection. Whereas the continued presence of small interfering/short hairpin RNA (si/shRNA) mediators is needed for RNAi to be effective, the continued expression of nucleases in the gene-editing systems is undesirable. Thus, RNAi provides the only practical way for expression of multiple silencers in infected and uninfected cells, which is needed for effective prevention/treatment of infection. There have been several advances in the RNAi field in terms of si/shRNA design, targeted delivery to HIV-1 susceptible cells, and testing for efficacy in preclinical humanized mouse models. Here, we comprehensively review the latest advances in RNAi technology towards prevention and treatment of HIV-1.
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Affiliation(s)
- Manjunath N Swamy
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
| | - Haoquan Wu
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
| | - Premlata Shankar
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
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