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Ta TM, Malik S, Anderson EM, Jones AD, Perchik J, Freylikh M, Sardo L, Klase ZA, Izumi T. Insights Into Persistent HIV-1 Infection and Functional Cure: Novel Capabilities and Strategies. Front Microbiol 2022; 13:862270. [PMID: 35572626 PMCID: PMC9093714 DOI: 10.3389/fmicb.2022.862270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/23/2022] Open
Abstract
Although HIV-1 replication can be efficiently suppressed to undetectable levels in peripheral blood by combination antiretroviral therapy (cART), lifelong medication is still required in people living with HIV (PLWH). Life expectancies have been extended by cART, but age-related comorbidities have increased which are associated with heavy physiological and economic burdens on PLWH. The obstacle to a functional HIV cure can be ascribed to the formation of latent reservoir establishment at the time of acute infection that persists during cART. Recent studies suggest that some HIV reservoirs are established in the early acute stages of HIV infection within multiple immune cells that are gradually shaped by various host and viral mechanisms and may undergo clonal expansion. Early cART initiation has been shown to reduce the reservoir size in HIV-infected individuals. Memory CD4+ T cell subsets are regarded as the predominant cellular compartment of the HIV reservoir, but monocytes and derivative macrophages or dendritic cells also play a role in the persistent virus infection. HIV latency is regulated at multiple molecular levels in transcriptional and post-transcriptional processes. Epigenetic regulation of the proviral promoter can profoundly regulate the viral transcription. In addition, transcriptional elongation, RNA splicing, and nuclear export pathways are also involved in maintaining HIV latency. Although most proviruses contain large internal deletions, some defective proviruses may induce immune activation by expressing viral proteins or producing replication-defective viral-like particles. In this review article, we discuss the state of the art on mechanisms of virus persistence in the periphery and tissue and summarize interdisciplinary approaches toward a functional HIV cure, including novel capabilities and strategies to measure and eliminate the infected reservoirs and induce immune control.
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Affiliation(s)
- Tram M. Ta
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Sajjaf Malik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Elizabeth M. Anderson
- Office of the Assistant Secretary for Health, Region 3, U.S. Department of Health and Human Services, Washington, DC, United States
| | - Amber D. Jones
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jocelyn Perchik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Maryann Freylikh
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Luca Sardo
- Department of Infectious Disease and Vaccines, Merck & Co., Inc., Kenilworth, NJ, United States
| | - Zackary A. Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Neuroimmunology and CNS Therapeutics, Institute of Molecular Medicine and Infectious Diseases, Drexel University of Medicine, Philadelphia, PA, United States
| | - Taisuke Izumi
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,*Correspondence: Taisuke Izumi,
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2
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Patters BJ, Kumar S. The role of exosomal transport of viral agents in persistent HIV pathogenesis. Retrovirology 2018; 15:79. [PMID: 30577804 PMCID: PMC6303896 DOI: 10.1186/s12977-018-0462-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection, despite great advances in antiretroviral therapy, remains a lifelong affliction. Though current treatment regimens can effectively suppress viral load to undetectable levels and preserve healthy immune function, they cannot fully alleviate all symptoms caused by the presence of the virus, such as HIV-associated neurocognitive disorders. Exosomes are small vesicles that transport cellular proteins, RNA, and small molecules between cells as a mechanism of intercellular communication. Recent research has shown that HIV proteins and RNA can be packaged into exosomes and transported between cells, to pathogenic effect. This review summarizes the current knowledge on the diverse mechanisms involved in the sorting of viral elements into exosomes and the damage those exosomal agents can inflict. In addition, potential therapeutic options to counteract exosome-mediated HIV pathogenesis are reviewed and considered.
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Affiliation(s)
- Benjamin J Patters
- Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Santosh Kumar
- Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
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Abstract
When a virus infects a host cell, it hijacks the biosynthetic capacity of the cell to produce virus progeny, a process that may take less than an hour or more than a week. The overall time required for a virus to reproduce depends collectively on the rates of multiple steps in the infection process, including initial binding of the virus particle to the surface of the cell, virus internalization and release of the viral genome within the cell, decoding of the genome to make viral proteins, replication of the genome, assembly of progeny virus particles, and release of these particles into the extracellular environment. For a large number of virus types, much has been learned about the molecular mechanisms and rates of the various steps. However, in only relatively few cases during the last 50 years has an attempt been made-using mathematical modeling-to account for how the different steps contribute to the overall timing and productivity of the infection cycle in a cell. Here we review the initial case studies, which include studies of the one-step growth behavior of viruses that infect bacteria (Qβ, T7, and M13), human immunodeficiency virus, influenza A virus, poliovirus, vesicular stomatitis virus, baculovirus, hepatitis B and C viruses, and herpes simplex virus. Further, we consider how such models enable one to explore how cellular resources are utilized and how antiviral strategies might be designed to resist escape. Finally, we highlight challenges and opportunities at the frontiers of cell-level modeling of virus infections.
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Affiliation(s)
- John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacob Redovich
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Noncoding RNAs in Retrovirus Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7173536 DOI: 10.1016/b978-0-12-811185-7.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although a limited percentage of the genome produces proteins, approximately 90% is transcribed, indicating important roles for noncoding RNA (ncRNA). It is now known that these ncRNAs have a multitude of cellular functions ranging from the regulation of gene expression to roles as structural elements in ribonucleoprotein complexes. ncRNA is also represented at nearly every step of viral life cycles. This chapter will focus on ncRNAs of both host and viral origin and their roles in retroviral life cycles. Cellular ncRNA represents a significant portion of material packaged into retroviral virions and includes transfer RNAs, 7SL RNA, U RNA, and vault RNA. Initially thought to be random packaging events, these host RNAs are now proposed to contribute to viral assembly and infectivity. Within the cell, long ncRNA and endogenous retroviruses have been found to regulate aspects of the retroviral life cycle in diverse ways. Additionally, the HIV-1 transactivating response element RNA is thought to impact viral infection beyond the well-characterized role as a transcription activator. RNA interference, thought to be an early version of the innate immune response to viral infection, can still be observed in plants and invertebrates today. The ability of retroviral infection to manipulate the host RNAi pathway is described here. Finally, RNA-based therapies, including gene editing approaches, are being explored as antiretroviral treatments and are discussed.
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5
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Attacking HIV-1 RNA versus DNA by sequence-specific approaches: RNAi versus CRISPR-Cas. Biochem Soc Trans 2016; 44:1355-1365. [DOI: 10.1042/bst20160060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/09/2016] [Accepted: 06/21/2016] [Indexed: 01/02/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection can be effectively controlled by potent antiviral drugs, but this never results in a cure. The patient should therefore take these drugs for the rest of his/her life, which can cause drug-resistance and adverse effects. Therefore, more durable therapeutic strategies should be considered, such as a stable gene therapy to protect the target T cells against HIV-1 infection. The development of potent therapeutic regimens based on the RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats (CRISPR-Cas) mechanisms will be described, which can be delivered by lentiviral vectors. These mechanisms attack different forms of the viral genome, the RNA and DNA, respectively, but both mechanisms act in a strictly sequence-specific manner. Early RNAi experiments demonstrated profound virus inhibition, but also indicated that viral escape is possible. Such therapy failure can be prevented by the design of a combinatorial RNAi attack on the virus and this gene therapy is currently being tested in a preclinical humanized mouse model. Recent CRISPR-Cas studies also document robust virus inhibition, but suggest a novel viral escape route that is induced by the cellular nonhomologous end joining DNA repair pathway, which is activated by CRISPR-Cas-induced DNA breaks. We will compare these two approaches for durable HIV-1 suppression and discuss the respective advantages and disadvantages. The potential for future clinical applications will be described.
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6
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Limsirichai P, Gaj T, Schaffer DV. CRISPR-mediated Activation of Latent HIV-1 Expression. Mol Ther 2016; 24:499-507. [PMID: 26607397 PMCID: PMC4786916 DOI: 10.1038/mt.2015.213] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/20/2015] [Indexed: 01/02/2023] Open
Abstract
Complete eradication of HIV-1 infection is impeded by the existence of cells that harbor chromosomally integrated but transcriptionally inactive provirus. These cells can persist for years without producing viral progeny, rendering them refractory to immune surveillance and antiretroviral therapy and providing a permanent reservoir for the stochastic reactivation and reseeding of HIV-1. Strategies for purging this latent reservoir are thus needed to eradicate infection. Here, we show that engineered transcriptional activation systems based on CRISPR/Cas9 can be harnessed to activate viral gene expression in cell line models of HIV-1 latency. We further demonstrate that complementing Cas9 activators with latency-reversing compounds can enhance latent HIV-1 transcription and that epigenome modulation using CRISPR-based acetyltransferases can also promote viral gene activation. Collectively, these results demonstrate that CRISPR systems are potentially effective tools for inducing latent HIV-1 expression and that their use, in combination with antiretroviral therapy, could lead to improved therapies for HIV-1 infection.
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Affiliation(s)
- Prajit Limsirichai
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Gaj
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, USA
| | - David V Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
- Department of Cell and Molecular Biology, University of California, Berkeley, Berkeley, California, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, California, USA
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7
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Jung U, Takahashi M, Rossi JJ, Burnett JC. LGIT In Vitro Latency Model in Primary and T Cell Lines to Test HIV-1 Reactivation Compounds. Methods Mol Biol 2016; 1354:255-264. [PMID: 26714717 DOI: 10.1007/978-1-4939-3046-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Persistent latent HIV-1 reservoirs pose a major barrier for combinatorial antiretroviral therapy (cART) to achieve eradication of the virus. A variety of mechanisms likely contribute to HIV-1 persistence, including establishment of post-integration latency in resting CD4+ T-lymphocytes, the proliferation of these latently infected cells, and the induced or spontaneous reactivation of latent virus. To elucidate the mechanisms of latency and to investigate therapeutic strategies for reactivating and purging the latent reservoir, investigators have developed in vitro models of HIV-1 latency using primary CD4+ T-lymphocytes and CD4+ T-cell lines. Several types of in vitro latency models range from replication-competent to single-round, replication-deficient viruses exhibiting different degrees of viral genomic deletion. Working under the hypothesis that HIV-1 post-integration latency is directly linked to HIV-1 promoter activity, which can be obscured by additional proteins expressed during replication, we focus here on the creation of latently infected primary human T-cells and cell lines through the single-round, replication deficient HIV-1 LGIT model. In this model the long terminal repeat (LTR) of the HIV-1 virus drives a cassette of GFP-IRES-Tat that allows testing of reactivating components and initiates a positive feedback loop through Tat expression.
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Affiliation(s)
- Ulrike Jung
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Mayumi Takahashi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Fox North, 1001A, 1500 Duarte Rd., Duarte, CA, 91010, USA
| | - John C Burnett
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Fox North, 1001A, 1500 Duarte Rd., Duarte, CA, 91010, USA.
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8
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Presloid JB, Novella IS. RNA Viruses and RNAi: Quasispecies Implications for Viral Escape. Viruses 2015; 7:3226-40. [PMID: 26102581 PMCID: PMC4488735 DOI: 10.3390/v7062768] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/04/2015] [Accepted: 06/17/2015] [Indexed: 12/16/2022] Open
Abstract
Due to high mutation rates, populations of RNA viruses exist as a collection of closely related mutants known as a quasispecies. A consequence of error-prone replication is the potential for rapid adaptation of RNA viruses when a selective pressure is applied, including host immune systems and antiviral drugs. RNA interference (RNAi) acts to inhibit protein synthesis by targeting specific mRNAs for degradation and this process has been developed to target RNA viruses, exhibiting their potential as a therapeutic against infections. However, viruses containing mutations conferring resistance to RNAi were isolated in nearly all cases, underlining the problems of rapid viral evolution. Thus, while promising, the use of RNAi in treating or preventing viral diseases remains fraught with the typical complications that result from high specificity of the target, as seen in other antiviral regimens.
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Affiliation(s)
- John B Presloid
- Department of Medical Microbiology and Immunology, College of Medicine, The University of Toledo, 3055 Arlington Avenue, Toledo, OH 43614, USA.
| | - Isabel S Novella
- Department of Medical Microbiology and Immunology, College of Medicine, The University of Toledo, 3055 Arlington Avenue, Toledo, OH 43614, USA.
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9
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Bobbin ML, Burnett JC, Rossi JJ. RNA interference approaches for treatment of HIV-1 infection. Genome Med 2015; 7:50. [PMID: 26019725 PMCID: PMC4445287 DOI: 10.1186/s13073-015-0174-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/13/2015] [Indexed: 01/05/2023] Open
Abstract
HIV/AIDS is a chronic and debilitating disease that cannot be cured with current antiretroviral drugs. While combinatorial antiretroviral therapy (cART) can potently suppress HIV-1 replication and delay the onset of AIDS, viral mutagenesis often leads to viral escape from multiple drugs. In addition to the pharmacological agents that comprise cART drug cocktails, new biological therapeutics are reaching the clinic. These include gene-based therapies that utilize RNA interference (RNAi) to silence the expression of viral or host mRNA targets that are required for HIV-1 infection and/or replication. RNAi allows sequence-specific design to compensate for viral mutants and natural variants, thereby drastically expanding the number of therapeutic targets beyond the capabilities of cART. Recent advances in clinical and preclinical studies have demonstrated the promise of RNAi therapeutics, reinforcing the concept that RNAi-based agents might offer a safe, effective, and more durable approach for the treatment of HIV/AIDS. Nevertheless, there are challenges that must be overcome in order for RNAi therapeutics to reach their clinical potential. These include the refinement of strategies for delivery and to reduce the risk of mutational escape. In this review, we provide an overview of RNAi-based therapies for HIV-1, examine a variety of combinatorial RNAi strategies, and discuss approaches for ex vivo delivery and in vivo delivery.
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Affiliation(s)
- Maggie L Bobbin
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA
| | - John C Burnett
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
| | - John J Rossi
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
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10
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Herrera-Carrillo E, Berkhout B. Gene therapy strategies to block HIV-1 replication by RNA interference. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 848:71-95. [PMID: 25757616 DOI: 10.1007/978-1-4939-2432-5_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cellular mechanism of RNA interference (RNAi) plays an antiviral role in many organisms and can be used for the development of therapeutic strategies against viral pathogens. Persistent infections like the one caused by the human immunodeficiency virus type 1 (HIV-1) likely require a durable gene therapy approach. The continuous expression of the inhibitory RNA molecules in T cells is needed to effectively block HIV-1 replication. We discuss here several issues, ranging from the choice of RNAi inhibitor and vector system, finding the best target in the HIV-1 RNA genome, alternatively by targeting host mRNAs that encode important viral cofactors, to the setup of appropriate preclinical test systems. Finally, we briefly discuss the relevance of this topic for other viral pathogens that cause a chronic infection in humans.
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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 of the University of Amsterdam, K3-110 Meibergdreef 15, Amsterdam, 1105 AS, The Netherlands
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11
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Fritz AL, Mao SR, West MG, Schaffer DV. A medium-throughput analysis of signaling pathways involved in early stages of stem cell reprogramming. Biotechnol Bioeng 2014; 112:209-19. [PMID: 25065366 DOI: 10.1002/bit.25336] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/28/2014] [Accepted: 07/07/2014] [Indexed: 02/06/2023]
Abstract
The induction of pluripotency from adult cells has enormous potential in regenerative medicine. While initial efforts to study mechanisms and improve efficiency of induced pluripotent stem cell (iPSC) reprogramming focused on the direct roles of transcriptional regulators, increasing evidence indicates that cellular signal transduction pathways can modulate this process. Here, we present a medium-throughput system to study the effect of signaling pathways on the early stages of reprogramming. We generated a set of lentiviral vectors encoding 38 genes that upregulate or downregulate major signal transduction pathways and quantified each signaling factor's effect on reprogramming. This approach confirmed the role of several factors previously implicated in reprogramming, as well as identified several GTPases-factors that to date have not been largely studied in reprogramming-that improve or hinder iPSC reprogramming. In addition, this methodology is useful in determining new targets for enhancing pluripotency reprogramming, lineage reprogramming, and/or cell differentiation.
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Affiliation(s)
- Ashley L Fritz
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, 94720
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12
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Liang Z, Wang X, Li H, Liu B, Zhao X, Liu C, Kong XH. Silencing of HIV-1 gag gene from epidemic strains among men who have sex with men (MSM) in Tianjin, China by a broad-spectrum short hairpin RNA. Virusdisease 2014; 25:294-301. [DOI: 10.1007/s13337-014-0209-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/12/2014] [Indexed: 11/30/2022] Open
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13
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Ouellet DL, Vigneault-Edwards J, Létourneau K, Gobeil LA, Plante I, Burnett JC, Rossi JJ, Provost P. Regulation of host gene expression by HIV-1 TAR microRNAs. Retrovirology 2013; 10:86. [PMID: 23938024 PMCID: PMC3751525 DOI: 10.1186/1742-4690-10-86] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/06/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The transactivating response (TAR) element of human immunodeficiency virus type 1 (HIV-1) is the source of two functional microRNAs (miRNAs), miR-TAR-5p and miR-TAR-3p. The objective of this study was to characterize the post-transcriptional regulation of host messenger RNAs (mRNAs) relevant to HIV-1 pathogenesis by HIV-1 TAR miRNAs. RESULTS We demonstrated that TAR miRNAs derived from HIV-1 can incorporate into host effector Argonaute protein complexes, which is required if these miRNAs are to regulate host mRNA expression. Bioinformatic predictions and reporter gene activity assays identified regulatory elements complementary and responsive to miR-TAR-5p and miR-TAR-3p in the 3' untranslated region (UTR) of several candidate genes involved in apoptosis and cell survival. These include Caspase 8, Aiolos, Ikaros and Nucleophosmin (NPM)/B23. Analyses of Jurkat cells that stably expressed HIV-1 TAR or contained a full-length latent HIV provirus suggested that HIV-1 TAR miRNAs could regulate the expression of genes in T cells that affect the balance between apoptosis and cell survival. CONCLUSIONS HIV-1 TAR miRNAs may contribute to the replication cycle and pathogenesis of HIV-1, by regulating host genes involved in the intricate balance between apoptosis and infected cell, to induce conditions that promote HIV-1 propagation and survival.
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Affiliation(s)
- Dominique L Ouellet
- Department of Molecular and Cellular Biology, Beckman Research Institute at City of Hope, 1500 E Duarte Road, Duarte, CA 91010, USA
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14
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Miller-Jensen K, Skupsky R, Shah PS, Arkin AP, Schaffer DV. Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression. PLoS Comput Biol 2013; 9:e1003135. [PMID: 23874178 PMCID: PMC3708878 DOI: 10.1371/journal.pcbi.1003135] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/16/2013] [Indexed: 12/13/2022] Open
Abstract
The sequence of a promoter within a genome does not uniquely determine gene expression levels and their variability; rather, promoter sequence can additionally interact with its location in the genome, or genomic context, to shape eukaryotic gene expression. Retroviruses, such as human immunodeficiency virus-1 (HIV), integrate their genomes into those of their host and thereby provide a biomedically-relevant model system to quantitatively explore the relationship between promoter sequence, genomic context, and noise-driven variability on viral gene expression. Using an in vitro model of the HIV Tat-mediated positive-feedback loop, we previously demonstrated that fluctuations in viral Tat-transactivating protein levels generate integration-site-dependent, stochastically-driven phenotypes, in which infected cells randomly ‘switch’ between high and low expressing states in a manner that may be related to viral latency. Here we extended this model and designed a forward genetic screen to systematically identify genetic elements in the HIV LTR promoter that modulate the fraction of genomic integrations that specify ‘Switching’ phenotypes. Our screen identified mutations in core promoter regions, including Sp1 and TATA transcription factor binding sites, which increased the Switching fraction several fold. By integrating single-cell experiments with computational modeling, we further investigated the mechanism of Switching-fraction enhancement for a selected Sp1 mutation. Our experimental observations demonstrated that the Sp1 mutation both impaired Tat-transactivated expression and also altered basal expression in the absence of Tat. Computational analysis demonstrated that the observed change in basal expression could contribute significantly to the observed increase in viral integrations that specify a Switching phenotype, provided that the selected mutation affected Tat-mediated noise amplification differentially across genomic contexts. Our study thus demonstrates a methodology to identify and characterize promoter elements that affect the distribution of stochastic phenotypes over genomic contexts, and advances our understanding of how promoter mutations may control the frequency of latent HIV infection. The sequence of a gene within a cellular genome does not uniquely determine its expression level, even for a single type of cell under fixed conditions. Numerous other factors, including gene location on the chromosome and random gene-expression “noise,” can alter expression patterns and cause differences between otherwise identical cells. This poses new challenges for characterizing the genotype–phenotype relationship. Infection by the human immunodeficiency virus-1 (HIV-1) provides a biomedically important example in which transcriptional noise and viral genomic location impact the decision between viral replication and latency, a quiescent but reversible state that cannot be eliminated by anti-viral therapies. Here, we designed a forward genetic screen to systematically identify mutations in the HIV promoter that alter the fraction of genomic integrations that specify noisy/reactivating expression phenotypes. The mechanisms by which the selected mutations specify the observed phenotypic enrichments are investigated through a combination of single-cell experiments and computational modeling. Our study provides a framework for identifying genetic sequences that alter the distribution of stochastic expression phenotypes over genomic locations and for characterizing their mechanisms of regulation. Our results also may yield further insights into the mechanisms by which HIV sequence evolution can alter the propensity for latent infections.
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Affiliation(s)
- Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail: (KMJ); (DVS)
| | - Ron Skupsky
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Priya S. Shah
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - David V. Schaffer
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
- * E-mail: (KMJ); (DVS)
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15
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Harper SJ. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups. Front Microbiol 2013; 4:93. [PMID: 23630519 PMCID: PMC3632782 DOI: 10.3389/fmicb.2013.00093] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/03/2013] [Indexed: 12/22/2022] Open
Abstract
Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes.
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Affiliation(s)
- S J Harper
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida Lake Alfred, FL, USA
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Boutimah F, Eekels JJM, Liu YP, Berkhout B. Antiviral strategies combining antiretroviral drugs with RNAi-mediated attack on HIV-1 and cellular co-factors. Antiviral Res 2013; 98:121-9. [PMID: 23439083 DOI: 10.1016/j.antiviral.2013.02.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 02/06/2013] [Accepted: 02/12/2013] [Indexed: 12/31/2022]
Abstract
To improve the care of HIV-1/AIDS patients there is a critical need to develop tools capable of blocking viral evolution and circumventing therapy-associated problems. An emerging solution is gene therapy either as a stand-alone approach or as an adjuvant to pharmacological drug regimens. Combinatorial RNAi by multiplexing antiviral RNAi inhibitors through vector-mediated delivery has recently shown significant superiority over conventional mono-therapies. Viral as well as cellular co-factor targets have been identified, but they are generally attacked separately. Here, we hypothesized that a mixture of shRNAs directed against highly conserved viral RNA sequences and the mRNAs of cellular components that are involved in HIV replication could restrict mutational escape by enhanced synergistic inhibition. We screened for potent silencer cocktails blending inhibitors acting scattered along the viral replication cycle. The results show enhanced and extended suppression of viral replication for some combinations. To further explore the power of combinatorial approaches, we tested the influence of RNAi-mediated knockdown on the activity of conventional antiretroviral drugs (fusion, RT, integrase and protease inhibitors). We compared the fold-change in IC₅₀ (FCIC₅₀) of these drugs in cell lines stably expressing anti-HIV and anti-host shRNAs and measured increased values that are up by several logs for some combinations. We show that high levels of additivity and synergy can be obtained by combining gene therapy with conventional drugs. These results support the idea to validate the therapeutic potential of this anti-HIV approach in appropriate in vivo models.
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Affiliation(s)
- Fatima Boutimah
- Department of Medical Microbiology, Center for Infection and Immunity Amsterdam-CINIMA, Academic Medical Center, University of Amsterdam, The Netherlands
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17
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siRNA Genome Screening Approaches to Therapeutic Drug Repositioning. Pharmaceuticals (Basel) 2013; 6:124-60. [PMID: 24275945 PMCID: PMC3816683 DOI: 10.3390/ph6020124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/10/2013] [Accepted: 01/22/2013] [Indexed: 01/21/2023] Open
Abstract
Bridging high-throughput screening (HTS) with RNA interference (RNAi) has allowed for rapid discovery of the molecular basis of many diseases, and identification of potential pathways for developing safe and effective treatments. These features have identified new host gene targets for existing drugs paving the pathway for therapeutic drug repositioning. Using RNAi to discover and help validate new drug targets has also provided a means to filter and prioritize promising therapeutics. This review summarizes these approaches across a spectrum of methods and targets in the host response to pathogens. Particular attention is given to the utility of drug repurposing utilizing the promiscuous nature of some drugs that affect multiple molecules or pathways, and how these biological pathways can be targeted to regulate disease outcome.
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18
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Burnett JC, Zaia JA, Rossi JJ. Creating genetic resistance to HIV. Curr Opin Immunol 2012; 24:625-32. [PMID: 22985479 PMCID: PMC3478429 DOI: 10.1016/j.coi.2012.08.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/23/2012] [Indexed: 11/26/2022]
Abstract
HIV/AIDS remains a chronic and incurable disease, in spite of the notable successes of combination antiretroviral therapy. Gene therapy offers the prospect of creating genetic resistance to HIV that supplants the need for antiviral drugs. In sight of this goal, a variety of anti-HIV genes have reached clinical testing, including gene-editing enzymes, protein-based inhibitors, and RNA-based therapeutics. Combinations of therapeutic genes against viral and host targets are designed to improve the overall antiviral potency and reduce the likelihood of viral resistance. In cell-based therapies, therapeutic genes are expressed in gene modified T lymphocytes or in hematopoietic stem cells that generate an HIV-resistant immune system. Such strategies must promote the selective proliferation of the transplanted cells and the prolonged expression of therapeutic genes. This review focuses on the current advances and limitations in genetic therapies against HIV, including the status of several recent and ongoing clinical studies.
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Affiliation(s)
- John C. Burnett
- Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - John A. Zaia
- Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - John J. Rossi
- Beckman Research Institute of the City of Hope, Duarte, CA, USA
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Shah PS, Schaffer DV. Response to "HIV Escape From RNAi Antivirals: Yet Another Houdini Action?". MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e28. [PMID: 23344080 PMCID: PMC3390221 DOI: 10.1038/mtna.2012.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Priya S Shah
- 1] Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA [2] Current address: Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
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Berkhout B, Das AT. HIV-1 Escape From RNAi Antivirals: Yet Another Houdini Action? MOLECULAR THERAPY-NUCLEIC ACIDS 2012; 1:e26. [PMID: 23344078 PMCID: PMC3390223 DOI: 10.1038/mtna.2012.22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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21
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HIV develops indirect cross-resistance to combinatorial RNAi targeting two distinct and spatially distant sites. Mol Ther 2012; 20:840-8. [PMID: 22294151 DOI: 10.1038/mt.2012.3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Resistance to existing HIV therapies is an increasing problem, and alternative treatments are urgently needed. RNA interference (RNAi), an innate mechanism for sequence-specific gene silencing, can be harnessed therapeutically to treat viral infections, yet viral resistance can still emerge. Here, we demonstrate that HIV can develop indirect resistance to individual and combinatorial RNAi-targeting protein-coding regions up to 5,500 nucleotides (nt) downstream of the viral promoter. We identify several variants harboring mutations in the HIV promoter, and not within the RNAi targets, that produce more fully elongated transcripts. Furthermore, these variants are resistant to the RNAi, potentially by stoichiometrically overwhelming this cellular mechanism. Alarmingly, virus resistant to one short hairpin RNA (shRNA) also exhibits cross-resistance to a different shRNA, which targets a distinct and spatially distant region to which the virus has not been previously exposed. To our knowledge, this is the first example of HIV "cross-resistance" to viral inhibitors targeting different loci. Finally, combining anti-HIV RNAi with a small molecule enhancer of RNAi can inhibit the replication of an indirectly resistant mutant. These results suggest that indirect resistance to RNAi is a general mechanism that should be considered when investigating viral resistance and designing combinatorial RNAi therapies.
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22
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Shah PS, Schaffer DV. Antiviral RNAi: translating science towards therapeutic success. Pharm Res 2011; 28:2966-82. [PMID: 21826573 PMCID: PMC5012899 DOI: 10.1007/s11095-011-0549-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/25/2011] [Indexed: 01/07/2023]
Abstract
Viruses continuously evolve to contend with an ever-changing environment that involves transmission between hosts and sometimes species, immune responses, and in some cases therapeutic interventions. Given the high mutation rate of viruses relative to the timescales of host evolution and drug development, novel drug classes that are readily screened and translated to the clinic are needed. RNA interference (RNAi)—a natural mechanism for specific degradation of target RNAs that is conserved from plants to invertebrates and vertebrates—can potentially be harnessed to yield therapies with extensive specificity, ease of design, and broad application. In this review, we discuss basic mechanisms of action and therapeutic applications of RNAi, including design considerations and areas for future development in the field.
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Affiliation(s)
- Priya S Shah
- Department of Chemical and Biolmolecular Engineering, University of California, Berkeley, California 94720, USA
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23
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Abstract
It is generally acknowledged that the Tat protein has a pivotal role in HIV-1 replication because it stimulates transcription from the viral long terminal repeat (LTR) promoter by binding to the TAR hairpin in the nascent RNA transcript. However, a multitude of additional Tat functions have been suggested. The importance of these functions is difficult to assess in replication studies with Tat-mutated HIV-1 variants because of the dominant negative effect on viral gene expression. We therefore used an HIV-1 construct that does not depend on the Tat-TAR interaction for transcription to reevaluate whether or not Tat has a second essential function in HIV-1 replication. This HIV-rtTA variant uses the incorporated Tet-On gene expression system for activation of transcription and replicates efficiently upon complete TAR deletion. Here we demonstrated that Tat inactivation does nevertheless severely inhibit replication. Upon long-term culturing, the Tat-minus HIV-rtTA variant acquired mutations in the U3 region that improved promoter activity and reestablished replication. We showed that in the absence of a functional TAR, Tat remains important for viral transcription via Sp1 sequence elements in the U3 promoter region. Substitution of these U3 sequences with nonrelated promoter elements created a virus that replicates efficiently without Tat in SupT1 T cells. These results indicate that Tat has a versatile role in transcription via TAR and U3 elements. The results also imply that Tat has no other essential function in viral replication in cultured T cells.
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MicroRNAs and human retroviruses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:686-93. [PMID: 21640212 PMCID: PMC3177989 DOI: 10.1016/j.bbagrm.2011.05.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that control a multitude of critical processes in mammalian cells. Increasing evidence has emerged that host miRNAs serve in animal cells to restrict viral infections. In turn, many viruses encode RNA silencing suppressors (RSS) which are employed to moderate the potency of the cell's miRNA selection against viral replication. Some viruses also encode viral miRNAs. In this review, we summarize findings from human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus type 1 (HTLV-1) that illustrate examples of host cell miRNAs that target the viruses, of RSS encoded by viruses, and of host cell miRNA profile changes that are seen in infected cells. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.
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Narayanan A, Kehn-Hall K, Bailey C, Kashanchi F. Analysis of the roles of HIV-derived microRNAs. Expert Opin Biol Ther 2011; 11:17-29. [PMID: 21133815 DOI: 10.1517/14712598.2011.540564] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE OF THE FIELD HIV-1 is a retrovirus that has infected millions in recent decades. The level of life cycle complexity and host control exerted by this small virus with only nine proteins is astonishing. An interesting direction that has emerged in recent years is the role of small non-coding RNAs in viral gene expression. AREAS COVERED IN THIS REVIEW We focus on HIV-1 produced microRNAs (miRNAs), namely, TAR, Nef and miR-H1, and their roles in HIV-1 biogenesis. The article provides insights into TAR miRNA-mediated downregulation of viral and host gene expression by recruitment of chromatin remodeling components (HDAC1). WHAT THE READER WILL GAIN We address the influence of TAR miRNA on host cell cycle progression and apoptosis, and the role of Nef miRNA in the regulation of viral and host gene expression. The review also highlights an intriguing connection between miR-H1 and HIV-1-associated neurological pathogenesis, and the influence of the miRNA machinery in the establishment of latency. In the Expert Opinion section, we analyze the issue of host-based therapeutics against HIV-1 and how transcription inhibitors are influenced by viral miRNA production. TAKE HOME MESSAGE HIV-derived miRNAs are of significance not only to understand host-virus interactions, but also for the design of effective therapeutics.
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Affiliation(s)
- Aarthi Narayanan
- George Mason University, National Center for Biodefense and Infectious Diseases, Manassas, VA 20110, USA
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26
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An evolved adeno-associated viral variant enhances gene delivery and gene targeting in neural stem cells. Mol Ther 2011; 19:667-75. [PMID: 21224831 DOI: 10.1038/mt.2010.287] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gene delivery to, and gene targeting in, stem cells would be a highly enabling technology for basic science and biomedical application. Adeno-associated viral (AAV) vectors have demonstrated the capacity for efficient delivery to numerous cells, but their application to stem cells has been limited by low transduction efficiency. Due to their considerable advantages, however, engineering AAV delivery systems to enhance gene delivery to stem cells may have an impact in stem cell biology and therapy. Therefore, using several diverse AAV capsid libraries-including randomly mutagenized, DNA shuffled, and random peptide insertion variants-we applied directed evolution to create a "designer" AAV vector with enhanced delivery efficiency for neural stem cells (NSCs). A novel AAV variant, carrying an insertion of a selected peptide sequence on the surface of the threefold spike within the heparin-binding site, emerged from this evolution. Importantly, this evolved AAV variant mediated efficient gene delivery to rat, mouse, and human NSCs, as well as efficient gene targeting within adult NSCs, and it is thus promising for applications ranging from basic stem cell biology to clinical translation.
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27
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Dutta S, Bhaduri N, Rastogi N, Chandel SG, Vandavasi JK, Upadhayaya RS, Chattopadhyaya J. Carba-LNA modified siRNAs targeting HIV-1 TAR region downregulate HIV-1 replication successfully with enhanced potency. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00225a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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28
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Willerth SM, Pedro HAM, Pachter L, Humeau LM, Arkin AP, Schaffer DV. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One 2010; 5:e13564. [PMID: 21042592 PMCID: PMC2962647 DOI: 10.1371/journal.pone.0013564] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 10/01/2010] [Indexed: 12/21/2022] Open
Abstract
Background With an estimated 38 million people worldwide currently infected with human immunodeficiency virus (HIV), and an additional 4.1 million people becoming infected each year, it is important to understand how this virus mutates and develops resistance in order to design successful therapies. Methodology/Principal Findings We report a novel experimental method for amplifying full-length HIV genomes without the use of sequence-specific primers for high throughput DNA sequencing, followed by assembly of full length viral genome sequences from the resulting large dataset. Illumina was chosen for sequencing due to its ability to provide greater coverage of the HIV genome compared to prior methods, allowing for more comprehensive characterization of the heterogeneity present in the HIV samples analyzed. Our novel amplification method in combination with Illumina sequencing was used to analyze two HIV populations: a homogenous HIV population based on the canonical NL4-3 strain and a heterogeneous viral population obtained from a HIV patient's infected T cells. In addition, the resulting sequence was analyzed using a new computational approach to obtain a consensus sequence and several metrics of diversity. Significance This study demonstrates how a lower bias amplification method in combination with next generation DNA sequencing provides in-depth, complete coverage of the HIV genome, enabling a stronger characterization of the quasispecies present in a clinically relevant HIV population as well as future study of how HIV mutates in response to a selective pressure.
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Affiliation(s)
- Stephanie M. Willerth
- Department of Chemical Engineering and the Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
| | - Hélder A. M. Pedro
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Lior Pachter
- Department of Mathematics and Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Laurent M. Humeau
- VIRxSYS Corporation, Gaithersburg, Maryland, United States of America
| | - Adam P. Arkin
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- * E-mail: (DVS); (APA)
| | - David V. Schaffer
- Department of Chemical Engineering and the Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- * E-mail: (DVS); (APA)
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29
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Applegate TL, Birkett DJ, Mcintyre GJ, Jaramillo AB, Symonds G, Murray JM. In silico modeling indicates the development of HIV-1 resistance to multiple shRNA gene therapy differs to standard antiretroviral therapy. Retrovirology 2010; 7:83. [PMID: 20932334 PMCID: PMC2959037 DOI: 10.1186/1742-4690-7-83] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Accepted: 10/09/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Gene therapy has the potential to counter problems that still hamper standard HIV antiretroviral therapy, such as toxicity, patient adherence and the development of resistance. RNA interference can suppress HIV replication as a gene therapeutic via expressed short hairpin RNAs (shRNAs). It is now clear that multiple shRNAs will likely be required to suppress infection and prevent the emergence of resistant virus. RESULTS We have developed the first biologically relevant stochastic model in which multiple shRNAs are introduced into CD34+ hematopoietic stem cells. This model has been used to track the production of gene-containing CD4+ T cells, the degree of HIV infection, and the development of HIV resistance in lymphoid tissue for 13 years. In this model, we found that at least four active shRNAs were required to suppress HIV infection/replication effectively and prevent the development of resistance. The inhibition of incoming virus was shown to be critical for effective treatment. The low potential for resistance development that we found is largely due to a pool of replicating wild-type HIV that is maintained in non-gene containing CD4+ T cells. This wild-type HIV effectively out-competes emerging viral strains, maintaining the viral status quo. CONCLUSIONS The presence of a group of cells that lack the gene therapeutic and is available for infection by wild-type virus appears to mitigate the development of resistance observed with systemic antiretroviral therapy.
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Affiliation(s)
- Tanya Lynn Applegate
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- The National Centre in HIV Epidemiology and Clinical Research, University of New South Wales, Level 9 Lowy Packer Building, 405 Liverpool St, Darlinghurst, NSW, 2010, Australia
| | - Donald John Birkett
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- 9 Raglan St, Mosman, NSW, 2088, Australia
| | - Glen John Mcintyre
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- School of Molecular and Microbial Biosciences, School of Biological Sciences, University of Sydney, NSW, 2006, Australia
| | - Angel Belisario Jaramillo
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital Missenden Road, Camperdown, NSW, 2050, Australia
| | - Geoff Symonds
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- Faculty of Medicine, Level 8, Lowy Packer Building, 405 Liverpool St, Darlinghurst, NSW, 2010, Australia
| | - John Michael Murray
- The National Centre in HIV Epidemiology and Clinical Research, University of New South Wales, Level 9 Lowy Packer Building, 405 Liverpool St, Darlinghurst, NSW, 2010, Australia
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW, 2052, Australia
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30
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Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. PLoS Comput Biol 2010; 6. [PMID: 20711350 PMCID: PMC2920833 DOI: 10.1371/journal.pcbi.1000883] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 07/13/2010] [Indexed: 12/27/2022] Open
Abstract
Gene therapy is an emerging alternative to conventional anti-HIV-1 drugs, and can potentially control the virus while alleviating major limitations of current approaches. Yet, HIV-1's ability to rapidly acquire mutations and escape therapy presents a critical challenge to any novel treatment paradigm. Viral escape is thus a key consideration in the design of any gene-based technique. We develop a computational model of HIV's evolutionary dynamics in vivo in the presence of a genetic therapy to explore the impact of therapy parameters and strategies on the development of resistance. Our model is generic and captures the properties of a broad class of gene-based agents that inhibit early stages of the viral life cycle. We highlight the differences in viral resistance dynamics between gene and standard antiretroviral therapies, and identify key factors that impact long-term viral suppression. In particular, we underscore the importance of mutationally-induced viral fitness losses in cells that are not genetically modified, as these can severely constrain the replication of resistant virus. We also propose and investigate a novel treatment strategy that leverages upon gene therapy's unique capacity to deliver different genes to distinct cell populations, and we find that such a strategy can dramatically improve efficacy when used judiciously within a certain parametric regime. Finally, we revisit a previously-suggested idea of improving clinical outcomes by boosting the proliferation of the genetically-modified cells, but we find that such an approach has mixed effects on resistance dynamics. Our results provide insights into the short- and long-term effects of gene therapy and the role of its key properties in the evolution of resistance, which can serve as guidelines for the choice and optimization of effective therapeutic agents. A primary obstacle to the success of any anti-HIV treatment is HIV's ability to rapidly resist it by generating new viral strains whose vulnerability to the treatment is reduced. Gene therapies represent a novel class of treatments for HIV infection that may supplement or replace present therapies, as they alleviate some of their major shortcomings. The design of gene therapeutic agents that effectively reduce viral resistance can be aided by a quantitative elucidation of the processes by which resistance is acquired following therapy initiation. We developed a computational model that describes a patient's response to therapy and used it to quantify the influence of therapy parameters and strategies on the development of viral resistance. We find that gene therapy induces different clinical conditions and a much slower viral response than present therapies. These dictate different design principles such as a greater significance to the virus' competence in the absence of therapy. We also show that one can effectively delay emergence of resistance by delivering distinct therapeutic genes into separate cell populations. Our results highlight the differences between traditional and gene therapies and provide a basic understanding of how key controllable parameters and strategies affect resistance development.
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31
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Das AT, Berkhout B. HIV-1 evolution: frustrating therapies, but disclosing molecular mechanisms. Philos Trans R Soc Lond B Biol Sci 2010; 365:1965-73. [PMID: 20478891 PMCID: PMC2880118 DOI: 10.1098/rstb.2010.0072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Replication of HIV-1 under selective pressure frequently results in the evolution of virus variants that replicate more efficiently under the applied conditions. For example, in patients on antiretroviral therapy, such evolution can result in variants that are resistant to the HIV-1 inhibitors, thus frustrating the therapy. On the other hand, virus evolution can help us to understand the molecular mechanisms that underlie HIV-1 replication. For example, evolution of a defective virus mutant can result in variants that overcome the introduced defect by restoration of the original sequence or by the introduction of additional mutations in the viral genome. Analysis of the evolution pathway can reveal the requirements of the element under study and help to understand its function. Analysis of the escape routes may generate new insight in the viral life cycle and result in the identification of unexpected biological mechanisms. We have developed in vitro HIV-1 evolution into a systematic research tool that allows the study of different aspects of the viral replication cycle. We will briefly review this method of forced virus evolution and provide several examples that illustrate the power of this approach.
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Affiliation(s)
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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32
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Burnett JC, Lim KI, Calafi A, Rossi JJ, Schaffer DV, Arkin AP. Combinatorial latency reactivation for HIV-1 subtypes and variants. J Virol 2010; 84:5958-74. [PMID: 20357084 PMCID: PMC2876650 DOI: 10.1128/jvi.00161-10] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 03/24/2010] [Indexed: 12/11/2022] Open
Abstract
The eradication of HIV-1 will likely require novel clinical approaches to purge the reservoir of latently infected cells from a patient. We hypothesize that this therapy should target a wide range of latent integration sites, act effectively against viral variants that have acquired mutations in their promoter regions, and function across multiple HIV-1 subtypes. By using primary CD4(+) and Jurkat cell-based in vitro HIV-1 latency models, we observe that single-agent latency reactivation therapy is ineffective against most HIV-1 subtypes. However, we demonstrate that the combination of two clinically promising drugs-namely, prostratin and suberoylanilide hydroxamic acid (SAHA)-overcomes the limitations of single-agent approaches and can act synergistically for many HIV-1 subtypes, including A, B, C, D, and F. Finally, by identifying the proviral integration position of latent Jurkat cell clones, we demonstrate that this drug combination does not significantly enhance the expression of endogenous genes nearest to the proviral integration site, indicating that its effects may be selective.
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Affiliation(s)
- John C. Burnett
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Kwang-il Lim
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Arash Calafi
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - John J. Rossi
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - David V. Schaffer
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Adam P. Arkin
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
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33
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Sun D, Rösler C, Kidd-Ljunggren K, Nassal M. Quantitative assessment of the antiviral potencies of 21 shRNA vectors targeting conserved, including structured, hepatitis B virus sites. J Hepatol 2010; 52:817-26. [PMID: 20400195 DOI: 10.1016/j.jhep.2009.10.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 10/16/2009] [Accepted: 10/19/2009] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS RNA interference (RNAi) may offer new treatment options for chronic hepatitis B. Replicating via an RNA intermediate, hepatitis B virus (HBV) is known to be principally vulnerable to RNAi. However, beyond delivery, the relevant issues of potential off-target effects, target site conservation in circulating HBV strains, and efficacy of RNAi itself have not systematically been addressed, nor can the different existing data be quantitatively compared. The aim of this study was to provide such information. METHODS To focus on the intracellular RNAi process itself and minimise other variables affecting overall RNAi efficacy, we used a robust co-transfection system to quantitatively assess the relative potencies of 21 small-hairpin (sh) RNA vectors, targeting conserved sites throughout the HBV genome, against viral RNAs, proteins, nucleocapsids, and secreted virions under standardised conditions. RESULTS The approach enabled a distinct efficacy ranking, with the six most potent shRNAs achieving 95% reductions in virion formation, sequence-specifically and without detectable interferon induction, yet by differentially affecting different steps. Efficacy correlated poorly with predictions and was not principally abolished by target structure. Sequence comparisons suggest that truly conserved, RNAi-targetable sequences comprise less than 500 nucleotides of the circulating HBV genomes. CONCLUSIONS The HBV genome can harbour only a finite number of optimal target sites, but current predictions are poorly suited to constrain the number of possible candidates. However, the small size of the highly conserved sequence space suggests experimental identification as a viable option.
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Affiliation(s)
- Dianxing Sun
- Bethune International Peace Hospital, Departmrnt of Liver Disease, 398 West Zhongshan Road, 050082 Shijiazhuang, PR China
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Coley W, Kehn-Hall K, Van Duyne R, Kashanchi F. Novel HIV-1 therapeutics through targeting altered host cell pathways. Expert Opin Biol Ther 2009; 9:1369-82. [PMID: 19732026 DOI: 10.1517/14712590903257781] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The emergence of drug-resistant HIV-1 strains presents a challenge for the design of new drugs. Anti-HIV compounds currently in use are the subject of advanced clinical trials using either HIV-1 reverse transcriptase, viral protease or integrase inhibitors. Recent studies show an increase in the number of HIV-1 variants resistant to anti-retroviral agents in newly infected individuals. Targeting host cell factors involved in the regulation of HIV-1 replication might be one way to combat HIV-1 resistance to the currently available anti-viral agents. A specific inhibition of HIV-1 gene expression could be expected from the development of compounds targeting host cell factors that participate in the activation of the HIV-1 LTR promoter. Here we discuss how targeting the host can be accomplished either by using small molecules to alter the function of the host's proteins such as p53 or cdk9, or by utilizing new advances in siRNA therapies to knock down essential host factors such as CCR5 and CXCR4. Finally, we will discuss how the viral protein interactomes should be used to better design therapeutics against HIV-1.
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Affiliation(s)
- William Coley
- George Washington University, School of Medicine, Department of Microbiology, Immunology and Tropical Medicine, Washington, DC 20037, USA
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Abstract
While the discovery of RNA interference (RNAi) has been considered one of the most significant breakthroughs in biomedicine, its prospects for novel therapeutic applications are even more exciting. The high specificity, exquisite selectivity and chemical homogeneity of small interfering RNAs (siRNA; intermediates in RNAi activity), provide unique advantages for these moieties as multi-targeted inhibitory drugs. Many such applications have demonstrated significant benefit compared with single gene-targeted siRNA inhibitors. In this article, we will review the current status of using a multi-targeted siRNA cocktail for novel therapeutic development in the treatment of cancer and viral infections. We will also propose the characteristics of various types of siRNA cocktails and their design, while recognizing the potential future impact of and challenges facing this unique therapeutic modality.
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Abstract
Basic research in the field of molecular biology led to the discovery of the mechanism of RNA interference (RNAi) in Caenorhabditis elegans in 1998. RNAi is now widely appreciated as an important gene control mechanism in mammals, and several RNAi‐based gene‐silencing applications have already been used in clinical trials. In this review I will discuss RNAi approaches to inhibit the pathogenic human immunodeficiency virus type 1 (HIV‐1), which establishes a chronic infection that would most likely require a durable gene therapy approach. Viruses, such as HIV‐1, are particularly difficult targets for RNAi attack because they mutate frequently, which allows viral escape by mutation of the RNAi target sequence. Combinatorial RNAi strategies are required to prevent viral escape.
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Affiliation(s)
- Ben Berkhout
- Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, the Netherlands.
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Berkhout B. A new Houdini act: multiple routes for HIV-1 escape from RNAi-mediated inhibition. Future Microbiol 2009; 4:151-4. [DOI: 10.2217/17460913.4.2.151] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Evaluation of: Leonard JN, Shah PS, Burnett JC, Schaffer DV: HIV evades RNA interference directed at TAR by an indirect compensatory mechanism. Cell Host Microbe 4, 484–494 (2008). RNAi can be used to induce the silencing of messenger RNAs in a sequence-specific manner. Several therapeutic RNAi applications are actively being pursued, including the targeting of the RNA genome of human pathogenic viruses such as HIV-1. Viruses are able to escape from RNAi attack by mutation of the targeted sequence. In this report, Leonard and co-workers present evidence of a more indirect viral escape route by selection of up-mutations in the promoter that boosts viral gene expression. This indirect route may serve as a general viral evasion mechanism.
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Affiliation(s)
- Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection & Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
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