1
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Asadbeigi A, Bakhtiarizadeh MR, Saffari M, Modarressi MH, Sadri N, Kafi ZZ, Fazilaty H, Ghalyanchilangeroudi A, Esmaeili H. Protection of animals against devastating RNA viruses using CRISPR-Cas13s. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102235. [PMID: 39021763 PMCID: PMC11253668 DOI: 10.1016/j.omtn.2024.102235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
The intrinsic nature of CRISPR-Cas in conferring immunity to bacteria and archaea has been repurposed to combat pathogenic agents in mammalian and plant cells. In this regard, CRISPR-Cas13 systems have proved their remarkable potential for single-strand RNA viruses targeting. Here, different types of Cas13 orthologs were applied to knockdown foot-and-mouth disease virus (FMDV), a highly contagious disease of a wide variety of species with genetically diverse strains and is widely geographically distributed. Using programmable CRISPR RNAs capable of targeting conserved regions of the viral genome, all Cas13s from CRISPR system type VI (subtype A/B/D) could comprehensively target and repress different serotypes of FMDV virus. This approach has the potential to destroy all strains of a virus as targets the ultra-conserved regions of genome. We experimentally compared the silencing efficiency of CRISPR and RNAi by designing the most effective short hairpin RNAs according to our developed scoring system and observed comparable results. This study showed successful usage of various Cas13 enzymes for suppression of FMDV, which provides a flexible strategy to battle with other animal infectious RNA viruses, an underdeveloped field in the biotechnology scope.
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Affiliation(s)
- Adnan Asadbeigi
- Cancer Institute, Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran 1417613151, Iran
| | | | - Mojtaba Saffari
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran 1417613151, Iran
| | - Mohammad Hossein Modarressi
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran 1417613151, Iran
| | - Naser Sadri
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
| | - Zahra Ziafati Kafi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
| | - Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
| | - Hossein Esmaeili
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
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2
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Becker J, Stanifer ML, Leist SR, Stolp B, Maiakovska O, West A, Wiedtke E, Börner K, Ghanem A, Ambiel I, Tse LV, Fackler OT, Baric RS, Boulant S, Grimm D. Ex vivo and in vivo suppression of SARS-CoV-2 with combinatorial AAV/RNAi expression vectors. Mol Ther 2022; 30:2005-2023. [PMID: 35038579 PMCID: PMC8758558 DOI: 10.1016/j.ymthe.2022.01.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/11/2021] [Accepted: 01/12/2022] [Indexed: 11/24/2022] Open
Abstract
Despite rapid development and deployment of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinically relevant modalities to curb the pandemic by directly attacking the virus on a genetic level remain highly desirable and are urgently needed. Here we comprehensively illustrate the capacity of adeno-associated virus (AAV) vectors co-expressing a cocktail of three short hairpin RNAs (shRNAs; RNAi triggers) directed against the SARS-CoV-2 RdRp and N genes as versatile and effective antiviral agents. In cultured monkey cells and human gut organoids, our most potent vector, SAVIOR (SARS virus repressor), suppressed SARS-CoV-2 infection to background levels. Strikingly, in control experiments using single shRNAs, multiple SARS-CoV-2 escape mutants quickly emerged from infected cells within 24-48 h. Importantly, such adverse viral adaptation was fully prevented with the triple-shRNA AAV vector even during long-term cultivation. In addition, AAV-SAVIOR efficiently purged SARS-CoV-2 in a new model of chronically infected human intestinal cells. Finally, intranasal AAV-SAVIOR delivery using an AAV9 capsid moderately diminished viral loads and/or alleviated disease symptoms in hACE2-transgenic or wild-type mice infected with human or mouse SARS-CoV-2 strains, respectively. Our combinatorial and customizable AAV/RNAi vector complements ongoing global efforts to control the coronavirus disease 2019 (COVID-19) pandemic and holds great potential for clinical translation as an original and flexible preventive or therapeutic antiviral measure.
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Affiliation(s)
- Jonas Becker
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - Megan Lynn Stanifer
- Department of Infectious Diseases/Molecular Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Sarah Rebecca Leist
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Bettina Stolp
- Department of Infectious Diseases/Integrative Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany
| | - Olena Maiakovska
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ande West
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Ellen Wiedtke
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany; Department of Infectious Diseases/Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany
| | - Ali Ghanem
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ina Ambiel
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Longping Victor Tse
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Oliver Till Fackler
- Department of Infectious Diseases/Integrative Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Ralph Steven Baric
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32611, USA; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany; Department of Infectious Diseases/Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, 69120 Heidelberg, Germany.
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3
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Ahmadi A, Moradi S. In silico analysis suggests the RNAi-enhancing antibiotic enoxacin as a potential inhibitor of SARS-CoV-2 infection. Sci Rep 2021; 11:10271. [PMID: 33986351 PMCID: PMC8119475 DOI: 10.1038/s41598-021-89605-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19 has currently become the biggest challenge in the world. There is still no specific medicine for COVID-19, which leaves a critical gap for the identification of new drug candidates for the disease. Recent studies have reported that the small-molecule enoxacin exerts an antiviral activity by enhancing the RNAi pathway. The aim of this study is to analyze if enoxacin can exert anti-SARS-CoV-2 effects. We exploit multiple computational tools and databases to examine (i) whether the RNAi mechanism, as the target pathway of enoxacin, could act on the SARS-CoV-2 genome, and (ii) microRNAs induced by enoxacin might directly silence viral components as well as the host cell proteins mediating the viral entry and replication. We find that the RNA genome of SARS-CoV-2 might be a suitable substrate for DICER activity. We also highlight several enoxacin-enhanced microRNAs which could target SARS-CoV-2 components, pro-inflammatory cytokines, host cell components facilitating viral replication, and transcription factors enriched in lung stem cells, thereby promoting their differentiation and lung regeneration. Finally, our analyses identify several enoxacin-targeted regulatory modules that were critically associated with exacerbation of the SARS-CoV-2 infection. Overall, our analysis suggests that enoxacin could be a promising candidate for COVID-19 treatment through enhancing the RNAi pathway.
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Affiliation(s)
- Amirhossein Ahmadi
- Department of Biological Science and Technology, Faculty of Nano and Bio Science and Technology, Persian Gulf University, Bushehr, 75169,, Iran
| | - Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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4
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Yin L, Zhao F, Sun H, Wang Z, Huang Y, Zhu W, Xu F, Mei S, Liu X, Zhang D, Wei L, Cen S, Hu S, Liang C, Guo F. CRISPR-Cas13a Inhibits HIV-1 Infection. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:147-155. [PMID: 32585623 PMCID: PMC7321785 DOI: 10.1016/j.omtn.2020.05.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/15/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas provides bacteria and archaea with immunity against invading phages and foreign plasmid DNA and has been successfully adapted for gene editing in a variety of species. The class 2 type VI CRISPR-Cas effector Cas13a targets and cleaves RNA, providing protection against RNA phages. Here we report the repurposing of CRISPR-Cas13a to inhibit human immunodeficiency virus type 1 (HIV-1) infection through targeting HIV-1 RNA and diminishing viral gene expression. We observed strong inhibition of HIV-1 infection by CRISPR-Cas13a in human cells. We showed that CRISPR-Cas13a not only diminishes the level of newly synthesized viral RNA, either from the transfected plasmid DNA or from the viral DNA, which is integrated into cellular DNA, but it also targets and destroys the viral RNA that enters cells within viral capsid, leading to strong inhibition of HIV-1 infection. Together, our results suggest that CRISPR-Cas13a provides a potential novel tool to treat viral diseases in humans.
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Affiliation(s)
- Lijuan Yin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Hong Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Zhen Wang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Weijun Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Di Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Siqi Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China.
| | - Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China.
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5
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Carbonell A, Lisón P, Daròs J. Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:720-737. [PMID: 31350772 PMCID: PMC6899541 DOI: 10.1111/tpj.14466] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 05/15/2023]
Abstract
RNA interference (RNAi)-based tools are used in multiple organisms to induce antiviral resistance through the sequence-specific degradation of target RNAs by complementary small RNAs. In plants, highly specific antiviral RNAi-based tools include artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs). syn-tasiRNAs have emerged as a promising antiviral tool allowing for the multi-targeting of viral RNAs through the simultaneous expression of several syn-tasiRNAs from a single precursor. Here, we compared in tomato plants the effects of an amiRNA construct expressing a single amiRNA and a syn-tasiRNA construct expressing four different syn-tasiRNAs against Tomato spotted wilt virus (TSWV), an economically important pathogen affecting tomato crops worldwide. Most of the syn-tasiRNA lines were resistant to TSWV, whereas the majority of the amiRNA lines were susceptible and accumulated viral progenies with mutations in the amiRNA target site. Only the two amiRNA lines with higher amiRNA accumulation were resistant, whereas resistance in syn-tasiRNA lines was not exclusive of lines with high syn-tasiRNA accumulation. Collectively, these results suggest that syn-tasiRNAs induce enhanced antiviral resistance because of the combined silencing effect of each individual syn-tasiRNA, which minimizes the possibility that the virus simultaneously mutates all different target sites to fully escape each syn-tasiRNA.
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Affiliation(s)
- Alberto Carbonell
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
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De Silva Feelixge HS, Stone D, Roychoudhury P, Aubert M, Jerome KR. CRISPR/Cas9 and Genome Editing for Viral Disease-Is Resistance Futile? ACS Infect Dis 2018; 4:871-880. [PMID: 29522311 PMCID: PMC5993632 DOI: 10.1021/acsinfecdis.7b00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chronic viral infections remain a major public health issue affecting millions of people worldwide. Highly active antiviral treatments have significantly improved prognosis and infection-related morbidity and mortality but have failed to eliminate persistent viral forms. Therefore, new strategies to either eradicate or control these viral reservoirs are paramount to allow patients to stop antiretroviral therapy and realize a cure. Viral genome disruption based on gene editing by programmable endonucleases is one promising curative gene therapy approach. Recent findings on RNA-guided human immunodeficiency virus 1 (HIV-1) genome cleavage by Cas9 and other gene-editing enzymes in latently infected cells have shown high levels of site-specific genome disruption and potent inhibition of virus replication. However, HIV-1 can readily develop resistance to genome editing at a single antiviral target site. Current data suggest that cellular repair associated with DNA double-strand breaks can accelerate the emergence of resistance. On the other hand, a combination antiviral target strategy can exploit the same repair mechanism to functionally cure HIV-1 infection in vitro while avoiding the development of resistance. This perspective summarizes recent findings on the biology of resistance to genome editing and discusses the significance of viral genetic diversity on the application of gene editing strategies toward cure.
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Affiliation(s)
- Harshana S De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
| | - Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
- Department of Microbiology, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
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7
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Are microRNAs Important Players in HIV-1 Infection? An Update. Viruses 2018; 10:v10030110. [PMID: 29510515 PMCID: PMC5869503 DOI: 10.3390/v10030110] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 12/15/2022] Open
Abstract
HIV-1 has already claimed over 35 million human lives globally. No curative treatments are currently available, and the only treatment option for over 36 million people currently living with HIV/AIDS are antiretroviral drugs that disrupt the function of virus-encoded proteins. However, such virus-targeted therapeutic strategies are constrained by the ability of the virus to develop drug-resistance. Despite major advances in HIV/AIDS research over the years, substantial knowledge gaps exist in many aspects of HIV-1 replication, especially its interaction with the host. Hence, understanding the mechanistic details of virus–host interactions may lead to novel therapeutic strategies for the prevention and/or management of HIV/AIDS. Notably, unprecedented progress in deciphering host gene silencing processes mediated by several classes of cellular small non-coding RNAs (sncRNA) presents a promising and timely opportunity for developing non-traditional antiviral therapeutic strategies. Cellular microRNAs (miRNA) belong to one such important class of sncRNAs that regulate protein synthesis. Evidence is mounting that cellular miRNAs play important roles in viral replication, either usurped by the virus to promote its replication or employed by the host to control viral infection by directly targeting the viral genome or by targeting cellular proteins required for productive virus replication. In this review, we summarize the findings to date on the role of miRNAs in HIV-1 biology.
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8
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Liu C, Liang Z, Kong X. Efficacy Analysis of Combinatorial siRNAs against HIV Derived from One Double Hairpin RNA Precursor. Front Microbiol 2017; 8:1651. [PMID: 28900421 PMCID: PMC5581867 DOI: 10.3389/fmicb.2017.01651] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/15/2017] [Indexed: 01/18/2023] Open
Abstract
Combinatorial small interfering RNA duplexes (siRNAs) have the potential to be a gene therapy against HIV-1, and some studies have reported that transient combinatorial siRNA expression represses HIV replication, but the effects of long-term siRNA expression on HIV replication have not been studied in detail. In this study, HIV-1 replication under the influence of stable combinatorial siRNA expression from a single RNA transcript was analyzed. First, a series of cassettes encoding short hairpin RNA (shRNA)/long hairpin RNA (lhRNA)/double long hairpins (dlhRNA) was constructed and subjected to an analysis of inhibitory efficacy. Next, an optimized dlhRNA encoding cassette was selected and inserted into lentiviral delivery vector FG12. Transient dlhRNA expression reduced replication of HIV-1 in TZM-bl cells and CD4+ T cells successfully. HIV-1 susceptible TZM-bl cells were transducted with the dlhRNA expressing lentiviral vector and sorted by fluorescence-activated cell sorting to obtain stable dlhRNA expressing cells. The generation of four anti-HIV siRNAs in these dlhRNA expressing cells was verified by stem-loop RT-PCR assay. dlhRNA expression did not activate a non-specific interferon response. The dlhRNA expressing cells were also challenged with HIV-1 NL4-3, which revealed that stable expression of combinatorial siRNAs repressed HIV-1 replication for 8 days, after which HIV-1 overcame the inhibitory effect of siRNA expression by expressing mutant versions of RNAi targets. The results of this evaluation of the long-term inhibitory effects of combinatorial siRNAs against HIV-1 provide a reference for researchers who utilize combinatorial RNA interference against HIV-1 or other error-prone viruses.
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Affiliation(s)
- Chang Liu
- Medical Molecular Virology Laboratory, School of Medicine, Nankai UniversityTianjin, China
| | - Zhipin Liang
- Medical Molecular Virology Laboratory, School of Medicine, Nankai UniversityTianjin, China
| | - Xiaohong Kong
- Medical Molecular Virology Laboratory, School of Medicine, Nankai UniversityTianjin, China
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Paavilainen H, Lehtinen J, Romanovskaya A, Nygårdas M, Bamford DH, Poranen MM, Hukkanen V. Inhibition of clinical pathogenic herpes simplex virus 1 strains with enzymatically created siRNA pools. J Med Virol 2016; 88:2196-2205. [PMID: 27191509 DOI: 10.1002/jmv.24578] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 12/11/2022]
Abstract
Herpes simplex virus (HSV) is a common human pathogen causing severe diseases such as encephalitis, keratitis, and neonatal herpes. There is no vaccine against HSV and the current antiviral chemotherapy fails to treat certain forms of the disease. Here, we evaluated the antiviral activity of enzymatically created small interfering (si)RNA pools against various pathogenic HSV strains as potential candidates for antiviral therapies. Pools of siRNA targeting 0.5-0.8 kbp of essential HSV genes UL54, UL29, or UL27 were enzymatically synthesized. Efficacy of inhibition of each siRNA pool was evaluated against multiple clinical isolates and laboratory wild type HSV-1 strains using three cell lines representing host tissues that support HSV-1 replication: epithelial, ocular, and cells that originated from the nervous system. The siRNA pools targeting UL54, UL29, and UL27, as well as their equimolar mixture, inhibited HSV replication, with the pool targeting UL29 having the most prominent antiviral effect. In contrast, the non-specific control siRNA pool did not have such an effect. Moreover, the UL29 pool elicited only a minimal innate immune response in the HSV-infected cells, thus evidencing the safety of its potential clinical use. These results are promising for the development of a topical RNA interference approach for clinical treatment of HSV infection. J. Med. Virol. 88:2196-2205, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Henrik Paavilainen
- Department of Virology, University of Turku, Turku, Finland.
- Drug Research Doctoral Program, University of Turku, Turku, Finland.
| | - Jenni Lehtinen
- Department of Virology, University of Turku, Turku, Finland
- Drug Research Doctoral Program, University of Turku, Turku, Finland
| | | | | | - Dennis H Bamford
- Department of Biosciences, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Veijo Hukkanen
- Department of Virology, University of Turku, Turku, Finland
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10
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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: 2.3] [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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11
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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: 5.5] [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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12
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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: 0.9] [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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13
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Berkhout B, Liu YP. Towards improved shRNA and miRNA reagents as inhibitors of HIV1 replication. Future Microbiol 2014; 9:561-71. [DOI: 10.2217/fmb.14.5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT: miRNAs are the key players of the RNAi mechanism, which regulates the expression of a large number of mRNAs in human cells. shRNAs are man-made synthetic miRNA mimics that exploit similar intracellular RNA processing routes. Massive amounts of data derived from next-generation sequencing have revealed miRNA species that are derived from alternative biosynthesis pathways. Here, we review recent progress in our understanding of these noncanonical routes of miRNA and shRNA biosynthesis. We focus on ways to use these novel insights for the design of more potent and specific RNAi reagents for therapeutic applications, including the AgoshRNA design, which is processed differently than regular shRNAs. We will also discuss the development of a durable gene therapy against HIV1.
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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
| | - Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection & Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
- Current address: uniQure biopharma BV, Department of Research & Development, The Netherlands
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Herrera-Carrillo E, Liu YP, Berkhout B. The impact of unprotected T cells in RNAi-based gene therapy for HIV-AIDS. Mol Ther 2014; 22:596-606. [PMID: 24336172 PMCID: PMC3944328 DOI: 10.1038/mt.2013.280] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/01/2013] [Indexed: 12/18/2022] Open
Abstract
RNA interference (RNAi) is highly effective in inhibiting human immunodeficiency virus type 1 (HIV-1) replication by the expression of antiviral short hairpin RNA (shRNA) in stably transduced T-cell lines. For the development of a durable gene therapy that prevents viral escape, we proposed to combine multiple shRNAs against highly conserved regions of the HIV-1 RNA genome. The future in vivo application of such a gene therapy protocol will reach only a fraction of the T cells, such that HIV-1 replication will continue in the unmodified T cells, thereby possibly frustrating the therapy by generation of HIV-1 variants that escape from the inhibition imposed by the protected cells. We studied virus inhibition and evolution in pure cultures of shRNA-expressing cells versus mixed cell cultures of protected and unprotected T cells. The addition of the unprotected T cells indeed seems to accelerate HIV-1 evolution and escape from a single shRNA inhibitor. However, expression of three antiviral shRNAs from a single lentiviral vector prevents virus escape even in the presence of unprotected cells. 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)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, 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, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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Bao Y, Tian D, Zheng YY, Xi HL, Liu D, Yu M, Xu XY. Characteristics of HIV-1 natural drug resistance-associated mutations in former paid blood donors in Henan Province, China. PLoS One 2014; 9:e89291. [PMID: 24586665 PMCID: PMC3929713 DOI: 10.1371/journal.pone.0089291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/18/2014] [Indexed: 12/29/2022] Open
Abstract
Background Natural drug resistance is a major cause of antiviral treatment failure. The characteristics of HIV-1 natural drug resistance-associated mutations in former paid blood donors in Henan Province remain unclear. Methods One hundred and fifty HIV-1-positive plasma samples were collected. Plasma viral RNA was extracted for pol gene amplification and sequencing. The sequencing results were submitted to the HIV-1 drug resistance database for drug-resistance analysis. Results The rates of natural drug resistance and resistance-associated mutations were 17.7% (19/107) and 40.2% (43/107), respectively. The rates of PI major, PI minor, NRTI, and NNRTI mutations were: 0, 30.8% (33/107), 10.3% (11/107), and 18.7% (20/107), respectively. Nine cases (8.4%) had both NRTI and NNRTI resistance-associated mutations. Seven cases (6.5%) had PI minor, NRTI and NNRTI resistance-associated mutations. NNRTI resistance was the most serious, followed by NRTI resistance and PI resistance. Polymorphism mutation sites with mutation rates in the protease region higher than 60.0% were: L63A/P/S/T 89.7%, V77I 82.2%, I72E/M/K/T/V 80.4%, I93L 75.7%, and E35D 72.9%. Polymorphism mutation sites with mutation rates in the RT region higher than 60.0% were: I135A/L/M/R/T/V 93.5%, T200A/E/I/P/V 89.7%, Q278E/K/N/T 88.8%, S162C/Y 82.2%, and K277R/S 66.4%. The distribution of 107 gene sequences was scattered, with some drug-resistant strains grouped in the same cluster. Conclusion The natural drug resistance mutation rate of HIV-1 in former paid blood donors in Henan Province was 17.7%, with NNRTI resistance the most serious. The distribution of drug-resistant strains was scattered, with some correlations found in certain resistance loci.
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Affiliation(s)
- Yi Bao
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Di Tian
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Ying-Ying Zheng
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Hong-Li Xi
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Dan Liu
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Min Yu
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Xiao-Yuan Xu
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
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Inhibition of hepatitis C virus in chimeric mice by short synthetic hairpin RNAs: sequence analysis of surviving virus shows added selective pressure of combination therapy. J Virol 2014; 88:4647-56. [PMID: 24478422 DOI: 10.1128/jvi.00105-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED We have recently shown that a cocktail of two short synthetic hairpin RNAs (sshRNAs), targeting the internal ribosome entry site of hepatitis C virus (HCV) formulated with lipid nanoparticles, was able to suppress viral replication in chimeric mice infected with HCV GT1a by up to 2.5 log10 (H. Ma et al., Gastroenterology 146:63-66.e5, http://dx.doi.org/10.1053/j.gastro.2013.09.049) Viral load remained about 1 log10 below pretreatment levels 21 days after the end of dosing. We have now sequenced the HCV viral RNA amplified from serum of treated mice after the 21-day follow-up period. Viral RNA from the HCV sshRNA-treated groups was altered in sequences complementary to the sshRNAs and nowhere else in the 500-nucleotide sequenced region, while the viruses from the control group that received an irrelevant sshRNA had no mutations in that region. The ability of the most commonly selected mutations to confer resistance to the sshRNAs was confirmed in vitro by introducing those mutations into HCV-luciferase reporters. The mutations most frequently selected by sshRNA treatment within the sshRNA target sequence occurred at the most polymorphic residues, as identified from an analysis of available clinical isolates. These results demonstrate a direct antiviral activity with effective HCV suppression, demonstrate the added selective pressure of combination therapy, and confirm an RNA interference (RNAi) mechanism of action. IMPORTANCE This study presents a detailed analysis of the impact of treating a hepatitis C virus (HCV)-infected animal with synthetic hairpin-shaped RNAs that can degrade the virus's RNA genome. These RNAs can reduce the viral load in these animals by over 99% after 1 to 2 injections. The study results confirm that the viral rebound that often occurred a few weeks after treatment is due to emergence of a virus whose genome is mutated in the sequences targeted by the RNAs. The use of two RNA inhibitors, which is more effective than use of either one by itself, requires that any resistant virus have mutations in the targets sites of both agents, a higher hurdle, if the virus is to retain the ability to replicate efficiently. These results demonstrate a direct antiviral activity with effective HCV suppression, demonstrate the added selective pressure of combination therapy, and confirm an RNAi mechanism of action.
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Suzuki K, Hattori S, Marks K, Ahlenstiel C, Maeda Y, Ishida T, Millington M, Boyd M, Symonds G, Cooper DA, Okada S, Kelleher AD. Promoter Targeting shRNA Suppresses HIV-1 Infection In vivo Through Transcriptional Gene Silencing. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e137. [PMID: 24301868 PMCID: PMC3894581 DOI: 10.1038/mtna.2013.64] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022]
Abstract
Despite prolonged and intensive application, combined antiretroviral therapy cannot eradicate human immunodeficiency virus (HIV)-1 because it is harbored as a latent infection, surviving for long periods of time. Alternative approaches are required to overcome the limitations of current therapy. We have been developing a short interfering RNA (siRNA) gene silencing approach. Certain siRNAs targeting promoter regions of genes induce transcriptional gene silencing. We previously reported substantial transcriptional gene silencing of HIV-1 replication by an siRNA targeting the HIV-1 promoter in vitro. In this study, we show that this siRNA, expressed as a short hairpin RNA (shRNA) (shPromA-JRFL) delivered by lentiviral transduction of human peripheral blood mononuclear cells (PBMCs), which are then used to reconstitute NOJ mice, is able to inhibit HIV-1 replication in vivo, whereas a three-base mismatched variant (shPromA-M2) does not. In shPromA-JRFL-treated mice, HIV-1 RNA in serum is significantly reduced, and the ratio of CD4(+)/CD8(+) T cells is significantly elevated. Expression levels of the antisense RNA strand inversely correlates with HIV-1 RNA in serum. The silenced HIV-1 can be reactivated by T-cell activation in ex vivo cultures. HIV-1 suppression is not due to offtarget effects of shPromA-JRFL. These data provide "proof-of principle" that an shRNA targeting the HIV-1 promoter is able to suppress HIV-1 replication in vivo.Molecular Therapy-Nucleic Acids (2013) 2, e137; doi:10.1038/mtna.2013.64; published online 3 December 2013.
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Affiliation(s)
- Kazuo Suzuki
- St. Vincent's Centre for Applied Medical Research, Darlinghurst, New South Wales, Australia
| | | | - Katherine Marks
- St. Vincent's Centre for Applied Medical Research, Darlinghurst, New South Wales, Australia
| | - Chantelle Ahlenstiel
- The Kirby Institute, The University of New South Wales, New South Wales, Australia
| | - Yosuke Maeda
- Department of Medical Virology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takaomi Ishida
- Research Center for Asian Infectious Disease, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | | | - Geoff Symonds
- St. Vincent's Centre for Applied Medical Research, Darlinghurst, New South Wales, Australia
- Calimmune, Sydney, Australia
| | - David A Cooper
- St. Vincent's Centre for Applied Medical Research, Darlinghurst, New South Wales, Australia
- The Kirby Institute, The University of New South Wales, New South Wales, Australia
| | - Seiji Okada
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Anthony D Kelleher
- St. Vincent's Centre for Applied Medical Research, Darlinghurst, New South Wales, Australia
- The Kirby Institute, The University of New South Wales, New South Wales, Australia
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Lafforgue G, Martínez F, Niu QW, Chua NH, Daròs JA, Elena SF. Improving the effectiveness of artificial microRNA (amiR)-mediated resistance against Turnip mosaic virus by combining two amiRs or by targeting highly conserved viral genomic regions. J Virol 2013; 87:8254-6. [PMID: 23698292 PMCID: PMC3700214 DOI: 10.1128/jvi.00914-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/10/2013] [Indexed: 01/04/2023] Open
Abstract
A drawback of recent antiviral therapies based on the transgenic expression of artificial microRNAs (amiRs) is the ease with which viruses generate escape mutations. Here, we show two alternative strategies for improving the effectiveness of resistance in plants. First, we expressed two amiRs complementary to independent targets in the viral genome, and second, we designed amiRs complementary to highly conserved RNA motifs in the viral genome.
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Affiliation(s)
- Guillaume Lafforgue
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Fernando Martínez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Qi-Wen Niu
- Laboratory of Plant Biology, Rockefeller University, New York, New York, USA
| | - Nam-Hai Chua
- Laboratory of Plant Biology, Rockefeller University, New York, New York, USA
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
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Functional in vivo delivery of multiplexed anti-HIV-1 siRNAs via a chemically synthesized aptamer with a sticky bridge. Mol Ther 2012; 21:192-200. [PMID: 23164935 PMCID: PMC3538316 DOI: 10.1038/mt.2012.226] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
One of the most formidable impediments to clinical translation of RNA interference (RNAi) is safe and effective delivery of the siRNAs to the desired target tissue at therapeutic doses. We previously described in vivo cell type-specific delivery of anti-HIV small-interfering RNAs (siRNAs) through covalent conjugation to an anti-gp120 aptamer. In order to improve the utility of aptamers as siRNA delivery vehicles, we chemically synthesized the gp120 aptamer with a 3′ 7-carbon linker (7C3), which in turn is attached to a 16-nucleotide 2′ OMe/2′ Fl GC-rich bridge sequence. This bridge facilitates the noncovalent binding and interchange of various siRNAs with the same aptamer. We show here that this aptamer-bridge-construct complexed with three different Dicer substrate siRNAs (DsiRNAs) results in effective delivery of the cocktail of DsiRNAs in vivo, resulting in knockdown of target mRNAs and potent inhibition of HIV-1 replication. Following cessation of the aptamer-siRNA cocktail treatment, HIV levels rebounded facilitating a follow-up treatment with the aptamer cocktail of DsiRNAs. This follow-up injection resulted in complete suppression of HIV-1 viral loads that extended several weeks beyond the final injection. Collectively, these data demonstrate a facile, targeted approach for combinatorial delivery of antiviral and host DsiRNAs for HIV-1 therapy in vivo.
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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: 2.8] [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: 0.9] [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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