1
|
Shibata A, Shirohzu H, Iwakami Y, Abe T, Emura C, Aoki E, Ohgi T. Terminal bridging of siRNA duplex at the ribose 2' position controls strand bias and target sequence preference. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:468-477. [PMID: 37168798 PMCID: PMC10165404 DOI: 10.1016/j.omtn.2023.04.013] [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: 11/04/2022] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
Small interfering RNA (siRNA) and short hairpin RNA (shRNA) are widely used as RNA interference (RNAi) reagents. Recently, truncated shRNAs that trigger RNAi in a Dicer-independent manner have been developed. We generated a novel class of RNAi reagent, designated enforced strand bias (ESB) RNA, in which an siRNA duplex was chemically bridged between the 3' terminal overhang region of the guide strand and the 5' terminal nucleotide of the passenger strand. ESB RNA, which is chemically bridged at the 2' positions of ribose (2'-2' ESB RNA), functions in a Dicer-independent manner and was highly effective at triggering RNAi without the passenger strand-derived off-target effect. In addition, the 2'-2' ESB RNA exhibited a unique target sequence preference that differs from siRNA and silenced target sequences that could not be effectively suppressed by siRNA. Our results indicate that ESB RNA has the potential to be an effective RNAi reagent even when the target sequence is not suitable for siRNA.
Collapse
Affiliation(s)
- Atsushi Shibata
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
- Corresponding author Atsushi Shibata, Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan.
| | - Hisao Shirohzu
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
- Fukuoka Center for Disease Control and Prevention, Kurume, Fukuoka, Japan
| | - Yusuke Iwakami
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Tomoaki Abe
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Chisato Emura
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Eriko Aoki
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Tadaaki Ohgi
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| |
Collapse
|
2
|
Hill A, van Leeuwen D, Schlösser V, Behera A, Mateescu B, Hall J. Chemically synthesized, self-assembling small interfering RNA-prohead RNA molecules trigger Dicer-independent gene silencing. Chemistry 2021; 28:e202103995. [PMID: 34879171 PMCID: PMC9305526 DOI: 10.1002/chem.202103995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 11/07/2022]
Abstract
RNA interference (RNAi) mediated by small interfering RNA (siRNA) duplexes is a powerful therapeutic modality, but the translation of siRNAs from the bench into clinical application has been hampered by inefficient delivery in vivo. An innovative delivery strategy involves fusing siRNAs to a three‐way junction (3WJ) motif derived from the phi29 bacteriophage prohead RNA (pRNA). Chimeric siRNA‐3WJ molecules are presumed to enter the RNAi pathway through Dicer cleavage. Here, we fused siRNAs to the phi29 3WJ and two phylogenetically related 3WJs. We confirmed that the siRNA‐3WJs are substrates for Dicer in vitro. However, our results reveal that siRNA‐3WJs transfected into Dicer‐deficient cell lines trigger potent gene silencing. Interestingly, siRNA‐3WJs transfected into an Argonaute 2‐deficient cell line also retain some gene silencing activity. siRNA‐3WJs are most efficient when the antisense strand of the siRNA duplex is positioned 5′ of the 3WJ (5′‐siRNA‐3WJ) relative to 3′ of the 3WJ (3′‐siRNA‐3WJ). This work sheds light on the functional properties of siRNA‐3WJs and offers a design rule for maximizing their potency in the human RNAi pathway.
Collapse
Affiliation(s)
- Alyssa Hill
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, SWITZERLAND
| | - Daniël van Leeuwen
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Verena Schlösser
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Alok Behera
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Bogdan Mateescu
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Jonathan Hall
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| |
Collapse
|
3
|
Lennox KA, Behlke MA. Chemical Modifications in RNA Interference and CRISPR/Cas Genome Editing Reagents. Methods Mol Biol 2020; 2115:23-55. [PMID: 32006393 DOI: 10.1007/978-1-0716-0290-4_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chemically modified oligonucleotides (ONs) are routinely used in the laboratory to assess gene function, and clinical advances are rapidly progressing as continual efforts are being made to optimize ON efficacy. Over the years, RNA interference (RNAi) has become one of the main tools used to inhibit RNA expression across a wide variety of species. Efforts have been made to improve the exogenous delivery of the double-stranded RNA components to the endogenous intracellular RNAi machinery to direct efficacious degradation of a user-defined RNA target. More recently, synthetic RNA ONs are being used to mimic the bacterial-derived CRISPR/Cas system to direct specific editing of the mammalian genome. Both of these techniques rely on the use of various chemical modifications to the RNA phosphate backbone or sugar in specific positions throughout the ONs to improve the desired biological outcome. Relevant chemical modifications also include conjugated targeting ligands to assist ON delivery to specific cell types. Chemical modifications are most beneficial for therapeutically relevant ONs, as they serve to enhance target binding, increase drug longevity, facilitate cell-specific targeting, improve internalization into productive intracellular compartments, and mitigate both sequence-specific as well as immune-related off-target effects (OTEs). The knowledge gained from years of optimizing RNAi reagents and characterizing the biochemical and biophysical properties of each chemical modification will hopefully accelerate the CRISPR/Cas technology into the clinic, as well as further expand the use of RNAi to treat currently undruggable diseases. This review discusses the most commonly employed chemical modifications in RNAi reagents and CRISPR/Cas guide RNAs and provides an overview of select publications that have demonstrated success in improving ON efficacy and/or mitigating undesired OTEs.
Collapse
Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA, USA.
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| |
Collapse
|
4
|
Sun G, Wang J, Huang Y, Yuan CWY, Zhang K, Hu S, Chen L, Lin RJ, Yen Y, Riggs AD. Differences in silencing of mismatched targets by sliced versus diced siRNAs. Nucleic Acids Res 2019; 46:6806-6822. [PMID: 29718312 PMCID: PMC6061797 DOI: 10.1093/nar/gky287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 04/20/2018] [Indexed: 01/11/2023] Open
Abstract
It has been reported that the two major types of RNA interference triggers, the classical Dicer-generated small RNAs (siRNAs), which function with all members of the Argonaute (Ago) protein family in mammals, and the Ago2-sliced small RNAs (sli-siRNAs), which function solely through Ago2, have similar potency in target cleavage and repression. Here, we show that sli-siRNAs are generally more potent than siRNAs in silencing mismatched targets. This phenomenon is usually more apparent in targets that have mismatched nucleotides in the 3′ supplementary region than in targets with mismatches in the seed region. We demonstrate that Ago2 slicer activity is a major factor contributing to the greater silencing efficiency of sli-siRNA against mismatched targets and that participation of non-slicing Agos in silencing mismatched siRNA targets may dilute the slicing ability of Ago2. The difference in length of the mature guide RNA used in sli-RISCs and si-RISCs may also contribute to the observed difference in knockdown efficiency. Our data suggest that a sli-siRNA guide strand is likely to have substantially stronger off-target effects than a guide strand with the same sequence in a classical siRNA and that Dicer and non-slicing Agos may play pivotal roles in controlling siRNA target specificity.
Collapse
Affiliation(s)
- Guihua Sun
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Jinghan Wang
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Yasheng Huang
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Christine Wan-Yin Yuan
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Keqiang Zhang
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Shuya Hu
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Linling Chen
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Ren-Jang Lin
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| | - Yun Yen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan
| | - Arthur D Riggs
- Department of Diabetes Complications & Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA
| |
Collapse
|
5
|
Gao Z, Berkhout B, Herrera-Carrillo E. Boosting AgoshRNA activity by optimized 5'-terminal nucleotide selection. RNA Biol 2019; 16:890-898. [PMID: 30991896 PMCID: PMC6546398 DOI: 10.1080/15476286.2019.1599259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RNA interference (RNAi) can be triggered by synthetic small interfering RNAs (siRNAs) or transgene-expressed short hairpin RNAs (shRNAs). Recent evidence indicates that shRNA molecules, with a relatively short stem and small loop, are processed by Argonaute 2 protein (Ago2). We named these molecules AgoshRNA as Ago2 is involved in both the processing and the subsequent mRNA-silencing reaction. This alternative processing route yields only a single guide strand, which thus avoids potential off-target effects induced by the passenger strand of a regular shRNA. We recently described that the introduction of a 5ʹ-terminal purine (A or G) and a mismatch at the bottom of the hairpin enhances the AgoshRNA activity. The critical 5ʹ-terminal nucleotide (nt) represents the +1 position of the transcriptional promoter, which influences the transcriptional efficiency and initiation accuracy as demonstrated for the H1 RNA polymerase (Pol) III promoter. These findings highlight the necessity of considering Pol III requirements in the design of optimized AgoshRNA cassettes. In this study, we report the design and expression of potent AgoshRNAs by two other popular Pol III promoters: U6 and 7SK, which were recently reported to have a distinct transcription profile compared to the H1 promoter. We propose general rules for the design and expression of potent AgoshRNA molecules using Pol III cassettes, which should augment the application of novel AgoshRNA reagents for basic research and therapeutic purposes.
Collapse
Affiliation(s)
- Zongliang Gao
- a Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC , University of Amsterdam , Amsterdam , the Netherlands
| | - Ben Berkhout
- a Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC , University of Amsterdam , Amsterdam , the Netherlands
| | - Elena Herrera-Carrillo
- a Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC , University of Amsterdam , Amsterdam , the Netherlands
| |
Collapse
|
6
|
Herrera-Carrillo E, Gao Z, Berkhout B. Influence of a 3' Terminal Ribozyme on AgoshRNA Biogenesis and Activity. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:452-462. [PMID: 31048184 PMCID: PMC6488825 DOI: 10.1016/j.omtn.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022]
Abstract
Short hairpin RNAs (shRNAs) can induce gene silencing via the RNA interference (RNAi) mechanism. We designed an alternative shRNA molecule with a relatively short base-paired stem that bypasses Dicer and instead is processed by the Argonaute 2 (Ago2) protein into a single guide RNA strand that effectively induces RNAi. We called these molecules AgoshRNAs. Active anti-HIV AgoshRNAs were developed, but their RNAi activity was generally reduced compared with the matching shRNAs. In an attempt to further optimize the AgoshRNA design, we inserted several self-cleaving ribozymes at the 3′ terminus of the transcribed AgoshRNA and evaluated the impact on AgoshRNA processing and activity. The hepatitis delta virus (HDV) ribozyme is efficiently removed from the transcribed AgoshRNAs and generates a uniform 3′ overhang, which translates into the enhanced antiviral activity of these molecules.
Collapse
Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands.
| |
Collapse
|
7
|
Kaadt E, Alsing S, Cecchi CR, Damgaard CK, Corydon TJ, Aagaard L. Efficient Knockdown and Lack of Passenger Strand Activity by Dicer-Independent shRNAs Expressed from Pol II-Driven MicroRNA Scaffolds. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:318-328. [PMID: 30654192 PMCID: PMC6348697 DOI: 10.1016/j.omtn.2018.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
The expression of short hairpin RNAs (shRNAs) may result in unwanted activity from the co-processed passenger strand. Recent studies have shown that shortening the stem of conventional shRNAs abolishes passenger strand release. These Dicer-independent shRNAs, expressed from RNA polymerase III (Pol III) promoters, rely on Ago2 processing in resemblance to miR-451. Using strand-specific reporters, we tested two designs, and our results support the loss of passenger strand activity. We demonstrate that artificial primary microRNA (pri-miRNA) transcripts, expressed from Pol II promoters, can potently silence a gene of choice. Among six different scaffolds tested, miR-324 and miR-451 were readily re-targeted to direct efficient knockdown from either a CMV or a U1 snRNA promoter. Importantly, the miR-shRNAs have no passenger strand activity and remain active in Dicer-knockout cells. Our vectors are straightforward to design, as we replace the pre-miR-324 or -451 sequences with a Dicer-independent shRNA mimicking miR-451 with unpaired A-C nucleotides at the base. The use of Pol II promoters allows for controlled expression, while the inclusion of pri-miRNA sequences likely requires Drosha processing and, as such, mimics microRNA biogenesis. Since this improved and tunable system bypasses the requirement for Dicer activity and abolishes passenger strand activity completely, it will likely prove favorable in both research and therapeutic applications in terms of versatility and enhanced safety.
Collapse
Affiliation(s)
- Erik Kaadt
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Sidsel Alsing
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Claudia R Cecchi
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Ophthalmology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark.
| |
Collapse
|
8
|
Dallas A, Trotsyuk A, Ilves H, Bonham CA, Rodrigues M, Engel K, Barrera JA, Kosaric N, Stern-Buchbinder ZA, White A, Mandell KJ, Hammond PT, Mansbridge J, Jayasena S, Gurtner GC, Johnston BH. Acceleration of Diabetic Wound Healing with PHD2- and miR-210-Targeting Oligonucleotides. Tissue Eng Part A 2018; 25:44-54. [PMID: 29644938 DOI: 10.1089/ten.tea.2017.0484] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In diabetes-associated chronic wounds, the normal response to hypoxia is impaired and many cellular processes involved in wound healing are hindered. Central to the hypoxia response is hypoxia-inducible factor-1α (HIF-1α), which activates multiple factors that enhance wound healing by promoting cellular motility and proliferation, new vessel formation, and re-epithelialization. Prolyl hydroxylase domain-containing protein 2 (PHD2) regulates HIF-1α activity by targeting it for degradation under normoxia. HIF-1α also upregulates microRNA miR-210, which in turn regulates proteins involved in cell cycle control, DNA repair, and mitochondrial respiration in ways that are antagonistic to wound repair. We have identified a highly potent short synthetic hairpin RNA (sshRNA) that inhibits expression of PHD2 and an antisense oligonucleotide (antimiR) that inhibits miR-210. Both oligonucleotides were chemically modified for improved biostability and to mitigate potential immunostimulatory effects. Using the sshRNA to silence PHD2 transcripts stabilizes HIF-1α and, in combination with the antimiR targeting miR-210, increases proliferation and migration of keratinocytes in vitro. To assess activity and delivery in an impaired wound healing model in diabetic mice, PHD2-targeting sshRNAs and miR-210 antimiRs both alone and in combination were formulated for local delivery to wounds using layer-by-layer (LbL) technology. LbL nanofabrication was applied to incorporate sshRNA into a thin polymer coating on a Tegaderm mesh. This coating gradually degrades under physiological conditions, releasing sshRNA and antimiR for sustained cellular uptake. Formulated treatments were applied directly to splinted full-thickness excisional wounds in db/db mice. Cellular uptake was confirmed using fluorescent sshRNA. Wounds treated with a single application of PHD2 sshRNA or antimiR-210 closed 4 days faster than untreated wounds, and wounds treated with both oligonucleotides closed on average 4.75 days faster. Markers for neovascularization and cell proliferation (CD31 and Ki67, respectively) were increased in the wound area following treatment, and vascular endothelial growth factor (VEGF) was increased in sshRNA-treated wounds. Our results suggest that silencing of PHD2 and miR-210 either together or separately by localized delivery of sshRNAs and antimiRs is a promising approach for the treatment of chronic wounds, with the potential for rapid clinical translation.
Collapse
Affiliation(s)
| | - Artem Trotsyuk
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, California
| | | | - Clark A Bonham
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Melanie Rodrigues
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Karl Engel
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Janos A Barrera
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Nina Kosaric
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, California
| | | | | | | | - Paula T Hammond
- 4 Koch Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | | | - Geoffrey C Gurtner
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, California
| | | |
Collapse
|
9
|
Herrera-Carrillo E, Liu YP, Berkhout B. Improving miRNA Delivery by Optimizing miRNA Expression Cassettes in Diverse Virus Vectors. Hum Gene Ther Methods 2018; 28:177-190. [PMID: 28712309 DOI: 10.1089/hgtb.2017.036] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The RNA interference pathway is an evolutionary conserved post-transcriptional gene regulation mechanism that is exclusively triggered by double-stranded RNA inducers. RNAi-based methods and technologies have facilitated the discovery of many basic science findings and spurred the development of novel RNA therapeutics. Transient induction of RNAi via transfection of synthetic small interfering RNAs can trigger the selective knockdown of a target mRNA. For durable silencing of gene expression, either artificial short hairpin RNA or microRNA encoding transgene constructs were developed. These miRNAs are based on the molecules that induce the natural RNAi pathway in mammals and humans: the endogenously expressed miRNAs. Significant efforts focused on the construction and delivery of miRNA cassettes in order to solve basic biology questions or to design new therapy strategies. Several viral vectors have been developed, which are particularly useful for the delivery of miRNA expression cassettes to specific target cells. Each vector system has its own unique set of distinct properties. Thus, depending on the specific application, a particular vector may be most suitable. This field was previously reviewed for different viral vector systems, and now the recent progress in the field of miRNA-based gene-silencing approaches using lentiviral vectors is reported. The focus is on the unique properties and respective limitations of the available vector systems for miRNA delivery.
Collapse
Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam , Amsterdam, The Netherlands
| | - Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam , Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam , Amsterdam, The Netherlands
| |
Collapse
|
10
|
Herrera-Carrillo E, Harwig A, Berkhout B. Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity. RNA Biol 2017; 14:1559-1569. [PMID: 28569591 PMCID: PMC5785215 DOI: 10.1080/15476286.2017.1328349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are widely used for gene silencing by the RNA interference (RNAi) mechanism. The shRNA precursor is processed by the Dicer enzyme into active small interfering RNAs (siRNAs) that subsequently target a complementary mRNA for cleavage by the Argonaute 2 (Ago2) complex. Recent evidence indicates that shRNAs with a relatively short basepaired stem bypass Dicer and are instead processed by Ago2. We termed these molecules AgoshRNAs as both processing and silencing steps are mediated by Ago2 and proposed rules for the design of effective AgoshRNA molecules. Active and non-cytotoxic AgoshRNAs against HIV-1 RNA were generated, but their silencing activity was generally reduced compared with the matching shRNAs. Thus, further optimization of the AgoshRNA design is needed. In this study, we evaluated the importance of the single-stranded loop, in particular its size and nucleotide sequence, in AgoshRNA-mediated silencing. We document that the pyrimidine/purine content is important for AgoshRNA-mediated silencing activity.
Collapse
Affiliation(s)
- Elena Herrera-Carrillo
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Alex Harwig
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Ben Berkhout
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| |
Collapse
|
11
|
Herrera-Carrillo E, Berkhout B. Dicer-independent processing of small RNA duplexes: mechanistic insights and applications. Nucleic Acids Res 2017; 45:10369-10379. [PMID: 28977573 PMCID: PMC5737282 DOI: 10.1093/nar/gkx779] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages. As an example, we will present the route towards development of a durable gene therapy against HIV-1.
Collapse
Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| |
Collapse
|
12
|
Hagopian JC, Hamil AS, van den Berg A, Meade BR, Eguchi A, Palm-Apergi C, Dowdy SF. Induction of RNAi Responses by Short Left-Handed Hairpin RNAi Triggers. Nucleic Acid Ther 2017; 27:260-271. [PMID: 28933656 DOI: 10.1089/nat.2017.0686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Small double-stranded, left-handed hairpin (LHP) RNAs containing a 5'-guide-loop-passenger-3' structure induce RNAi responses by a poorly understood mechanism. To explore LHPs, we synthesized fully 2'-modified LHP RNAs targeting multiple genes and found all to induce robust RNAi responses. Deletion of the loop and nucleotides at the 5'-end of the equivalent passenger strand resulted in a smaller LHP that still induced strong RNAi responses. Surprisingly, progressive deletion of up to 10 nucleotides from the 3'-end of the guide strand resulted in a 32mer LHP capable of inducing robust RNAi responses. However, further guide strand deletion inhibited LHP activity, thereby defining the minimal length guide targeting length to 13 nucleotides. To dissect LHP processing, we examined LHP species that coimmunoprecipitated with Argonaute 2 (Ago2), the catalytic core of RNA-induced silencing complex, and found that the Ago2-associated processed LHP species was of a length that correlated with Ago2 cleavage of the passenger strand. Placement of a blocking 2'-OMe blocking modification at the LHP predicted Ago2 cleavage site resulted in an intact LHP loaded into Ago2 and no RNAi response. Taken together, these data argue that in the absence of a substantial loop, this novel class of small LHP RNAs enters the RNAi pathway by a Dicer-independent mechanism that involves Ago2 cleavage and results in an extended guide strand. This work establishes LHPs as an alternative RNAi trigger that can be produced from a single synthesis for potential use as an RNAi therapeutic.
Collapse
Affiliation(s)
- Jonathan C Hagopian
- Department of Cellular and Molecular Medicine, UCSD School of Medicine , La Jolla, California
| | - Alexander S Hamil
- Department of Cellular and Molecular Medicine, UCSD School of Medicine , La Jolla, California
| | - Arjen van den Berg
- Department of Cellular and Molecular Medicine, UCSD School of Medicine , La Jolla, California
| | - Bryan R Meade
- Department of Cellular and Molecular Medicine, UCSD School of Medicine , La Jolla, California
| | - Akiko Eguchi
- Department of Cellular and Molecular Medicine, UCSD School of Medicine , La Jolla, California
| | - Caroline Palm-Apergi
- Department of Cellular and Molecular Medicine, UCSD School of Medicine , La Jolla, California
| | - Steven F Dowdy
- Department of Cellular and Molecular Medicine, UCSD School of Medicine , La Jolla, California
| |
Collapse
|
13
|
Herrera-Carrillo E, Gao ZL, Harwig A, Heemskerk MT, Berkhout B. The influence of the 5΄-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site. Nucleic Acids Res 2017; 45:4036-4050. [PMID: 27928054 PMCID: PMC5397164 DOI: 10.1093/nar/gkw1203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
Recent evidence indicates that shRNAs with a relatively short basepaired stem do not require Dicer processing, but instead are processed by the Argonaute 2 protein (Ago2). We named these molecules AgoshRNAs as both their processing and silencing function are mediated by Ago2. This alternative processing yields only a single RNA guide strand, which can avoid off-target effects induced by the passenger strand of regular shRNAs. It is important to understand this alternative processing route in mechanistic detail such that one can design improved RNA reagents. We verified that AgoshRNAs trigger site-specific cleavage of a complementary mRNA. Second, we document the importance of the identity of the 5΄-terminal nucleotide and its basepairing status for AgoshRNA activity. AgoshRNA activity is significantly reduced or even abrogated with C or U at the 5΄-terminal and is enhanced by introduction of a bottom mismatch and 5΄-terminal nucleotide A or G. The 5΄-terminal RNA nucleotide also represents the +1 position of the transcriptional promoter in the DNA, thus further complicating the analysis. Indeed, we report that +1 modification affects the transcriptional efficiency and accuracy of start site selection, with A or G as optimal nucleotide. These combined results allow us to propose general rules for the design and expression of potent AgoshRNA molecules.
Collapse
Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Zong-Liang Gao
- 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
| | - Alex Harwig
- 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
| | - Matthias T Heemskerk
- 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
| | - 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
| |
Collapse
|
14
|
Herrera-Carrillo E, Harwig A, Berkhout B. Silencing of HIV-1 by AgoshRNA molecules. Gene Ther 2017; 24:453-461. [DOI: 10.1038/gt.2017.44] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/13/2017] [Accepted: 05/12/2017] [Indexed: 12/17/2022]
|
15
|
Cambon K, Zimmer V, Martineau S, Gaillard MC, Jarrige M, Bugi A, Miniarikova J, Rey M, Hassig R, Dufour N, Auregan G, Hantraye P, Perrier AL, Déglon N. Preclinical Evaluation of a Lentiviral Vector for Huntingtin Silencing. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 5:259-276. [PMID: 28603746 PMCID: PMC5453866 DOI: 10.1016/j.omtm.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/07/2017] [Indexed: 01/12/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder resulting from a polyglutamine expansion in the huntingtin (HTT) protein. There is currently no cure for this disease, but recent studies suggest that RNAi to downregulate the expression of both normal and mutant HTT is a promising therapeutic approach. We previously developed a small hairpin RNA (shRNA), vectorized in an HIV-1-derived lentiviral vector (LV), that reduced pathology in an HD rodent model. Here, we modified this vector for preclinical development by using a tat-independent third-generation LV (pCCL) backbone and removing the original reporter genes. We demonstrate that this novel vector efficiently downregulated HTT expression in vitro in striatal neurons derived from induced pluripotent stem cells (iPSCs) of HD patients. It reduced two major pathological HD hallmarks while triggering a minimal inflammatory response, up to 6 weeks after injection, when administered by stereotaxic surgery in the striatum of an in vivo rodent HD model. Further assessment of this shRNA vector in vitro showed proper processing by the endogenous silencing machinery, and we analyzed gene expression changes to identify potential off-targets. These preclinical data suggest that this new shRNA vector fulfills primary biosafety and efficiency requirements for further development in the clinic as a cure for HD.
Collapse
Affiliation(s)
- Karine Cambon
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Virginie Zimmer
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Sylvain Martineau
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Marie-Claude Gaillard
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Margot Jarrige
- Institut National de la Santé et de la Recherche Médicale UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
- UEVE UMR861, I-STEM, AFM, 91100 Corbeil-Essonnes, France
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Aurore Bugi
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Jana Miniarikova
- Department of Research & Development, uniQure, 1105 Amsterdam, the Netherlands
| | - Maria Rey
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Raymonde Hassig
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Noelle Dufour
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Gwenaelle Auregan
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Anselme L. Perrier
- Institut National de la Santé et de la Recherche Médicale UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
- UEVE UMR861, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Nicole Déglon
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Corresponding author: Nicole Déglon, Lausanne University Hospital (CHUV), Laboratory of Cellular and Molecular Neurotherapies (LNCM), Pavillon 3, Avenue de Beaumont, 1011 Lausanne, Switzerland.
| |
Collapse
|
16
|
Ohno SI, Itano K, Harada Y, Asada K, Oikawa K, Kashiwazako M, Okuyama H, Kumagai K, Takanashi M, Sudo K, Ikeda N, Kuroda M. Development of Novel Small Hairpin RNAs That do not Require Processing by Dicer or AGO2. Mol Ther 2016; 24:1278-89. [PMID: 27109632 PMCID: PMC5088761 DOI: 10.1038/mt.2016.81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/04/2016] [Indexed: 01/08/2023] Open
Abstract
The innate cytokine response to nucleic acid is the most challenging problem confronting the practical use of nucleic acid medicine. The degree of stimulation of the innate cytokine response strongly depends on the length of the nucleic acid. In this study, we developed a 30-nucleotide single-strand RNA, termed "guide hairpin RNA (ghRNA, ghR)", that has a physiological function similar to that of miRNA and siRNA. The ghR caused no innate cytokine response either in vitro or in vivo. In addition, its structure does not contain a passenger strand seed sequence, reducing the unwanted gene repression relative to existing short RNA reagents. Systemic and local injection of ghR-form miR-34a (ghR-34a) suppressed tumor growth in a mouse model of RAS-induced lung cancer. Furthermore, Dicer and AGO2 are not required for ghR-34a function. This novel RNA interference (RNAi) technology may provide a novel, safe, and effective nucleic acid drug platform that will increase the clinical usefulness of nucleic acid therapy.
Collapse
Affiliation(s)
- Shin-ichiro Ohno
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Karen Itano
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Yuichirou Harada
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Koutaro Asada
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Keiki Oikawa
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Mikie Kashiwazako
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Hikaru Okuyama
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Katsuyoshi Kumagai
- Department of Animal Research Center,
Tokyo Medical University, Tokyo, Japan
| | | | - Katsuko Sudo
- Department of Animal Research Center,
Tokyo Medical University, Tokyo, Japan
| | - Norihiko Ikeda
- Department of Respiratory Surgery,
Tokyo Medical University, Tokyo, Japan
| | - Masahiko Kuroda
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| |
Collapse
|
17
|
Herrera-Carrillo E, Harwig A, Berkhout B. Toward optimization of AgoshRNA molecules that use a non-canonical RNAi pathway: variations in the top and bottom base pairs. RNA Biol 2016; 12:447-56. [PMID: 25747107 DOI: 10.1080/15476286.2015.1022024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are widely used for gene knockdown by inducing the RNA interference (RNAi) mechanism. The shRNA precursor is processed by Dicer into small interfering RNAs (siRNAs) and subsequently programs the RNAi-induced silencing complex (RISC) to find a complementary target mRNA (mRNA) for post-transcriptional gene silencing. Recent evidence indicates that shRNAs with a relatively short basepaired stem bypass Dicer to be processed directly by the Ago2 nuclease of the RISC complex. We named this design AgoshRNA as these molecules depend on Ago2 both for processing and subsequent silencing activity. This alternative AgoshRNA processing route yields only a single active RNA strand, an important feature to restrict off-target effects induced by the passenger strand of regular shRNAs. It is therefore important to understand this novel AgoshRNA processing route in mechanistic detail such that one can design the most effective and selective RNA reagents. We performed a systematic analysis of the optimal base pair (bp) composition at the top and bottom of AgoshRNA molecules. In this study, we document the importance of the 5' end nucleotide (nt) and a bottom mismatch. The optimized AgoshRNA design exhibits improved RNAi activity across cell types. These results have important implications for the future design of more specific RNAi therapeutics.
Collapse
Affiliation(s)
- Elena Herrera-Carrillo
- a Laboratory of Experimental Virology; Department of Medical Microbiology; Center for Infection and Immunity Amsterdam (CINIMA); Academic Medical Center ; University of Amsterdam ; Amsterdam , The Netherlands
| | | | | |
Collapse
|
18
|
He J, Huang L, Qiu H, Li J, Luo L, Li Y, Tian S, Kang K, Luo J, Liu L, Gou D. A new design of a lentiviral shRNA vector with inducible co-expression of ARGONAUTE 2 for enhancing gene silencing efficiency. Cell Biosci 2015; 5:67. [PMID: 26649169 PMCID: PMC4672530 DOI: 10.1186/s13578-015-0058-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/19/2015] [Indexed: 12/13/2022] Open
Abstract
Background RNA interference (RNAi) is a robust tool for inhibiting specific gene expression, but it is limited by the uncertain efficiency of siRNA or shRNA constructs. It has been shown that the overexpression of ARGONAUTE 2 (AGO2) protein increases silencing efficiency. However, the key elements required for AGO2-mediated enhancement of gene silencing in lentiviral vector has not been well studied. Results To explore the application of AGO2-based shRNA system in mammalian cells, we designed shRNA vectors targeting the EGFP reporter gene and evaluated the effects of various factors on silencing efficiency including stem length, loop sequence, antisense location as well as the ratio between AGO2 and shRNA. We found that 19 ~ 21-bp stem and 6- or 9-nt loop structure in the sense-loop-antisense (S-L-AS) orientation was an optimal design in the AGO2-shRNA system. Then, we constructed a single lentiviral vector co-expressing shRNA and AGO2 and demonstrated that the simultaneous expression of shRNA and AGO2 can achieve robust silencing of exogenous DsRed2 and endogenous ID1 and P65 genes. However, the titers of packaged lentivirus from constitutive expression of AGO2 vector were extremely low, severely limiting its broad application. For the first time, we demonstrated that the problem can be significantly improved by using the inducible expression of AGO2 lentiviral system. Conclusions We reported a novel lentiviral vector with an optimal design of shRNA and inducible AGO2 overexpression which provides a new tool for RNAi research.
Collapse
Affiliation(s)
- Jiening He
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Lian Huang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Huiling Qiu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Jiexuan Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Lan Luo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Yanjiao Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Shengli Tian
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Kang Kang
- Department of Physiology, Shenzhen University Health Science Center, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Jun Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Lin Liu
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078 USA
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| |
Collapse
|
19
|
Shang R, Zhang F, Xu B, Xi H, Zhang X, Wang W, Wu L. Ribozyme-enhanced single-stranded Ago2-processed interfering RNA triggers efficient gene silencing with fewer off-target effects. Nat Commun 2015; 6:8430. [PMID: 26455506 PMCID: PMC4633630 DOI: 10.1038/ncomms9430] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 08/21/2015] [Indexed: 02/06/2023] Open
Abstract
Short-hairpin RNAs (shRNAs) are widely used to produce small-interfering RNAs (siRNAs) for gene silencing. Here we design an alternative siRNA precursor, named single-stranded, Argonaute 2 (Ago2)-processed interfering RNA (saiRNA), containing a 16-18 bp stem and a loop complementary to the target transcript. The introduction of a self-cleaving ribozyme derived from hepatitis delta virus to the 3' end of the transcribed saiRNA dramatically improves its silencing activity by generating a short 3' overhang that facilitates the efficient binding of saiRNA to Ago2. The same ribozyme also enhances the activity of Dicer-dependent shRNAs. Unlike a classical shRNA, the strand-specific cleavage of saiRNA by Ago2 during processing eliminates the passenger strand and prevents the association of siRNA with non-nucleolytic Ago proteins. As a result, off-target effects are reduced. In addition, saiRNA exhibits less competition with the biogenesis of endogenous miRNAs. Therefore, ribozyme-enhanced saiRNA provides a reliable tool for RNA interference applications.
Collapse
Affiliation(s)
- Renfu Shang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.,Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fengjuan Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.,Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Beiying Xu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.,Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hairui Xi
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xue Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.,Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Weihua Wang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.,Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ligang Wu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.,Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
20
|
Deep Sequence Analysis of AgoshRNA Processing Reveals 3' A Addition and Trimming. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e247. [PMID: 26172504 PMCID: PMC4561654 DOI: 10.1038/mtna.2015.19] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/06/2015] [Indexed: 11/11/2022]
Abstract
The RNA interference (RNAi) pathway, in which microprocessor and Dicer collaborate to process microRNAs (miRNA), was recently expanded by the description of alternative processing routes. In one of these noncanonical pathways, Dicer action is replaced by the Argonaute2 (Ago2) slicer function. It was recently shown that the stem-length of precursor-miRNA or short hairpin RNA (shRNA) molecules is a major determinant for Dicer versus Ago2 processing. Here we present the results of a deep sequence study on the processing of shRNAs with different stem length and a top G·U wobble base pair (bp). This analysis revealed some unexpected properties of these so-called AgoshRNA molecules that are processed by Ago2 instead of Dicer. First, we confirmed the gradual shift from Dicer to Ago2 processing upon shortening of the hairpin length. Second, hairpins with a stem larger than 19 base pair are inefficiently cleaved by Ago2 and we noticed a shift in the cleavage site. Third, the introduction of a top G·U bp in a regular shRNA can promote Ago2-cleavage, which coincides with a loss of Ago2-loading of the Dicer-cleaved 3' strand. Fourth, the Ago2-processed AgoshRNAs acquire a short 3' tail of 1–3 A-nucleotides (nt) and we present evidence that this product is subsequently trimmed by the poly(A)-specific ribonuclease (PARN).
Collapse
|
21
|
Alleviation of off-target effects from vector-encoded shRNAs via codelivered RNA decoys. Proc Natl Acad Sci U S A 2015; 112:E4007-16. [PMID: 26170322 DOI: 10.1073/pnas.1510476112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Exogenous RNAi triggers such as shRNAs ideally exert their activities exclusively via the antisense strand that binds and silences designated target mRNAs. However, in principle, the sense strand also possesses silencing capacity that may contribute to adverse RNAi side effects including off-target gene regulation. Here, we address this concern with a novel strategy that reduces sense strand activity of vector-encoded shRNAs via codelivery of inhibitory tough decoy (TuD) RNAs. Using various shRNAs for proof of concept, we validate that coexpression of TuDs can sequester and inactivate shRNA sense strands in human cells selectively without affecting desired antisense activities from the same shRNAs. Moreover, we show how coexpressed TuDs can alleviate shRNA-mediated perturbation of global gene expression by specifically de-repressing off-target transcripts carrying seed matches to the shRNA sense strand. Our combination of shRNA and TuD in a single bicistronic gene transfer vector derived from Adeno-associated virus (AAV) enables a wide range of applications, including gene therapies. To this end, we engineered our constructs in a modular fashion and identified simple hairpin design rules permitting adaptation to preexisting or new shRNAs. Finally, we demonstrate the power of our vectors for combinatorial RNAi strategies by showing robust suppression of hepatitis C virus (HCV) with an AAV expressing a bifunctional TuD against an anti-HCV shRNA sense strand and an HCV-related cellular miRNA. The data and tools reported here represent an important step toward the next generation of RNAi triggers with increased specificity and thus ultimately safety in humans.
Collapse
|
22
|
Liu YP, Karg M, Herrera-Carrillo E, Berkhout B. Towards Antiviral shRNAs Based on the AgoshRNA Design. PLoS One 2015; 10:e0128618. [PMID: 26087209 PMCID: PMC4472832 DOI: 10.1371/journal.pone.0128618] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022] Open
Abstract
RNA interference (RNAi) can be induced by intracellular expression of a short hairpin RNA (shRNA). Processing of the shRNA requires the RNaseIII-like Dicer enzyme to remove the loop and to release the biologically active small interfering RNA (siRNA). Dicer is also involved in microRNA (miRNA) processing to liberate the mature miRNA duplex, but recent studies indicate that miR-451 is not processed by Dicer. Instead, this miRNA is processed by the Argonaute 2 (Ago2) protein, which also executes the subsequent cleavage of a complementary mRNA target. Interestingly, shRNAs that structurally resemble miR-451 can also be processed by Ago2 instead of Dicer. The key determinant of these "AgoshRNA" molecules is a relatively short basepaired stem, which avoids Dicer recognition and consequently allows alternative processing by Ago2. AgoshRNA processing yields a single active RNA strand, whereas standard shRNAs produce a duplex with guide and passenger strands and the latter may cause adverse off-target effects. In this study, we converted previously tested active anti-HIV-1 shRNA molecules into AgoshRNA. We tested several designs that could potentially improve AgoshRNA activity, including extension of the complementarity between the guide strand and the mRNA target and reduction of the thermodynamic stability of the hairpins. We demonstrate that active AgoshRNAs can be generated. However, the RNAi activity is reduced compared to the matching shRNAs. Despite reduced RNAi activity, comparison of an active AgoshRNA and the matching shRNA in a sensitive cell toxicity assay revealed that the AgoshRNA is much less toxic.
Collapse
Affiliation(s)
- Ying Poi Liu
- 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
| | - Margarete Karg
- 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
| | - Elena Herrera-Carrillo
- 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
| | - 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
- * E-mail:
| |
Collapse
|
23
|
Sun G, Yeh SY, Yuan CWY, Chiu MJY, Yung BSH, Yen Y. Molecular Properties, Functional Mechanisms, and Applications of Sliced siRNA. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e221. [PMID: 25602583 PMCID: PMC4345305 DOI: 10.1038/mtna.2014.73] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/06/2014] [Indexed: 11/09/2022]
Abstract
Using pre-miR-451 as a model molecule, we have characterized the general molecular properties of small hairpin RNAs that are processed into potent small interfering RNAs (siRNA) by Argonaute2 (Ago2). The Ago2-sliced siRNAs (sli-siRNAs) have the same silencing potency as the classical Dicer diced siRNAs (di-siRNAs) but have dramatically reduced unwanted sense strand activities. We have built vectors with the constitutive or inducible U6 promoter that can express sli-siRNAs in mammalian cells, in which the sli-siRNAs can be correctly processed to repress target genes. As a proof of principle for potential applications of sli-siRNAs in vivo, we show that the expression of one Ago2 shRNA-1148 in HCT-116 colon cancer cells knocked down RRM2 expression and reduced the proliferation and invasiveness of the cells. The defined sli-siRNA model molecules and the expression systems established in this study will facilitate the design and application of sli-siRNAs as novel potent RNAi triggers with reduced off-target effects.
Collapse
Affiliation(s)
- Guihua Sun
- Department of Molecular Pharmacology, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Spencer Yele Yeh
- Summer Interns, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | | | - Bryan Shing Hei Yung
- Summer Interns, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Yun Yen
- Department of Molecular Pharmacology, Beckman Research Institute of the City of Hope, Duarte, California, USA
| |
Collapse
|
24
|
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.
Collapse
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
| | | |
Collapse
|
25
|
Maruyama H, Nakashima Y, Shuto S, Matsuda A, Ito Y, Abe H. An intracellular buildup reaction of active siRNA species from short RNA fragments. Chem Commun (Camb) 2014; 50:1284-7. [PMID: 24365776 DOI: 10.1039/c3cc47529h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here we report a new strategy for the buildup reaction of active siRNA species from short RNA fragments in living cells using a chemical ligation reaction. This strategy could decrease undesired immune responses and provide more latitude for RNAi technology in the design and concentration of introduced RNA compared to traditional siRNA methods.
Collapse
Affiliation(s)
- Hideto Maruyama
- Nano Medical Engineering Laboratory, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan.
| | | | | | | | | | | |
Collapse
|
26
|
Herrera-Carrillo E, Harwig A, Liu YP, Berkhout B. Probing the shRNA characteristics that hinder Dicer recognition and consequently allow Ago-mediated processing and AgoshRNA activity. RNA (NEW YORK, N.Y.) 2014; 20:1410-8. [PMID: 25035295 PMCID: PMC4138324 DOI: 10.1261/rna.043950.113] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/22/2014] [Indexed: 06/03/2023]
Abstract
Recent evidence indicates the presence of alternative pathways for microRNA (miRNA) and short hairpin (shRNA) processing. Specifically, some of these molecules are refractory to Dicer-mediated processing, which allows alternative processing routes via the Ago2 endonuclease. The resulting RNA molecules differ in size and sequence and will thus trigger the silencing of different target RNAs. It is, therefore, important to understand these processing routes in mechanistic detail such that one can design exclusive RNA reagents for a specific processing route. The exact sh/miRNA properties that determine this routing toward Dicer or Ago2 are incompletely understood. The size of the base-paired stem seems an important determinant, but other RNA elements may contribute as well. In this study, we document the importance of a weak G-U or U-G base pair at the top of the hairpin stem.
Collapse
Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| |
Collapse
|
27
|
Designing Ago2-specific siRNA/shRNA to Avoid Competition with Endogenous miRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e176. [PMID: 25025466 PMCID: PMC4121517 DOI: 10.1038/mtna.2014.27] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 05/23/2014] [Indexed: 12/22/2022]
Abstract
Relatively large amounts of transfected siRNA can compete for Ago proteins and thus compromise endogenous miRNA function, potentially leading to toxicities. Here, we show that shRNA can also perturb endogenous miRNA function similarly. More importantly, we also show that the problem can be solved by designing shRNAs in the context of pre-miR-451 structure with completely complementary stem, which significantly improves the Ago2 specificity. This shRNA was shown to be Ago2-specific, and maintain target-silencing ability while avoiding competition with endogenous miRNAs by not competing for Agos 1, 3, and 4. We conclude that modified pre-miR-451 structure provides a general platform to design shRNAs that significantly reduce perturbation of miRNA function.
Collapse
|
28
|
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: 2.3] [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.
Collapse
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
| |
Collapse
|
29
|
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: 1.0] [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.
Collapse
|
30
|
Ma H, Dallas A, Ilves H, Shorenstein J, MacLachlan I, Klumpp K, Johnston BH. Formulated minimal-length synthetic small hairpin RNAs are potent inhibitors of hepatitis C virus in mice with humanized livers. Gastroenterology 2014; 146:63-6.e5. [PMID: 24076507 PMCID: PMC3896324 DOI: 10.1053/j.gastro.2013.09.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/16/2013] [Accepted: 09/22/2013] [Indexed: 12/02/2022]
Abstract
Short synthetic hairpin RNAs (sshRNAs) (SG220 and SG273) that target the internal ribosome entry site of the hepatitis C virus (HCV) were formulated into lipid nanoparticles and administered intravenously to HCV-infected urokinase plasminogen activator-severe combined immunodeficient mice with livers repopulated with human hepatocytes (humanized livers). Weekly administration of 2.5 mg/kg of each sshRNA for 2 weeks resulted in a maximal mean reduction in viral load of 2.5 log10 from baseline. The viral load remained reduced by more than 90% at 14 days after the last dose was given. The sshRNAs were well tolerated and did not significantly increase liver enzyme levels. These findings indicate the in vivo efficacy of a synthetic RNA inhibitor against the HCV genome in reducing HCV infection.
Collapse
Affiliation(s)
- Han Ma
- Hoffmann-La Roche, Nutley, New Jersey
| | | | | | | | - Ian MacLachlan
- Tekmira Pharmaceuticals, Burnaby, British Columbia, Canada
| | | | | |
Collapse
|
31
|
Human RNAi pathway: crosstalk with organelles and cells. Funct Integr Genomics 2013; 14:31-46. [PMID: 24197738 DOI: 10.1007/s10142-013-0344-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 12/12/2022]
Abstract
Understanding gene regulation mechanisms has been a serious challenge in biology. As a novel mechanism, small non-coding RNAs are an alternative means of gene regulation in a specific and efficient manner. There are growing reports on regulatory roles of these RNAs including transcriptional gene silencing/activation and post-transcriptional gene silencing events. Also, there are several known small non-coding RNAs which all work through RNA interference pathway. Interestingly, these small RNAs are secreted from cells toward targeted cells presenting new communication approach in cell-cell or cell-organ signal transduction. In fact, understanding cellular and molecular basis of these pathways will strongly improve developing targeted therapies and potent and specific regulatory tools. This study will review some of the most recent findings in this subject and will introduce a super-pathway RNA interference-based small RNA silencing network.
Collapse
|
32
|
Ramos J, Rege K. Poly(aminoether)-gold nanorod assemblies for shRNA plasmid-induced gene silencing. Mol Pharm 2013; 10:4107-19. [PMID: 24066795 DOI: 10.1021/mp400080f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gold nanorods (GNRs) have emerged as promising nanomaterials for biosensing, imaging, photothermal hyperthermia treatments, and therapeutic delivery for several diseases. We generated poly(aminoether)-GNR nanoassemblies using a layer-by-layer deposition approach based on the 1,4C-1,4Bis polymer from a library recently synthesized in our laboratory. Subtoxic concentrations of 1,4C-1,4Bis-GNR nanoassemblies were employed to deliver expression vectors that express shRNA ("shRNA plasmid") against firefly luciferase gene to knock down expression of the protein constitutively expressed in prostate cancer cells. The role of hydrodynamic size and zeta potential in determining nanoassembly mediated luciferase silencing was investigated. Finally, the theranostic potential of 1,4C-1,4Bis-GNR nanoassemblies was demonstrated using live cell two-photon induced luminescence bioimaging. Our results indicate that poly(aminoether)-GNR nanoassemblies are a promising theranostic platform for delivery of therapeutic payloads capable of simultaneous gene silencing and bioimaging.
Collapse
Affiliation(s)
- James Ramos
- Biomedical Engineering, School of Biological and Health Systems Engineering and ‡Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University , 501 E. Tyler Mall, ECG 303, Tempe, Arizona 85287-6106, United States
| | | |
Collapse
|
33
|
Dallas A, Ilves H, Shorenstein J, Judge A, Spitler R, Contag C, Wong SP, Harbottle RP, Maclachlan I, Johnston BH. Minimal-length Synthetic shRNAs Formulated with Lipid Nanoparticles are Potent Inhibitors of Hepatitis C Virus IRES-linked Gene Expression in Mice. MOLECULAR THERAPY-NUCLEIC ACIDS 2013; 2:e123. [PMID: 24045712 PMCID: PMC4028017 DOI: 10.1038/mtna.2013.50] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/08/2013] [Indexed: 12/19/2022]
Abstract
We previously identified short synthetic shRNAs (sshRNAs) that target a conserved hepatitis C virus (HCV) sequence within the internal ribosome entry site (IRES) of HCV and potently inhibit HCV IRES-linked gene expression. To assess in vivo liver delivery and activity, the HCV-directed sshRNA SG220 was formulated into lipid nanoparticles (LNP) and injected i.v. into mice whose livers supported stable HCV IRES-luciferase expression from a liver-specific promoter. After a single injection, RNase protection assays for the sshRNA and 3H labeling of a lipid component of the nanoparticles showed efficient liver uptake of both components and long-lasting survival of a significant fraction of the sshRNA in the liver. In vivo imaging showed a dose-dependent inhibition of luciferase expression (>90% 1 day after injection of 2.5 mg/kg sshRNA) with t1/2 for recovery of about 3 weeks. These results demonstrate the ability of moderate levels of i.v.-injected, LNP-formulated sshRNAs to be taken up by liver hepatocytes at a level sufficient to substantially suppress gene expression. Suppression is rapid and durable, suggesting that sshRNAs may have promise as therapeutic agents for liver indications.
Collapse
Affiliation(s)
- Anne Dallas
- SomaGenics, Inc., 2161 Delaware Ave., Santa Cruz, California, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Snead NM, Wu X, Li A, Cui Q, Sakurai K, Burnett JC, Rossi JJ. Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants. Nucleic Acids Res 2013; 41:6209-21. [PMID: 23620279 PMCID: PMC3695504 DOI: 10.1093/nar/gkt200] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The canonical exogenous trigger of RNA interference (RNAi) in mammals is small interfering RNA (siRNA). One promising application of RNAi is siRNA-based therapeutics, and therefore the optimization of siRNA efficacy is an important consideration. To reduce unfavorable properties of canonical 21mer siRNAs, structural and chemical variations to canonical siRNA have been reported. Several of these siRNA variants demonstrate increased potency in downstream readout-based assays, but the molecular mechanism underlying the increased potency is not clear. Here, we tested the performance of canonical siRNAs and several sequence-matched variants in parallel in gene silencing, RNA-induced silencing complex (RISC) assembly, stability and Argonaute (Ago) loading assays. The commonly used 19mer with two deoxythymidine overhangs (19merTT) variant performed similarly to canonical 21mer siRNA. A shorter 16mer variant (16merTT) did not perform comparably in our assays. Dicer substrate interfering RNA (dsiRNA) demonstrated better gene silencing by the guide strand (target complementary strand), better RISC assembly, persistence of the guide strand and relatively more loading of the guide strand into Ago. Hence, we demonstrate the advantageous properties of dsiRNAs at upstream, intermediate and downstream molecular steps of the RNAi pathway.
Collapse
Affiliation(s)
- Nicholas M Snead
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | | | | | | | | | | | | |
Collapse
|
35
|
Liu YP, Schopman NCT, Berkhout B. Dicer-independent processing of short hairpin RNAs. Nucleic Acids Res 2013; 41:3723-33. [PMID: 23376931 PMCID: PMC3616727 DOI: 10.1093/nar/gkt036] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/11/2012] [Accepted: 01/07/2013] [Indexed: 12/11/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are widely used to induce RNA interference (RNAi). We tested a variety of shRNAs that differed in stem length and terminal loop size and revealed strikingly different RNAi activities and shRNA-processing patterns. Interestingly, we identified a specific shRNA design that uses an alternative Dicer-independent processing pathway. Detailed analyses indicated that a short shRNA stem length is critical for avoiding Dicer processing and activation of the alternative processing route, in which the shRNA is incorporated into RISC and processed by the AGO2-mediated slicer activity. Such alternatively processed shRNAs (AgoshRNAs) yield only a single RNA strand that effectively induces RNAi, whereas conventional shRNA processing results in an siRNA duplex of which both strands can trigger RNAi. Both the processing and subsequent RNAi activity of these AgoshRNAs are thus mediated by the RISC-component AGO2. These results have important implications for the future design of more specific RNAi therapeutics.
Collapse
Affiliation(s)
| | | | - Ben Berkhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| |
Collapse
|
36
|
Design and chemical modification of synthetic short shRNAs as potent RNAi triggers. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 942:279-90. [PMID: 23027057 DOI: 10.1007/978-1-62703-119-6_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Synthetic shRNAs that are too short to be Dicer substrates (short shRNAs or sshRNAs) can be highly potent RNAi effectors when properly designed, with activities similar to or more potent than the more commonly used siRNAs targeting the same sequences. sshRNAs can be designed in two possible orientations: left- or right-hand loop, designated L-sshRNAs and R-sshRNAs, respectively. Because L- and R-sshRNAs are processed by the RNAi machinery in different ways, optimal designs for the two formats diverge in several key aspects. Here, we describe the principles of design and chemical modification of highly effective L- and R-sshRNAs.
Collapse
|
37
|
Johnston BH, Ge Q. Design of Synthetic shRNAs for Targeting Hepatitis C: A New Approach to Antiviral Therapeutics. FROM NUCLEIC ACIDS SEQUENCES TO MOLECULAR MEDICINE 2012. [PMCID: PMC7138429 DOI: 10.1007/978-3-642-27426-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Small hairpin RNAs (shRNAs) are widely used as gene silencing tools and typically consist of a duplex stem of 19–29 bp, a loop, and often a dinucleotide overhang at the 3′ end. Like siRNAs, shRNAs show promise as potential therapeutic agents due to their high level of specificity and potency, although effective delivery to target tissues remains a challenge. Algorithms used to predict siRNA performance are frequently used to design shRNAs as well. However, the differences between these two kinds of RNAi mediators indicate that the factors affecting target gene silencing will not be the same for siRNAs and shRNAs. Stem and loop lengths, structures of the termini, the identity of nucleotides adjacent to and near the loop, and the position of the guide (antisense) strand all affect the efficacy of shRNAs. In addition, shRNAs with 19-bp or shorter stem lengths are processed and function differently than those with longer stems. In this review, we describe studies of targeting the hepatitis C virus that have provided guidelines for an optimal design for short (19 bp) shRNAs (sshRNAs) that are highly potent, stable in biological fluids, and have minimal immunostimulatory properties.
Collapse
|