1
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Haldrup SH, Fabian-Jessing BK, Jakobsen TS, Lindholm AB, Adsersen RL, Aagaard L, Bek T, Askou AL, Corydon TJ. Subretinal AAV delivery of RNAi-therapeutics targeting VEGFA reduces choroidal neovascularization in a large animal model. Mol Ther Methods Clin Dev 2024; 32:101242. [PMID: 38605811 PMCID: PMC11007540 DOI: 10.1016/j.omtm.2024.101242] [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: 10/11/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024]
Abstract
Neovascular age-related macular degeneration (nAMD) is a frequent cause of vision loss among the elderly in the Western world. Current disease management with repeated injections of anti-VEGF agents accumulates the risk for adverse events and constitutes a burden for society and the individual patient. Sustained suppression of VEGF using gene therapy is an attractive alternative, which we explored using adeno-associated virus (AAV)-based delivery of novel RNA interference (RNAi) effectors in a porcine model of choroidal neovascularization (CNV). The potency of VEGFA-targeting, Ago2-dependent short hairpin RNAs placed in pri-microRNA scaffolds (miR-agshRNA) was established in vitro and in vivo in mice. Subsequently, AAV serotype 8 (AAV2.8) vectors encoding VEGFA-targeting or irrelevant miR-agshRNAs under the control of a tissue-specific promotor were delivered to the porcine retina via subretinal injection before CNV induction by laser. Notably, VEGFA-targeting miR-agshRNAs resulted in a significant and sizable reduction of CNV compared with the non-targeting control. We also demonstrated that single-stranded and self-complementary AAV2.8 vectors efficiently transduce porcine retinal pigment epithelium cells but differ in their transduction characteristics and retinal safety. Collectively, our data demonstrated a robust anti-angiogenic effect of VEGFA-targeting miR-aghsRNAs in a large translational animal model, thereby suggesting AAV-based delivery of anti-VEGFA RNAi therapeutics as a valuable tool for the management of nAMD.
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Affiliation(s)
- Silja Hansen Haldrup
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Bjørn K. Fabian-Jessing
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Thomas Stax Jakobsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Anna Bøgh Lindholm
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Rikke L. Adsersen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Toke Bek
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Anne Louise Askou
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Thomas J. Corydon
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
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2
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Bie Y, Zhang J, Chen J, Zhang Y, Huang M, Zhang L, Zhou X, Qiu Y. Design of antiviral AGO2-dependent short hairpin RNAs. Virol Sin 2024:S1995-820X(24)00069-5. [PMID: 38734183 DOI: 10.1016/j.virs.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024] Open
Abstract
The increasing emergence and re-emergence of RNA virus outbreaks underlines the urgent need to develop effective antivirals. RNA interference (RNAi) is a sequence-specific gene silencing mechanism that is triggered by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), which exhibits significant promise for antiviral therapy. AGO2-dependent shRNA (agshRNA) generates a single-stranded guide RNA and presents significant advantages over traditional siRNA and shRNA. In this study, we applied a logistic regression algorithm to a previously published chemically siRNA efficacy dataset and built a machine learning-based model with high predictive power. Using this model, we designed siRNA sequences targeting diverse RNA viruses, including human enterovirus A71 (EV71), Zika virus (ZIKV), dengue virus 2 (DENV2), mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and transformed them into agshRNAs. We validated the performance of our agshRNA design by evaluating antiviral efficacies of agshRNAs in cells infected with different viruses. Using the agshRNA targeting EV71 as an example, we showed that the anti-EV71 effect of agshRNA was more potent compared with the corresponding siRNA and shRNA. Moreover, the antiviral effect of agshRNA is dependent on AGO2-processed guide RNA, which can load into the RNA-induced silencing complex (RISC). We also confirmed the antiviral effect of agshRNA in vivo. Together, this work develops a novel antiviral strategy that combines machine learning-based algorithm with agshRNA design to custom design antiviral agshRNAs with high efficiency.
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Affiliation(s)
- Yuanyuan Bie
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jieling Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiyao Chen
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yumin Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Muhan Huang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Leike Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Zhou
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Yang Qiu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
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3
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Shang R, Lee S, Senavirathne G, Lai EC. microRNAs in action: biogenesis, function and regulation. Nat Rev Genet 2023; 24:816-833. [PMID: 37380761 PMCID: PMC11087887 DOI: 10.1038/s41576-023-00611-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/30/2023]
Abstract
Ever since microRNAs (miRNAs) were first recognized as an extensive gene family >20 years ago, a broad community of researchers was drawn to investigate the universe of small regulatory RNAs. Although core features of miRNA biogenesis and function were revealed early on, recent years continue to uncover fundamental information on the structural and molecular dynamics of core miRNA machinery, how miRNA substrates and targets are selected from the transcriptome, new avenues for multilevel regulation of miRNA biogenesis and mechanisms for miRNA turnover. Many of these latest insights were enabled by recent technological advances, including massively parallel assays, cryogenic electron microscopy, single-molecule imaging and CRISPR-Cas9 screening. Here, we summarize the current understanding of miRNA biogenesis, function and regulation, and outline challenges to address in the future.
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Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Gayan Senavirathne
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
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4
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Yu L, Fan G, Wang Q, Zhu Y, Zhu H, Chang J, Wang Z, Zhan S, Hua X, She D, Huang J, Wang Y, Zhao J, Zhang CY, Chen X, Zhou G. In vivo self-assembly and delivery of VEGFR2 siRNA-encapsulated small extracellular vesicles for lung metastatic osteosarcoma therapy. Cell Death Dis 2023; 14:626. [PMID: 37739958 PMCID: PMC10516902 DOI: 10.1038/s41419-023-06159-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/02/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
The prognosis of lung metastatic osteosarcoma (OS) remains disappointing. siRNA-based gene silencing of VEGFR2 is a promising treatment strategy for lung metastatic OS, but there is a lack of safe and efficient delivery systems to encapsulate siRNAs for in vivo administration. This study presented a synthetic biological strategy that remolds the host liver with synthesized genetic circuits for efficient in vivo VEGFR2 siRNA delivery. After being taken-up by hepatocytes, the genetic circuit (in the form of a DNA plasmid) reprogrammed the liver to drive the autonomous intrahepatic assembly and encapsulation of VEGFR2 siRNAs into secretory small extracellular vesicles (sEVs), thus allowing for the transport of self-assembled VEGFR2 siRNAs towards the lung. The results showed that our strategy was superior to the positive medicine (Apatinib) for OS lung metastasis in terms of therapeutic efficacy and toxic adverse effects and may provide a feasible and viable therapeutic solution for lung metastatic OS.
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Affiliation(s)
- Lingfeng Yu
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Gentao Fan
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Qingyan Wang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Yan Zhu
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Hao Zhu
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Jiang Chang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, 210029, China
| | - Zhen Wang
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Shoubin Zhan
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Xianming Hua
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Diankun She
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Jianhao Huang
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Yicun Wang
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Jianning Zhao
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Chen-Yu Zhang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China.
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, 210023, China.
| | - Xi Chen
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China.
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, 210023, China.
| | - Guangxin Zhou
- Department of Orthopedics, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China.
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, 210023, China.
- Wuxi Xishan NJU Institute of Applied Biotechnology, Wuxi, Jiangsu, 214101, China.
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5
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Lee S, Jee D, Srivastava S, Yang A, Ramidi A, Shang R, Bortolamiol-Becet D, Pfeffer S, Gu S, Wen J, Lai EC. Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals. Cell Rep 2023; 42:112111. [PMID: 36800291 PMCID: PMC10508058 DOI: 10.1016/j.celrep.2023.112111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/16/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Canonical microRNA (miRNA) hairpins are processed by the RNase III enzymes Drosha and Dicer into ∼22 nt RNAs loaded into an Argonaute (Ago) effector. In addition, splicing generates numerous intronic hairpins that bypass Drosha (mirtrons) to yield mature miRNAs. Here, we identify hundreds of previously unannotated, splicing-derived hairpins in intermediate-length (∼50-100 nt) but not small (20-30 nt) RNA data. Since we originally defined mirtrons from small RNA duplexes, we term this larger set as structured splicing-derived RNAs (ssdRNAs). These associate with Dicer and/or Ago complexes, but generally accumulate modestly and are poorly conserved. We propose they contaminate the canonical miRNA pathway, which consequently requires defense against the siege of splicing-derived substrates. Accordingly, ssdRNAs/mirtrons comprise dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. Overall, the rampant proliferation of young mammalian mirtrons/ssdRNAs, coupled with an inhibitory molecular defense, comprises a Red Queen's race of intragenomic conflict.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - David Jee
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sid Srivastava
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; High Technology High School, Lincroft, NJ 07738, USA
| | - Acong Yang
- RNA Biology Laboratory, Center for Cancer Research, 8 National Cancer Institute, Frederick, MD 21702, USA
| | - Abhinav Ramidi
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; High Technology High School, Lincroft, NJ 07738, USA
| | - Renfu Shang
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - Diane Bortolamiol-Becet
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France
| | - Shuo Gu
- RNA Biology Laboratory, Center for Cancer Research, 8 National Cancer Institute, Frederick, MD 21702, USA
| | - Jiayu Wen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
| | - Eric C Lai
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA.
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6
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Shang R, Kretov DA, Adamson SI, Treiber T, Treiber N, Vedanayagam J, Chuang J, Meister G, Cifuentes D, Lai E. Regulated dicing of pre-mir-144 via reshaping of its terminal loop. Nucleic Acids Res 2022; 50:7637-7654. [PMID: 35801921 PMCID: PMC9303283 DOI: 10.1093/nar/gkac568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/10/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
Although the route to generate microRNAs (miRNAs) is often depicted as a linear series of sequential and constitutive cleavages, we now appreciate multiple alternative pathways as well as diverse strategies to modulate their processing and function. Here, we identify an unusually profound regulatory role of conserved loop sequences in vertebrate pre-mir-144, which are essential for its cleavage by the Dicer RNase III enzyme in human and zebrafish models. Our data indicate that pre-mir-144 dicing is positively regulated via its terminal loop, and involves the ILF3 complex (NF90 and its partner NF45/ILF2). We provide further evidence that this regulatory switch involves reshaping of the pre-mir-144 apical loop into a structure that is appropriate for Dicer cleavage. In light of our recent findings that mir-144 promotes the nuclear biogenesis of its neighbor mir-451, these data extend the complex hierarchy of nuclear and cytoplasmic regulatory events that can control the maturation of clustered miRNAs.
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Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Dmitry A Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Scott I Adamson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Thomas Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Eric C Lai
- To whom correspondence should be addressed. Tel: +1 212 639 5578; Fax: +1 212 717 3604;
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7
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Alsing S, Doktor TK, Askou AL, Jensen EG, Ahmadov U, Kristensen LS, Andresen BS, Aagaard L, Corydon TJ. VEGFA-targeting miR-agshRNAs combine efficacy with specificity and safety for retinal gene therapy. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:58-76. [PMID: 35356684 PMCID: PMC8933642 DOI: 10.1016/j.omtn.2022.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
Retinal gene therapy using RNA interference (RNAi) to silence targeted genes requires both efficacy and safety. Short hairpin RNAs (shRNAs) are useful for RNAi, but high expression levels and activity from the co-delivered passenger strand may cause undesirable cellular responses. Ago2-dependent shRNAs (agshRNAs) produce no passenger strand activity. To enhance efficacy and to investigate improvements in safety, we have generated VEGFA-targeting agshRNAs and microRNA (miRNA)-embedded agshRNAs (miR-agshRNAs) and inserted these RNAi effectors in Pol II/III-driven expression cassettes and lentiviral vectors (LVs). Compared with corresponding shRNAs, agshRNAs and miR-agshRNAs increased specificity and safety, while retaining a high knockdown efficacy and abolishing passenger strand activity. The agshRNAs also caused significantly smaller reductions in cell viability and reduced competition with the processing of endogenous miR21 compared with their shRNA counterparts. RNA sequencing (RNA-seq) analysis of LV-transduced ARPE19 cells revealed that expression of shRNAs in general leads to more changes in gene expression levels compared with their agshRNA counterparts and activation of immune-related pathways. In mice, subretinal delivery of LVs encoding tissue-specific miR-agshRNAs resulted in retinal pigment epithelium (RPE)-restricted expression and significant knockdown of Vegfa in transduced RPE cells. Collectively, our data suggest that agshRNAs and miR-agshRNA possess important advantages over shRNAs, thereby posing a clinically relevant approach with respect to efficacy, specificity, and safety.
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8
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Downregulation of CIRP Prone Cells to Oxidative Injury via Regulating Nrf2 Signaling Pathway. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2416787. [PMID: 35800223 PMCID: PMC9256419 DOI: 10.1155/2022/2416787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 12/03/2022]
Abstract
Cold-inducible RNA-binding protein (CIRP) is a cellular stress-response protein, whose expression can be induced by a variety of stress conditions. Our previous study showed that intracellular CIRP is a protective factor against cellular oxidative stress and silencing of CIRP gene prone cells to apoptosis. However, the underlying mechanism remains unknown. The present study was aimed at investigating the possible mechanisms underlying the protective role of CIRP in oxidative stress injury. Herein, we used HEK293T cells as our cell model to investigate the relation between CIRP and the possible antioxidant pathways by using the latest genetic silencing technologies. Our results showed that silencing CIRP by using SaiRNA-based genetic silencing tool leads to the downregulation of Nrf2 and Nrf2-regulated antioxidant genes in HEK293T cells. Taken together, our study identified the antioxidant Nrf2 signaling pathway as a downstream target of CIRP, and silencing CIRP may prone cells to apoptosis by downregulating the Nrf2 antioxidant pathway in response to oxidative injury.
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9
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Fang X, Liu Y, Xiao W, Zhao N, Zhu C, Yu D, Zhao Y. Prognostic SLC family genes promote cell proliferation, migration, and invasion in hepatocellular carcinoma. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1065-1075. [PMID: 34128989 DOI: 10.1093/abbs/gmab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
The solute carrier (SLC) superfamily genes encode more than 300 members that are responsible for the transmembrane transportation of many essential endogenous and exogenous compounds ranging from nutrients to drugs. SLCs are highly expressed in metabolic organs such as the liver, regulating the homeostasis of metabolites and the disposition of drugs. In contrast to their well-studied roles in physiological and pharmacological processes, little is known about the relationship between SLCs and cancer progression. Here, we aimed to explore the potential role of SLCs in progression and prognosis of hepatocellular carcinoma (HCC), one of the most commonly diagnosed cancers and leading causes of death worldwide. By performing bioinformatics analyses of HCC dataset from The Cancer Genome Atlas database, we identified three novel signature SLCs (SLC51B, SLC22A15, and SLC2A1) that are indicative of poor prognosis. Further functional analyses suggested the potential regulation of the three prognostic SLCs on cell proliferation and metastasis. Subsequent knockdown experiments performed in HCC cell lines showed that all three prognostic SLCs positively regulated the proliferation of HCC cells, among which SLC22A15 and SLC2A1 were required for migration and invasion of the cells, demonstrating remarkable consistency with the roles identified by bioinformatics methods in HCC. Therefore, our study provides a novel prognostic biomarker for HCC and reveals the significant roles of SLCs in HCC progression, which might have been undervalued in the past.
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Affiliation(s)
- Xiao Fang
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225009, China
- Clinical Medical College, Yangzhou University, Yangzhou 225009, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Medical College, Yangzhou University, Yangzhou 225009, China
| | - Ying Liu
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225009, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225009, China
| | - Wangwen Xiao
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225009, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225009, China
| | - Nan Zhao
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225009, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225009, China
| | - Chunmiao Zhu
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225009, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225009, China
| | - Duonan Yu
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225009, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Medical College, Yangzhou University, Yangzhou 225009, China
| | - Ya Zhao
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225009, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Medical College, Yangzhou University, Yangzhou 225009, China
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10
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Fu Z, Zhang X, Zhou X, Ur-Rehman U, Yu M, Liang H, Guo H, Guo X, Kong Y, Su Y, Ye Y, Hu X, Cheng W, Wu J, Wang Y, Gu Y, Lu SF, Wu D, Zen K, Li J, Yan C, Zhang CY, Chen X. In vivo self-assembled small RNAs as a new generation of RNAi therapeutics. Cell Res 2021; 31:631-648. [PMID: 33782530 PMCID: PMC8169669 DOI: 10.1038/s41422-021-00491-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/22/2021] [Indexed: 02/01/2023] Open
Abstract
RNAi therapy has undergone two stages of development, direct injection of synthetic siRNAs and delivery with artificial vehicles or conjugated ligands; both have not solved the problem of efficient in vivo siRNA delivery. Here, we present a proof-of-principle strategy that reprogrammes host liver with genetic circuits to direct the synthesis and self-assembly of siRNAs into secretory exosomes and facilitate the in vivo delivery of siRNAs through circulating exosomes. By combination of different genetic circuit modules, in vivo assembled siRNAs are systematically distributed to multiple tissues or targeted to specific tissues (e.g., brain), inducing potent target gene silencing in these tissues. The therapeutic value of our strategy is demonstrated by programmed silencing of critical targets associated with various diseases, including EGFR/KRAS in lung cancer, EGFR/TNC in glioblastoma and PTP1B in obesity. Overall, our strategy represents a next generation RNAi therapeutics, which makes RNAi therapy feasible.
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Affiliation(s)
- Zheng Fu
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XChemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, Jiangsu, China ,grid.89957.3a0000 0000 9255 8984State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiang Zhang
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Xinyan Zhou
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Uzair Ur-Rehman
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Mengchao Yu
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China ,grid.412521.1Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Hongwei Liang
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Hongyuan Guo
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Xu Guo
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Yan Kong
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Yuanyuan Su
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Yangyang Ye
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Xiuting Hu
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Wei Cheng
- grid.410745.30000 0004 1765 1045Department of General Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jinrong Wu
- grid.440259.e0000 0001 0115 7868Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Yanbo Wang
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Yayun Gu
- grid.89957.3a0000 0000 9255 8984State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sheng-feng Lu
- grid.410745.30000 0004 1765 1045Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Dianqing Wu
- grid.47100.320000000419368710Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale University School of Medicine, New Haven, CT USA
| | - Ke Zen
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Jing Li
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Chao Yan
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XChemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, Jiangsu, China ,grid.89957.3a0000 0000 9255 8984State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chen-Yu Zhang
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Xi Chen
- grid.41156.370000 0001 2314 964XNanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XChemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, Jiangsu, China ,grid.89957.3a0000 0000 9255 8984State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
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11
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Dönmüş B, Ünal S, Kirmizitaş FC, Türkoğlu Laçin N. Virus-associated ribozymes and nano carriers against COVID-19. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:204-218. [PMID: 33645342 DOI: 10.1080/21691401.2021.1890103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoo tonic, highly pathogenic virus. The new type of coronavirus with contagious nature spread from Wuhan (China) to the whole world in a very short time and caused the new coronavirus disease (COVID-19). COVID-19 has turned into a global public health crisis due to spreading by close person-to-person contact with high transmission capacity. Thus, research about the treatment of the damages caused by the virus or prevention from infection increases everyday. Besides, there is still no approved and definitive, standardized treatment for COVID-19. However, this disaster experienced by human beings has made us realize the significance of having a system ready for use to prevent humanity from viral attacks without wasting time. As is known, nanocarriers can be targeted to the desired cells in vitro and in vivo. The nano-carrier system targeting a specific protein, containing the enzyme inhibiting the action of the virus can be developed. The system can be used by simple modifications when we encounter another virus epidemic in the future. In this review, we present a potential treatment method consisting of a nanoparticle-ribozyme conjugate, targeting ACE-2 receptors by reviewing the virus-associated ribozymes, their structures, types and working mechanisms.
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Affiliation(s)
- Beyza Dönmüş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Sinan Ünal
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Fatma Ceren Kirmizitaş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Nelisa Türkoğlu Laçin
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
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12
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Lessel D, Zeitler DM, Reijnders MRF, Kazantsev A, Hassani Nia F, Bartholomäus A, Martens V, Bruckmann A, Graus V, McConkie-Rosell A, McDonald M, Lozic B, Tan ES, Gerkes E, Johannsen J, Denecke J, Telegrafi A, Zonneveld-Huijssoon E, Lemmink HH, Cham BWM, Kovacevic T, Ramsdell L, Foss K, Le Duc D, Mitter D, Syrbe S, Merkenschlager A, Sinnema M, Panis B, Lazier J, Osmond M, Hartley T, Mortreux J, Busa T, Missirian C, Prasun P, Lüttgen S, Mannucci I, Lessel I, Schob C, Kindler S, Pappas J, Rabin R, Willemsen M, Gardeitchik T, Löhner K, Rump P, Dias KR, Evans CA, Andrews PI, Roscioli T, Brunner HG, Chijiwa C, Lewis MES, Jamra RA, Dyment DA, Boycott KM, Stegmann APA, Kubisch C, Tan EC, Mirzaa GM, McWalter K, Kleefstra T, Pfundt R, Ignatova Z, Meister G, Kreienkamp HJ. Germline AGO2 mutations impair RNA interference and human neurological development. Nat Commun 2020; 11:5797. [PMID: 33199684 PMCID: PMC7670403 DOI: 10.1038/s41467-020-19572-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
ARGONAUTE-2 and associated miRNAs form the RNA-induced silencing complex (RISC), which targets mRNAs for translational silencing and degradation as part of the RNA interference pathway. Despite the essential nature of this process for cellular function, there is little information on the role of RISC components in human development and organ function. We identify 13 heterozygous mutations in AGO2 in 21 patients affected by disturbances in neurological development. Each of the identified single amino acid mutations result in impaired shRNA-mediated silencing. We observe either impaired RISC formation or increased binding of AGO2 to mRNA targets as mutation specific functional consequences. The latter is supported by decreased phosphorylation of a C-terminal serine cluster involved in mRNA target release, increased formation of dendritic P-bodies in neurons and global transcriptome alterations in patient-derived primary fibroblasts. Our data emphasize the importance of gene expression regulation through the dynamic AGO2-RNA association for human neuronal development.
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Affiliation(s)
- Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Daniela M Zeitler
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Andriy Kazantsev
- Institute of Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Fatemeh Hassani Nia
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Alexander Bartholomäus
- Institute of Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Victoria Martens
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Veronika Graus
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, 27707, USA
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, 27707, USA
| | - Bernarda Lozic
- University Hospital of Split, Split, Croatia
- University of Split School of Medicine, Split, Croatia
| | - Ee-Shien Tan
- Genetics Service, Department of Paediatrics, KK Women's & Children's Hospital, Singapore, Singapore
| | - Erica Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | | | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Breana W M Cham
- Genetics Service, Department of Paediatrics, KK Women's & Children's Hospital, Singapore, Singapore
| | | | - Linda Ramsdell
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Kimberly Foss
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Diana Mitter
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Steffen Syrbe
- Department of General Paediatrics, Division of Pediatric Epileptology, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Bianca Panis
- Department of Pediatrics, Zuyderland Medical Center, Heerlen and Sittard, 6419, the Netherlands
| | - Joanna Lazier
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Jeremie Mortreux
- Département de Génétique Médicale, CHU Timone Enfants, Assistance Publique - Hôpitaux de Marseille AP-HM, Marseille, France
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Tiffany Busa
- Département de Génétique Médicale, CHU Timone Enfants, Assistance Publique - Hôpitaux de Marseille AP-HM, Marseille, France
| | - Chantal Missirian
- Département de Génétique Médicale, CHU Timone Enfants, Assistance Publique - Hôpitaux de Marseille AP-HM, Marseille, France
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Pankaj Prasun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sabine Lüttgen
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Ilaria Mannucci
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Ivana Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Claudia Schob
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stefan Kindler
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - John Pappas
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Rachel Rabin
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Marjolein Willemsen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Katharina Löhner
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrick Rump
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kerith-Rae Dias
- Neuroscience Research Australia (NeuRA), Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
- NSW Health Pathology Randwick Genetics, Sydney, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA), Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
- NSW Health Pathology Randwick Genetics, Sydney, Australia
| | - Peter Ian Andrews
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
- New South Wales Health Pathology Genomics Laboratory Randwick, Sydney, Australia
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Ene-Choo Tan
- Research Laboratory, KK Women's & Children's Hospital, Singapore, Singapore
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, US
| | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Zoya Ignatova
- Institute of Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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13
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Zhang Y, Teng Y, Xiao W, Xu B, Zhao Y, Li W, Wu L. Identifying Cleaved and Noncleaved Targets of Small Interfering RNAs and MicroRNAs in Mammalian Cells by SpyCLIP. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:900-909. [PMID: 33251041 PMCID: PMC7666362 DOI: 10.1016/j.omtn.2020.10.009] [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: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/03/2022]
Abstract
Recently, the US Food and Drug Administration (FDA) approved the first small interfering RNA (siRNA) drug, marking a significant milestone in the therapeutic use of RNA interference (RNAi) technology. However, off-target gene silencing by siRNA remains one of the major obstacles in siRNA therapy. Although siRNA off-target effects caused by a mechanism known for microRNA (miRNA)-mediated gene repression have been extensively discussed, whether RNAi can cause unintended cleavage through the effector protein AGO2 at sites harboring partially complementary sequences to the siRNA remains unknown. Here, we report a strategy to establish a comprehensive picture of siRNA cleaved and noncleaved off-targets by performing SpyCLIP using wild-type and catalytically inactive AGO2 mutants in parallel. Additionally, we investigated naturally occurring cleavage events mediated by endogenous miRNAs using the same strategy. Our results demonstrated that AGO2 SpyCLIP is a powerful method to identify both the cleaved and noncleaved targets of siRNAs, providing valuable information for improving siRNA design rules.
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Affiliation(s)
- Yao Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai 200032, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yilan Teng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wangwen Xiao
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Institute of Translational Medicine, School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Beiying Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ya Zhao
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Institute of Translational Medicine, School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Weihua Li
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai 200032, China
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
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14
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Sheng P, Flood KA, Xie M. Short Hairpin RNAs for Strand-Specific Small Interfering RNA Production. Front Bioeng Biotechnol 2020; 8:940. [PMID: 32850763 PMCID: PMC7427337 DOI: 10.3389/fbioe.2020.00940] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
RNA interference (RNAi) is an effective mechanism for inhibiting gene expression at the post-transcriptional level. Expression of a messenger RNA (mRNA) can be inhibited by a ∼22-nucleotide (nt) small interfering (si)RNA with the corresponding reverse complementary sequence. Typically, a duplex of siRNA, composed of the desired siRNA and a passenger strand, is processed from a short hairpin RNA (shRNA) precursor by Dicer. Subsequently, one strand of the siRNA duplex is associated with Argonaute (Ago) protein for RNAi. Although RNAi is widely used, the off-target effect induced by the passenger strand remains a potential problem. Here, based on current understanding of endogenous precursor microRNA (pre-miRNA) hairpins, called Ago-shRNA and m7G-capped pre-miRNA, we discuss the principles of shRNA designs that produce a single siRNA from one strand of the hairpin.
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Affiliation(s)
- Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States.,UF Health Cancer Center, University of Florida, Gainesville, FL, United States
| | - Krystal A Flood
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States.,UF Health Cancer Center, University of Florida, Gainesville, FL, United States
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States.,UF Health Cancer Center, University of Florida, Gainesville, FL, United States.,UF Genetics Institute, University of Florida, Gainesville, FL, United States
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15
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Shang R, Baek SC, Kim K, Kim B, Kim VN, Lai EC. Genomic Clustering Facilitates Nuclear Processing of Suboptimal Pri-miRNA Loci. Mol Cell 2020; 78:303-316.e4. [PMID: 32302542 PMCID: PMC7546447 DOI: 10.1016/j.molcel.2020.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/26/2019] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Abstract
Nuclear processing of most miRNAs is mediated by Microprocessor, comprised of RNase III enzyme Drosha and its cofactor DGCR8. Here, we uncover a hidden layer of Microprocessor regulation via studies of Dicer-independent mir-451, which is clustered with canonical mir-144. Although mir-451 is fully dependent on Drosha/DGCR8, its short stem and small terminal loop render it an intrinsically weak Microprocessor substrate. Thus, it must reside within a cluster for normal biogenesis, although the identity and orientation of its neighbor are flexible. We use DGCR8 tethering assays and operon structure-function assays to demonstrate that local recruitment and transfer of Microprocessor enhances suboptimal substrate processing. This principle applies more broadly since genomic analysis indicates suboptimal canonical miRNAs are enriched in operons, and we validate several of these experimentally. Proximity-based enhancement of suboptimal hairpin processing provides a rationale for genomic retention of certain miRNA operons and may explain preferential evolutionary emergence of miRNA operons.
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Affiliation(s)
- Renfu Shang
- Department of Developmental Biology, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA.
| | - S Chan Baek
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Boseon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Eric C Lai
- Department of Developmental Biology, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA.
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16
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Liao X, Pan J, Zhang X, Tang Q. Sensitive Detection of Argonaute2 by Triple-Helix Molecular Switch Reaction and Pyrene Excimer Switching. Aust J Chem 2020. [DOI: 10.1071/ch19485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RNA interference (RNAi) is a powerful tool for silencing target genes in a variety of cells and has great therapeutic potential. It is triggered by small interfering RNAs (siRNAs) and by an RNA-binding protein (argonaute, Ago). In this manuscript, we designed a simple fluorescence sensor strategy for sensitive detection of argonaute2 (Ago2) based on the base pairing principle of Watson–Crick and Hoogsteen and the pyrene excimer switch. The sensing platform has extremely high sensitivity and a detection limit of 0.1nM. It can be used to detect endogenous Ago2 in cancer cells and has great potential in clinical diagnosis and biomedical research.
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17
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Herrera-Carrillo E, Gao Z, Berkhout B. Influence of a 3' Terminal Ribozyme on AgoshRNA Biogenesis and Activity. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:452-462. [PMID: 31048184 PMCID: PMC6488825 DOI: 10.1016/j.omtn.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022]
Abstract
Short hairpin RNAs (shRNAs) can induce gene silencing via the RNA interference (RNAi) mechanism. We designed an alternative shRNA molecule with a relatively short base-paired stem that bypasses Dicer and instead is processed by the Argonaute 2 (Ago2) protein into a single guide RNA strand that effectively induces RNAi. We called these molecules AgoshRNAs. Active anti-HIV AgoshRNAs were developed, but their RNAi activity was generally reduced compared with the matching shRNAs. In an attempt to further optimize the AgoshRNA design, we inserted several self-cleaving ribozymes at the 3′ terminus of the transcribed AgoshRNA and evaluated the impact on AgoshRNA processing and activity. The hepatitis delta virus (HDV) ribozyme is efficiently removed from the transcribed AgoshRNAs and generates a uniform 3′ overhang, which translates into the enhanced antiviral activity of these molecules.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands.
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18
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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.
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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.
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19
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Herrera-Carrillo E, Berkhout B. Dicer-independent processing of small RNA duplexes: mechanistic insights and applications. Nucleic Acids Res 2017; 45:10369-10379. [PMID: 28977573 PMCID: PMC5737282 DOI: 10.1093/nar/gkx779] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages. As an example, we will present the route towards development of a durable gene therapy against HIV-1.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
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20
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Wang G, Cui T, Sun L, Peng N, Yang C. Long noncoding RNA LeXis promotes osteosarcoma growth through upregulation of CTNNB1 expression. Am J Cancer Res 2017; 7:1577-1587. [PMID: 28744406 PMCID: PMC5523037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023] Open
Abstract
Osteosarcoma (OS) is the most common primary bone cancer in adolescents and children. Long noncoding RNAs (lncRNAs) contain > 200 nucleotides and do not have protein-coding ability. Liver-expressed LXR-induced sequence (LeXis) is a newly identified functional lncRNA. However, its expression pattern, biological function, and molecular mechanism in OS progression are unclear. The present study is the first to show that LeXis expression was upregulated in OS tissues. Increased LeXis expression was significantly correlated with high tumor stage, large tumor size, and poor prognosis. Our findings highlight the oncogenic activity of lncRNA LeXis in OS growth. Results of functional assays showed that LeXis promoted OS growth both in vitro and in vivo. Mechanistic investigation showed that LeXis directly interacted with miR-199a and suppressed its expression. Moreover, LeXis increased CTNNB1 expression by functioning as a ceRNA of CTNNB1 against miR-199a. These findings may have important implications for developing novel therapeutic strategies for OS.
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Affiliation(s)
- Guijiang Wang
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Tao Cui
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Lishan Sun
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Ningning Peng
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Cheng Yang
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
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21
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Liu G, Wang L, Han H, Li Y, Lu S, Li T, Cheng C. LncRNA ZFAS1 promotes growth and metastasis by regulating BMI1 and ZEB2 in osteosarcoma. Am J Cancer Res 2017; 7:1450-1462. [PMID: 28744396 PMCID: PMC5523027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023] Open
Abstract
Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents. LncRNAs have recently gained widespread attention and have been shown to have crucial roles in various biological regulatory processes. ZFAS1, a newly identified lncRNA, was shown to be dysregulated in several cancers. However, little is known about the alteration and functional significance of ZFAS1 in OS. In the present study, for the first time, we revealed a functional role of ZFAS1 on OS growth and metastasis. The expression of ZFAS1 was significantly overexpressed in OS samples and cell lines, and upregulation of ZFAS1 is significantly associated with unfavorable prognosis of OS patients. Functional assays also demonstrated that ZFAS1 enhanced the growth and metastatic ability of OS cells in vitro and in vivo. Mechanistically, we found that ZFAS1 positively regulated malignant phenotypes by competitively binding the miR-200b and miR-200c and upregulating BMI1. ZFAS1 also interacted with ZEB2 and regulated ZEB2 protein stability. Furthermore, we demonstrated that SP1 functions as an upstream activated factor of ZFAS1. ZFAS1 may be a potential therapeutic target for OS tumorigenesis and progression.
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Affiliation(s)
- Guangfei Liu
- No.1 Orthopedics Department, Cangzhou Central Hospital of Hebei Medical UniversityCangzhou, Hebei Province, China
| | - Lu Wang
- No.1 Orthopedics Department, Cangzhou Central Hospital of Hebei Medical UniversityCangzhou, Hebei Province, China
| | - Hongmin Han
- No.1 Orthopedics Department, Cangzhou Central Hospital of Hebei Medical UniversityCangzhou, Hebei Province, China
| | - Yong Li
- No.1 Orthopedics Department, Cangzhou Central Hospital of Hebei Medical UniversityCangzhou, Hebei Province, China
| | - Shouliang Lu
- No.1 Orthopedics Department, Cangzhou Central Hospital of Hebei Medical UniversityCangzhou, Hebei Province, China
| | - Tiejun Li
- No.1 Orthopedics Department, Cangzhou Central Hospital of Hebei Medical UniversityCangzhou, Hebei Province, China
| | - Cai Cheng
- No.1 Orthopedics Department, Cangzhou Central Hospital of Hebei Medical UniversityCangzhou, Hebei Province, China
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22
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Bofill-De Ros X, Gu S. Guidelines for the optimal design of miRNA-based shRNAs. Methods 2016; 103:157-66. [PMID: 27083402 PMCID: PMC4921303 DOI: 10.1016/j.ymeth.2016.04.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is an extremely useful tool for inhibiting gene expression. It can be triggered by transfected synthetic small interfering RNA (siRNA) or by expressed small hairpin RNA (shRNA). The cellular machinery processes the latter into siRNA in vivo. shRNA is preferred or required in genetic screens and specific RNAi approaches in gene therapy settings. Despite its many successes, the field of shRNAs faces many challenges. Insufficient knockdowns and off-target effects become obstacles for shRNA usage in many applications. Numerous failures are triggered by pitfalls in shRNA design that is often associated with impoverished biogenesis. Here, based on current understanding of the miRNA maturation pathway, we discuss the principles of different shRNA design (pre-miRNA-like, pri-miRNA-like and Ago-shRNA) with an emphasis on the RNA structure. We also provide detailed instructions for an optimal design of pre-miRNA-like shRNA.
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Affiliation(s)
- Xavier Bofill-De Ros
- Gene Regulation and Chromosome Biology Laboratory, Center For Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Shuo Gu
- Gene Regulation and Chromosome Biology Laboratory, Center For Cancer Research, National Cancer Institute, Frederick, MD, United States.
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23
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Li M, Chen H, Zhao Y, Gao S, Cheng C. H19 Functions as a ceRNA in Promoting Metastasis Through Decreasing miR-200s Activity in Osteosarcoma. DNA Cell Biol 2016; 35:235-40. [DOI: 10.1089/dna.2015.3171] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Min Li
- Department of Orthopedics, Cangzhou Central Hospital, Hebei, China
| | - Hanwen Chen
- Department of Orthopedics, Cangzhou Central Hospital, Hebei, China
| | - Yuejiang Zhao
- Department of Orthopedics, Cangzhou Central Hospital, Hebei, China
| | - Shuming Gao
- Department of Orthopedics, Cangzhou Central Hospital, Hebei, China
| | - Cai Cheng
- Department of Orthopedics, Cangzhou Central Hospital, Hebei, China
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