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Hirota K, Yamashita A, Abe E, Yamaji T, Azushima K, Tanaka S, Taguchi S, Tsukamoto S, Wakui H, Tamura K. miR-125a-5p/miR-125b-5p contributes to pathological activation of angiotensin II-AT1R in mouse distal convoluted tubule cells by the suppression of Atrap. J Biol Chem 2023; 299:105478. [PMID: 37981211 PMCID: PMC10755798 DOI: 10.1016/j.jbc.2023.105478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023] Open
Abstract
The renin-angiotensin system plays a crucial role in the regulation of blood pressure. Activation of the angiotensin II (Ang II)-Ang II type 1 receptor (AT1R) signaling pathway contributes to the pathogenesis of hypertension and subsequent organ damage. AT1R-associated protein (ATRAP) has been identified as an endogenous inhibitory protein of the AT1R pathological activation. We have shown that mouse Atrap (Atrap) represses various Ang II-AT1R-mediated pathologies, including hypertension in mice. The expression of human ATRAP (ATRAP)/Atrap can be altered in various pathological states in humans and mice, such as Ang II stimulation and serum starvation. However, the regulatory mechanisms of ATRAP/Atrap are not yet fully elucidated. miRNAs are 21 to 23 nucleotides of small RNAs that post-transcriptionally repress gene expression. Single miRNA can act on hundreds of target mRNAs, and numerous miRNAs have been identified as the Ang II-AT1R signaling-associated disease phenotype modulator, but nothing is known about the regulation of ATRAP/Atrap. In the present study, we identified miR-125a-5p/miR-125b-5p as the evolutionarily conserved miRNAs that potentially act on ATRAP/Atrap mRNA. Further analysis revealed that miR-125a-5p/miR-125b-5p can directly repress both ATRAP and Atrap. In addition, the inhibition of miR-125a-5p/miR-125b-5p resulted in the suppression of the Ang II-AT1R signaling in mouse distal convoluted tubule cells. Taken together, miR-125a-5p/miR-125b-5p activates Ang II-AT1R signaling by the suppression of ATRAP/Atrap. Our results provide new insights into the potential approaches for achieving the organ-protective effects by the repression of the miR-125 family associated with the enhancement of ATRAP/Atrap expression.
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Affiliation(s)
- Keigo Hirota
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Akio Yamashita
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
| | - Eriko Abe
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takahiro Yamaji
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kengo Azushima
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shohei Tanaka
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shinya Taguchi
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shunichiro Tsukamoto
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromichi Wakui
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kouichi Tamura
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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2
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Han J, Mendell JT. MicroRNA turnover: a tale of tailing, trimming, and targets. Trends Biochem Sci 2023; 48:26-39. [PMID: 35811249 PMCID: PMC9789169 DOI: 10.1016/j.tibs.2022.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) post-transcriptionally repress gene expression by guiding Argonaute (AGO) proteins to target mRNAs. While much is known about the regulation of miRNA biogenesis, miRNA degradation pathways are comparatively poorly understood. Although miRNAs generally exhibit slow turnover, they can be rapidly degraded through regulated mechanisms that act in a context- or sequence-specific manner. Recent work has revealed a particularly important role for specialized target interactions in controlling rates of miRNA degradation. Engagement of these targets is associated with the addition and removal of nucleotides from the 3' ends of miRNAs, a process known as tailing and trimming. Here we review these mechanisms of miRNA modification and turnover, highlighting the contexts in which they impact miRNA stability and discussing important questions that remain unanswered.
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Affiliation(s)
- Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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3
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Li S, Liu Y, Zhang T, Lin S, Shi S, He J, Xie Y, Cai X, Tian T, Lin Y. A Tetrahedral Framework DNA-Based Bioswitchable miRNA Inhibitor Delivery System: Application to Skin Anti-Aging. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204287. [PMID: 35901292 DOI: 10.1002/adma.202204287] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/21/2022] [Indexed: 02/05/2023]
Abstract
MicroRNA (miR)-based therapy shows strong potential; however, structural limitations pose a challenge in fully exploiting its biomedical functionality. Tetrahedral framework DNA (tFNA) has proven to be an ideal vehicle for miR therapy. Inspired by the ancient Chinese myth "Sun and Immortal Birds," a novel bioswitchable miR inhibitor delivery system (BiRDS) is designed with three miR inhibitors (the three immortal birds) and a nucleic acid core (the central sun). The BiRDS fuses miR inhibitors within the framework, maximizing their loading capacity, while allowing the system to retain the characteristics of small-sized tFNA and avoiding uncertainty associated with RNA exposure in traditional loading protocols. The RNase H-responsive sequence at the tail of each "immortal bird" enables the BiRDS to transform from a 3D to a 2D structure upon entering cells, promoting the delivery of miR inhibitors. To confirm the application potential, the BiRDS is used to deliver the miR-31 inhibitor, with antiaging effects on hair follicle stem cells, into a skin aging model. Superior skin penetration ability and RNA delivery are observed with significant anti-aging effects. These findings demonstrate the capability and editability of the BiRDS to improve the stability and delivery efficacy of miRs for future innovations.
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Affiliation(s)
- Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yuhao Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shiyu Lin
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiajun He
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
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4
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Hirano Y, Komatsu Y. Promotion of cytoplasmic localization of oligonucleotides by connecting cross-linked duplexes. RSC Adv 2022; 12:24471-24477. [PMID: 36128385 PMCID: PMC9425837 DOI: 10.1039/d2ra04375k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/22/2022] [Indexed: 11/21/2022] Open
Abstract
An interstrand cross-linked duplex (CD) modification promoted antisense oligonucleotide to be localized in the cytoplasm, resulting in effective knockdown microRNA in cytoplasm. In contrast, single-stranded antisense was confined in the nucleus.
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Affiliation(s)
- Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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5
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Abdelhady AM, Hirano Y, Onizuka K, Okamura H, Komatsu Y, Nagatsugi F. Synthesis of crosslinked 2'-OMe RNA duplexes and their application for effective inhibition of miRNA function. Bioorg Med Chem Lett 2021; 48:128257. [PMID: 34246752 DOI: 10.1016/j.bmcl.2021.128257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 11/24/2022]
Abstract
The interstrand crosslinking of nucleic acids is one of the strategies to create the stable complex between an oligonucleotide and RNA by covalent bond formation. We previously reported that fully 2'-O-methylated (2'-OMe) RNAs having the 2-amino-6-vinylpurine (AVP) exhibited an efficient crosslinking to uracil in the target RNA. In this study, we established a chemical method to efficiently synthesize the crosslinked 2'-OMe RNA duplexes using AVP and prepared the anti-miRNA oligonucleotides (AMOs) containing the antisense targeting miR-21 and crosslinked duplex at the terminal sequences. These AMOs showed a markedly higher anti miRNA activity than that of the commercially-available miR-21 inhibitor which has locked nucleic acid (LNA) residues.
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Affiliation(s)
- Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan; Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, 11884 Cairo, Egypt
| | - Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan; Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
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6
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Okumura S, Hirano Y, Komatsu Y. Stable duplex-linked antisense targeting miR-148a inhibits breast cancer cell proliferation. Sci Rep 2021; 11:11467. [PMID: 34075147 PMCID: PMC8169724 DOI: 10.1038/s41598-021-90972-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/20/2021] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs) regulate cancer cell proliferation by binding directly to the untranslated regions of messenger RNA (mRNA). MicroRNA-148a (miR-148a) is expressed at low levels in breast cancer (BC). However, little attention has been paid to the sequestration of miR-148a. Here, we performed a knockdown of miR-148a using anti-miRNA oligonucleotides (AMOs) and investigated the effect on BC cell proliferation. BC cell proliferation was significantly suppressed by AMO flanked by interstrand cross-linked duplexes (CL-AMO), whereas single-stranded and commercially available AMOs had no effect. The suppression was caused by sequestering specifically miR-148a. Indeed, miR-148b, another member of the miR-148 family, was not affected. Importantly, the downregulation of miR-148a induced a greater and longer-lasting inhibition of BC cell proliferation than the targeting of oncogenic microRNA-21 (miR-21) did. We identified thioredoxin-interacting protein (TXNIP), a tumor suppressor gene, as a target of miR-148a and showed that CL-AMO provoked an increase in TXNIP mRNA expression. This study provide evidence that lowly expressed miRNAs such as miR-148a have an oncogenic function and might be a promising target for cancer treatment.
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Affiliation(s)
- Sho Okumura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan
- Graduate School of Life Science, Hokkaido University, 8, Kita 10-jo-Nishi, Kita-ku, Sapporo, 060-0810, Japan
- Cosmo Bio Co., Ltd., 3-513-2, Zenibako, Otaru, Hokkaido, 047-0261, Japan
| | - Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan
- Graduate School of Life Science, Hokkaido University, 8, Kita 10-jo-Nishi, Kita-ku, Sapporo, 060-0810, Japan
| | - Yasuo Komatsu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
- Graduate School of Life Science, Hokkaido University, 8, Kita 10-jo-Nishi, Kita-ku, Sapporo, 060-0810, Japan.
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7
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Landmesser U, Poller W, Tsimikas S, Most P, Paneni F, Lüscher TF. From traditional pharmacological towards nucleic acid-based therapies for cardiovascular diseases. Eur Heart J 2021; 41:3884-3899. [PMID: 32350510 DOI: 10.1093/eurheartj/ehaa229] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/17/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acid-based therapeutics are currently developed at large scale for prevention and management of cardiovascular diseases (CVDs), since: (i) genetic studies have highlighted novel therapeutic targets suggested to be causal for CVD; (ii) there is a substantial recent progress in delivery, efficacy, and safety of nucleic acid-based therapies; (iii) they enable effective modulation of therapeutic targets that cannot be sufficiently or optimally addressed using traditional small molecule drugs or antibodies. Nucleic acid-based therapeutics include (i) RNA-targeted therapeutics for gene silencing; (ii) microRNA-modulating and epigenetic therapies; (iii) gene therapies; and (iv) genome-editing approaches (e.g. CRISPR-Cas-based): (i) RNA-targeted therapeutics: several large-scale clinical development programmes, using antisense oligonucleotides (ASO) or short interfering RNA (siRNA) therapeutics for prevention and management of CVD have been initiated. These include ASO and/or siRNA molecules to lower apolipoprotein (a) [apo(a)], proprotein convertase subtilisin/kexin type 9 (PCSK9), apoCIII, ANGPTL3, or transthyretin (TTR) for prevention and treatment of patients with atherosclerotic CVD or TTR amyloidosis. (ii) MicroRNA-modulating and epigenetic therapies: novel potential therapeutic targets are continually arising from human non-coding genome and epigenetic research. First microRNA-based therapeutics or therapies targeting epigenetic regulatory pathways are in clinical studies. (iii) Gene therapies: EMA/FDA have approved gene therapies for non-cardiac monogenic diseases and LDL receptor gene therapy is currently being examined in patients with homozygous hypercholesterolaemia. In experimental studies, gene therapy has significantly improved cardiac function in heart failure animal models. (iv) Genome editing approaches: these technologies, such as using CRISPR-Cas, have proven powerful in stem cells, however, important challenges are remaining, e.g. low rates of homology-directed repair in somatic cells such as cardiomyocytes. In summary, RNA-targeted therapies (e.g. apo(a)-ASO and PCSK9-siRNA) are now in large-scale clinical outcome trials and will most likely become a novel effective and safe therapeutic option for CVD in the near future. MicroRNA-modulating, epigenetic, and gene therapies are tested in early clinical studies for CVD. CRISPR-Cas-mediated genome editing is highly effective in stem cells, but major challenges are remaining in somatic cells, however, this field is rapidly advancing.
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Affiliation(s)
- Ulf Landmesser
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Sotirios Tsimikas
- Division of Cardiovascular Medicine, Sulpizio Cardiovascular Center, University of California San Diego, 9500 Gilman Drive, BSB 1080, La Jolla, CA 92093-0682, USA
| | - Patrick Most
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany.,Center for Translational Medicine, Jefferson Medical College, 1020 Locust Street, Philadelphia, PA 19107, USA.,Molecular and Translational Cardiology, Department of Medicine III, Heidelberg University Hospital, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Rämistrasse 100, MOU2, 8091 Zurich, Switzerland
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Research, Education and Development, Royal Brompton and Harefield Hospital Trust and Imperial College London, National Heart and Lung Institute, Guy Scadding Building, Dovehouse Street, London SW3 6LY, UK
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8
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Aránega AE, Lozano-Velasco E, Rodriguez-Outeiriño L, Ramírez de Acuña F, Franco D, Hernández-Torres F. MiRNAs and Muscle Regeneration: Therapeutic Targets in Duchenne Muscular Dystrophy. Int J Mol Sci 2021; 22:ijms22084236. [PMID: 33921834 PMCID: PMC8072594 DOI: 10.3390/ijms22084236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
microRNAs (miRNAs) are small non-coding RNAs required for the post-transcriptional control of gene expression. MicroRNAs play a critical role in modulating muscle regeneration and stem cell behavior. Muscle regeneration is affected in muscular dystrophies, and a critical point for the development of effective strategies for treating muscle disorders is optimizing approaches to target muscle stem cells in order to increase the ability to regenerate lost tissue. Within this framework, miRNAs are emerging as implicated in muscle stem cell response in neuromuscular disorders and new methodologies to regulate the expression of key microRNAs are coming up. In this review, we summarize recent advances highlighting the potential of miRNAs to be used in conjunction with gene replacement therapies, in order to improve muscle regeneration in the context of Duchenne Muscular Dystrophy (DMD).
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Affiliation(s)
- Amelia Eva Aránega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje Las Lagunillas s/n, 23009 Jaen, Spain; (E.L.-V.); (L.R.-O.); (F.R.d.A.); (D.F.); (F.H.-T.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento 34, 18016 Granada, Spain
- Correspondence:
| | - Estefanía Lozano-Velasco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje Las Lagunillas s/n, 23009 Jaen, Spain; (E.L.-V.); (L.R.-O.); (F.R.d.A.); (D.F.); (F.H.-T.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento 34, 18016 Granada, Spain
| | - Lara Rodriguez-Outeiriño
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje Las Lagunillas s/n, 23009 Jaen, Spain; (E.L.-V.); (L.R.-O.); (F.R.d.A.); (D.F.); (F.H.-T.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento 34, 18016 Granada, Spain
| | - Felicitas Ramírez de Acuña
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje Las Lagunillas s/n, 23009 Jaen, Spain; (E.L.-V.); (L.R.-O.); (F.R.d.A.); (D.F.); (F.H.-T.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento 34, 18016 Granada, Spain
| | - Diego Franco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje Las Lagunillas s/n, 23009 Jaen, Spain; (E.L.-V.); (L.R.-O.); (F.R.d.A.); (D.F.); (F.H.-T.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento 34, 18016 Granada, Spain
| | - Francisco Hernández-Torres
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje Las Lagunillas s/n, 23009 Jaen, Spain; (E.L.-V.); (L.R.-O.); (F.R.d.A.); (D.F.); (F.H.-T.)
- Medina Foundation, Technology Park of Health Sciences, Av. del Conocimiento 34, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Avda. de la Investigación 11, 18016 Granada, Spain
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Grixti JM, Ayers D, Day PJR. An Analysis of Mechanisms for Cellular Uptake of miRNAs to Enhance Drug Delivery and Efficacy in Cancer Chemoresistance. Noncoding RNA 2021; 7:27. [PMID: 33923485 PMCID: PMC8167612 DOI: 10.3390/ncrna7020027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 12/15/2022] Open
Abstract
Up until recently, it was believed that pharmaceutical drugs and their metabolites enter into the cell to gain access to their targets via simple diffusion across the hydrophobic lipid cellular membrane, at a rate which is based on their lipophilicity. An increasing amount of evidence indicates that the phospholipid bilayer-mediated drug diffusion is in fact negligible, and that drugs pass through cell membranes via proteinaceous membrane transporters or carriers which are normally used for the transportation of nutrients and intermediate metabolites. Drugs can be targeted to specific cells and tissues which express the relevant transporters, leading to the design of safe and efficacious treatments. Furthermore, transporter expression levels can be manipulated, systematically and in a high-throughput manner, allowing for considerable progress in determining which transporters are used by specific drugs. The ever-expanding field of miRNA therapeutics is not without its challenges, with the most notable one being the safe and effective delivery of the miRNA mimic/antagonist safely to the target cell cytoplasm for attaining the desired clinical outcome, particularly in miRNA-based cancer therapeutics, due to the poor efficiency of neo-vascular systems revolting around the tumour site, brought about by tumour-induced angiogenesis. This acquisition of resistance to several types of anticancer drugs can be as a result of an upregulation of efflux transporters expression, which eject drugs from cells, hence lowering drug efficacy, resulting in multidrug resistance. In this article, the latest available data on human microRNAs has been reviewed, together with the most recently described mechanisms for miRNA uptake in cells, for future therapeutic enhancements against cancer chemoresistance.
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Affiliation(s)
- Justine M. Grixti
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK;
| | - Duncan Ayers
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida MSD 2080, Malta
- Faculty of Biology, Medicine and Human Sciences, The University of Manchester, Manchester M1 7DN, UK;
| | - Philip J. R. Day
- Faculty of Biology, Medicine and Human Sciences, The University of Manchester, Manchester M1 7DN, UK;
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10
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Friedrich M, Vaxevanis CK, Biehl K, Mueller A, Seliger B. Targeting the coding sequence: opposing roles in regulating classical and non-classical MHC class I molecules by miR-16 and miR-744. J Immunother Cancer 2021; 8:jitc-2019-000396. [PMID: 32571994 PMCID: PMC7307530 DOI: 10.1136/jitc-2019-000396] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 01/31/2023] Open
Abstract
Background To control gene expression, microRNAs (miRNAs) are of key importance and their deregulation is associated with the development and progression of various cancer types. In this context, a discordant messenger RNA/protein expression pointing to extensive post-transcriptional regulation of major histocompatibility complex (MHC) class I molecules was already shown. However, only a very limited number of miRNAs targeting these molecules have yet been identified. Despite an increasing evidence of coding sequence (CDS)-located miRNA binding sites, there exists so far, no detailed study of the interaction of miRNAs with the CDS of MHC class I molecules. Methods Using an MS2-tethering approach in combination with small RNA sequencing, a number of putative miRNAs binding to the CDS of human leukocyte antigen (HLA)-G were identified. These candidate miRNAs were extensively screened for their effects in the HLA-G-positive JEG3 cell line. Due to the high sequence similarity between HLA-G and classical MHC class I molecules, the impact of HLA-G candidate miRNAs on HLA class I surface expression was also analyzed. The Cancer Genome Atlas data were used to correlate candidate miRNAs and HLA class I gene expression. Results Transfection of candidate miRNAs revealed that miR-744 significantly downregulates HLA-G protein levels. In contrast, overexpression of the candidate miRNAs miR-15, miR-16, and miR-424 sharing the same seed sequence resulted in an unexpected upregulation of HLA-G. Comparable results were obtained for classical MHC class I members after transfection of miRNA mimics into HEK293T cells. Analyses of The Cancer Genome Atlas data sets for miRNA and MHC class I expression further validated the results. Conclusions Our data expand the knowledge about MHC class I regulation and showed for the first time an miRNA-dependent control of MHC class I antigens mediated by the CDS. CDS-located miRNA binding sites could improve the general use of miRNA-based therapeutic approaches as these sites are highly independent of structural variations (e.g. mutations) in the gene body. Surprisingly, miR-16 family members promoted MHC class I expression potentially in a gene activation-like mechanism.
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Affiliation(s)
- Michael Friedrich
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
| | | | - Katharina Biehl
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
| | - Anja Mueller
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
| | - Barbara Seliger
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
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11
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Hrdlicka HC, Pereira RC, Shin B, Yee SP, Deymier AC, Lee SK, Delany AM. Inhibition of miR-29-3p isoforms via tough decoy suppresses osteoblast function in homeostasis but promotes intermittent parathyroid hormone-induced bone anabolism. Bone 2021; 143:115779. [PMID: 33253931 PMCID: PMC7770763 DOI: 10.1016/j.bone.2020.115779] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 01/07/2023]
Abstract
miRNAs play a vital role in post-transcriptional regulation of gene expression in osteoblasts and osteoclasts, and the miR-29 family is expressed in both lineages. Using mice globally expressing a miR-29-3p tough decoy, we demonstrated a modest 30-60% decrease all three miR-29-3p isoforms: miR-29a, miR-29b, and miR-29c. While the miR-29-3p decoy did not impact osteoclast number or function, the tough decoy decreased bone formation in growing mice, which led to decreased trabecular bone volume in mature animals. These data support previous in vitro studies suggesting that miR-29-3p is a positive regulator of osteoblast differentiation. In contrast, when mice were treated with intermittent parathyroid hormone (PTH1-34), inhibition of miR-29-3p augmented the effect of PTH on cortical bone anabolism, increased bone formation rate and osteoblast surface, and increased levels of Ctnnb1/βcatenin mRNA, which is a miR-29 target. These findings highlight differences in the mechanisms controlling basal level bone formation and bone formation induced by intermittent PTH. Overall, the global miR-29-3p tough decoy model represents a modest loss-of-function, which could be a relevant tool for assessing the possible impact of systemically administered miR-29-3p inhibitors. Our studies provide a potential rationale for co-administration of PTH1-34 and miR-29-3p inhibitors, to boost bone formation in severely affected osteoporosis patients, particularly in the cortical compartment.
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Affiliation(s)
- Henry C Hrdlicka
- Center for Molecular Oncology, UConn Health Center, Farmington, CT, United States of America
| | - Renata C Pereira
- Division of Pediatric Nephrology, David Geffen School of Medicine at University of California, Los Angeles, United States of America
| | - Bongjin Shin
- Center on Aging, UConn Health Center, Farmington, CT, United States of America
| | - Siu-Pok Yee
- Center for Mouse Genome Modification, UConn Health Center, Farmington, CT, United States of America
| | - Alix C Deymier
- Institute of Material Sciences, UConn Health Center, Farmington, CT, United States of America
| | - Sun-Kyeong Lee
- Center on Aging, UConn Health Center, Farmington, CT, United States of America.
| | - Anne M Delany
- Center for Molecular Oncology, UConn Health Center, Farmington, CT, United States of America.
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12
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Tachibana A, Saito S, Fujiyama Y, Tanabe T. LidNA, a miRNA inhibitor constructed with unmodified DNA, requires an xxxA insertion sequence in miRNA binding site for its potent inhibitory activity. FEBS Lett 2020; 594:1608-1614. [DOI: 10.1002/1873-3468.13756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Akira Tachibana
- Department of Bioengineering Graduate School of Engineering Osaka City University JapanOsaka
| | - Satoshi Saito
- Department of Bioengineering Graduate School of Engineering Osaka City University JapanOsaka
| | - Yukiko Fujiyama
- Department of Bioengineering Graduate School of Engineering Osaka City University JapanOsaka
| | - Toshizumi Tanabe
- Department of Bioengineering Graduate School of Engineering Osaka City University JapanOsaka
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13
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Yoshioka K, Kunieda T, Asami Y, Guo H, Miyata H, Yoshida-Tanaka K, Sujino Y, Piao W, Kuwahara H, Nishina K, Hara RI, Nagata T, Wada T, Obika S, Yokota T. Highly efficient silencing of microRNA by heteroduplex oligonucleotides. Nucleic Acids Res 2019; 47:7321-7332. [PMID: 31214713 PMCID: PMC6698647 DOI: 10.1093/nar/gkz492] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022] Open
Abstract
AntimiR is an antisense oligonucleotide that has been developed to silence microRNA (miRNA) for the treatment of intractable diseases. Enhancement of its in vivo efficacy and improvement of its toxicity are highly desirable but remain challenging. We here design heteroduplex oligonucleotide (HDO)-antimiR as a new technology comprising an antimiR and its complementary RNA. HDO-antimiR binds targeted miRNA in vivo more efficiently by 12-fold than the parent single-stranded antimiR. HDO-antimiR also produced enhanced phenotypic effects in mice with upregulated expression of miRNA-targeting messenger RNAs. In addition, we demonstrated that the enhanced potency of HDO-antimiR was not explained by its bio-stability or delivery to the targeted cell, but reflected an improved intracellular potency. Our findings provide new insights into biology of miRNA silencing by double-stranded oligonucleotides and support the in vivo potential of this technology based on a new class of for the treatment of miRNA-related diseases.
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Affiliation(s)
- Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Taiki Kunieda
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yutaro Asami
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Huijia Guo
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Haruka Miyata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yumiko Sujino
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Wenying Piao
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hiroya Kuwahara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kazutaka Nishina
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Rintaro Iwata Hara
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Takeshi Wada
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Satoshi Obika
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
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14
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Hoshikawa N, Sakai A, Takai S, Suzuki H. Targeting Extracellular miR-21-TLR7 Signaling Provides Long-Lasting Analgesia in Osteoarthritis. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:199-207. [PMID: 31841992 PMCID: PMC6920297 DOI: 10.1016/j.omtn.2019.11.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/12/2022]
Abstract
Osteoarthritis (OA) is the most prevalent joint disorder associated with severe chronic pain. Although synovial inflammation is well correlated with pain severity, the molecular mechanism responsible for OA pain remains unclear. Here, we show that extracellular miR-21 released from synovial tissue mediates knee OA pain in surgical OA model rats. miR-21 was the most abundant among increased microRNAs (miRNAs) in the synovial tissue. miR-21 was released into extracellular space from the synovial tissue and increased in the synovial fluid. A single intra-articular injection of miR-21 inhibitor exerted long-term analgesia of knee OA pain, whereas miR-21 injection in naive rats caused knee joint pain. miR-21 mutant, which lacks the Toll-like receptor (TLR) binding motif, but not in the seed sequence, did not cause joint pain, suggesting a non-canonical mode of action different from translational repression. Consistent with this, the algesic effect of miR-21 was blocked by antagonizing TLR7. The TLR7 antagonist also exerted a long-lasting analgesic effect on knee OA pain. Therefore, extracellular miR-21 released from synovial tissue mediates knee OA pain through TLR7 activation in surgical OA model rats. Extracellular miRNA in the joint may be a plausible target for pain therapy, providing a novel analgesic strategy for OA.
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Affiliation(s)
- Naoya Hoshikawa
- Department of Pharmacology, Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan; Department of Orthopaedic Surgery, Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
| | - Atsushi Sakai
- Department of Pharmacology, Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan.
| | - Shinro Takai
- Department of Orthopaedic Surgery, Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
| | - Hidenori Suzuki
- Department of Pharmacology, Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
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15
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Hooykaas MJG, Soppe JA, De Buhr HM, Kruse E, Wiertz EJHJ, Lebbink RJ. RNA accessibility impacts potency of Tough Decoy microRNA inhibitors. RNA Biol 2018; 15:1410-1419. [PMID: 30339041 PMCID: PMC6284568 DOI: 10.1080/15476286.2018.1537746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that post-transcriptionally regulate gene expression through silencing of complementary target mRNAs. miRNAs are involved in many biological processes, including cell proliferation, differentiation, cell signaling and cellular defense responses to infection. Strategies that allow for strong and stable suppression of specific microRNA activity are needed to study miRNA functions and to develop therapeutic intervention strategies aimed at interfering with miRNA activity in vivo. One of these classes of miRNA inhibitors are Tough Decoys (TuD) RNAs, which comprise of an imperfect RNA hairpin structure that harbors two opposing miRNA binding sites. Upon developing TuDs targeting Epstein-Barr virus miRNAs, we observed a strong variation in inhibitory potential between different TuD RNAs targeting the same miRNA. We show that the composition of the 'bulge' sequence in the miRNA binding sites has a strong impact on the inhibitory potency of the TuD. Our data implies that miRNA inhibition correlates with the thermodynamic properties of the TuD and that design aimed at lowering the TuD opening energy increases TuD potency. Our study provides specific guidelines for the design and construction of potent decoy-based miRNA inhibitors, which may be used for future therapeutic intervention strategies.
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Affiliation(s)
- Marjolein J G Hooykaas
- a Department of Medical Microbiology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Jasper A Soppe
- a Department of Medical Microbiology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Hendrik M De Buhr
- a Department of Medical Microbiology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Elisabeth Kruse
- a Department of Medical Microbiology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Emmanuel J H J Wiertz
- a Department of Medical Microbiology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Robert J Lebbink
- a Department of Medical Microbiology , University Medical Center Utrecht , Utrecht , The Netherlands
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16
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Hirano Y, Kojima N, Komatsu Y. Synthesis and Application of Interstrand Cross-Linked Duplexes by Covalently Linking a Pair of Abasic Sites. ACTA ACUST UNITED AC 2018; 75:e63. [PMID: 30315733 DOI: 10.1002/cpnc.63] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Interstrand cross-linking of DNA or RNA inhibits the double strands from dissociating into single strands. This article contains detailed procedures for the synthesis of a novel interstrand cross-linker that comprises a bis-aminooxy naphthalene derivative and a description of its use in the preparation of sequence-specific interstrand cross-linked oligonucleotide duplexes. The interstrand cross-linker covalently connects a pair of apurinic/apyrimidinic sites in DNA/RNA duplexes with bis(aminooxy) groups. The resulting oxime linkages are stable under physiological conditions and greatly improve the thermal stability of the duplex. In addition, we construct a novel anti-miRNA oligonucleotide (AMO) flanked by interstrand cross-linked 2'-O-methylated RNA duplexes (CLs). AMO flanked by CLs at the 5'- and 3'-termini exhibited high inhibition activity toward miRNA function in cells. The novel interstrand cross-linker indicates potent activity and is applicable in biophysical studies, oligonucleotide therapeutics, and materials science. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Naoshi Kojima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
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17
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Poller W, Dimmeler S, Heymans S, Zeller T, Haas J, Karakas M, Leistner DM, Jakob P, Nakagawa S, Blankenberg S, Engelhardt S, Thum T, Weber C, Meder B, Hajjar R, Landmesser U. Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J 2018; 39:2704-2716. [PMID: 28430919 PMCID: PMC6454570 DOI: 10.1093/eurheartj/ehx165] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.
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Affiliation(s)
- Wolfgang Poller
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
- DZHK, Site Rhein-Main, Frankfurt, Germany
| | - Stephane Heymans
- Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Mahir Karakas
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - David-Manuel Leistner
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Philipp Jakob
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Stefan Engelhardt
- Institute for Pharmacology and Toxikology, Technische Universität München, Biedersteiner Strasse 29, München, Germany
- DZHK, Site Munich, Munich, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Christian Weber
- DZHK, Site Munich, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstrasse 8a/9, Munich, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Hajjar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulf Landmesser
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, Germany
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18
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Mie Y, Hirano Y, Kowata K, Nakamura A, Yasunaga M, Nakajima Y, Komatsu Y. Function Control of Anti-microRNA Oligonucleotides Using Interstrand Cross-Linked Duplexes. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:64-74. [PMID: 29499957 PMCID: PMC5734696 DOI: 10.1016/j.omtn.2017.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
Abstract
MicroRNA (miRNA)-guided argonaute (Ago) controls gene expression upon binding to the 3′ UTR of mRNA. The miRNA function can be competitively inhibited by single-stranded anti-miRNA oligonucleotides (AMOs). In this study, we constructed a novel type of AMO flanked by interstrand cross-linked 2′-O-methylated RNA duplexes (CLs) that confer a stable helical conformation. Compared with other structured AMOs, AMO flanked by CLs at the 5′ and 3′ termini exhibited much higher inhibitory activity in cells. Anti-miRNA activity, nuclease resistance, and miRNA modification pattern distinctly differed according to the CL-connected positions in AMOs. Moreover, we found that the 3′-side CL improves nuclease resistance, whereas the 5′-side CL contributes to stable binding with miRNA in Ago upon interaction with the 3′ part of miRNA. These structure-function relationship analyses of AMOs provide important insights into the function control of Ago-miRNA complexes, which will be useful for basic miRNA research as well as for determining therapeutic applications of AMO.
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Affiliation(s)
- Yasuhiro Mie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Keiko Kowata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Mayu Yasunaga
- Health Research Institute, AIST, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Yoshihiro Nakajima
- Health Research Institute, AIST, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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Zhao B, Lucas KJ, Saha TT, Ha J, Ling L, Kokoza VA, Roy S, Raikhel AS. MicroRNA-275 targets sarco/endoplasmic reticulum Ca2+ adenosine triphosphatase (SERCA) to control key functions in the mosquito gut. PLoS Genet 2017; 13:e1006943. [PMID: 28787446 PMCID: PMC5560755 DOI: 10.1371/journal.pgen.1006943] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 08/17/2017] [Accepted: 07/26/2017] [Indexed: 12/17/2022] Open
Abstract
The yellow fever mosquito Aedes aegypti is the major vector of arboviruses, causing numerous devastating human diseases, such as dengue and yellow fevers, Chikungunya and Zika. Female mosquitoes need vertebrate blood for egg development, and repeated cycles of blood feeding are tightly linked to pathogen transmission. The mosquito’s posterior midgut (gut) is involved in blood digestion and also serves as an entry point for pathogens. Thus, the mosquito gut is an important tissue to investigate. The miRNA aae-miR-275 (miR-275) has been shown to be required for normal blood digestion in the female mosquito; however, the mechanism of its action has remained unknown. Here, we demonstrate that miR-275 directly targets and positively regulates sarco/endoplasmic reticulum Ca2+adenosine triphosphatase, which is implicated in active transport of Ca2+ from the cytosol to the sarco/endoplasmic reticulum. We utilized a combination of the gut-specific yeast transcription activator protein Gal4/upstream activating sequence (Gal4/UAS) system and miRNA Tough Decoy technology to deplete the endogenous level of miR-275 in guts of transgenic mosquitoes. This gut-specific reduction of miR-275 post blood meal decreased SERCA mRNA and protein levels of the digestive enzyme late trypsin. It also resulted in a significant reduction of gut microbiota. Moreover, the decrease of miR-275 and SERCA correlated with defects in the Notch signaling pathway and assembly of the gut actin cytoskeleton. The adverse phenotypes caused by miR-275 silencing were rescued by injections of miR-275 mimic. Thus, we have discovered that miR-275 directly targets SERCA, and the maintenance of its level is critical for multiple gut functions in mosquitoes. Female mosquitoes transmit numerous devastating human diseases. The mosquito gut, in addition to its primary function as a site of blood digestion, represents the entry point for pathogen colonization in mosquito vectors. The conserved microRNA, miR-275, was shown to be required for blood digestion and egg development. In this study, we investigated the target of miR-275 contributing to the regulation of mosquito gut functions. We achieved spatiotemporal suppression of miR-275 using a transgenic Tough Decoy RNA approach in the A. aegypti female mosquito gut. Furthermore, we have uncovered that miR-275 targets sarco/endoplasmic reticulum Ca2+- adenosine triphosphatase (SERCA), affecting numerous gut functions including blood digestion, production of digestive proteases, and assembly of the gut actin cytoskeleton. SERCA is essential for maintenance of Ca2+ homeostasis, and its disturbance, in humans, leads to cardiac hypertrophy, heart failure and cancers. Therefore, the finding that the miRNA miR-275 targets SERCA not only contributes to the knowledge of mosquito gut regulation but also significantly adds to the general understanding of mechanisms governing this critical molecule.
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Affiliation(s)
- Bo Zhao
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Keira J Lucas
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Tusar T Saha
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Jisu Ha
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
| | - Lin Ling
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Vladimir A Kokoza
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Sourav Roy
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Alexander S Raikhel
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
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20
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Hollensen AK, Thomsen R, Bak RO, Petersen CC, Ermegaard ER, Aagaard L, Damgaard CK, Mikkelsen JG. Improved microRNA suppression by WPRE-linked tough decoy microRNA sponges. RNA (NEW YORK, N.Y.) 2017; 23:1247-1258. [PMID: 28487381 PMCID: PMC5513069 DOI: 10.1261/rna.061192.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/26/2017] [Indexed: 05/02/2023]
Abstract
Our genes are post-transcriptionally regulated by microRNAs (miRNAs) inducing translational suppression and degradation of targeted mRNAs. Strategies to inhibit miRNAs in a spatiotemporal manner in a desired cell type or tissue, or at a desired developmental stage, can be crucial for understanding miRNA function and for pushing forward miRNA suppression as a feasible rationale for genetic treatment of disease. For such purposes, RNA polymerase II (RNA Pol II)-transcribed tough decoy (TuD) miRNA inhibitors are particularly attractive. Here, we demonstrate augmented miRNA suppression capacity of TuD RNA hairpins linked to the Woodchuck hepatitis virus post-transcriptional regulatory element (WPRE). This effect is position-dependent and evident only when the WPRE is positioned upstream of the TuD. In accordance, inclusion of the WPRE does not change nuclear export, translation, total levels of TuD-containing RNA transcripts, or cytoplasmic P-body localization, suggesting that previously reported WPRE functions are negligible for improved TuD function. Notably, deletion analysis of TuD-fused WPRE unveils truncated WPRE variants resulting in optimized miRNA suppression. Together, our findings add to the guidelines for production of WPRE-supported anti-miRNA TuDs.
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Affiliation(s)
- Anne Kruse Hollensen
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Rune Thomsen
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
- Department of Pediatrics, Stanford University, Stanford, California 94305, USA
| | | | - Eva R Ermegaard
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Lars Aagaard
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Christian Kroun Damgaard
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-8000 Aarhus C, Denmark
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21
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A mammalian mirtron miR-1224 promotes tube-formation of human primary endothelial cells by targeting anti-angiogenic factor epsin2. Sci Rep 2017; 7:5541. [PMID: 28717225 PMCID: PMC5514154 DOI: 10.1038/s41598-017-05782-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 06/05/2017] [Indexed: 01/29/2023] Open
Abstract
Angiogenesis, new vessel formation from pre-existing vessels, is a highly conserved event through vertebrates. However, the system for tuning angiogenesis by species-intrinsic factors is totally unknown. miR-1224 is a member of mammal-specific mirtrons, which were identified as non-canonical microRNAs. We found that the expression of miR-1224 was upregulated in capillary-like tube-forming human umbilical vein endothelial cells on Matrigel. Enforced expression of miR-1224 stimulated tube formation, whereas repression of endogenous miR-1224 inhibited formation. Enforced expression of miR-1224 enhanced VEGF signaling and repressed NOTCH signaling. The adaptor protein of clathrin-dependent endocytosis, epsin2, which has been shown to be a suppressor of angiogenesis, was a direct target of miR-1224. Knockdown of EPN2 stimulated tube formation, while overexpression of EPN2 repressed miR-1224-mediated stimulation. Our findings indicate that miR-1224 is a mammal specific modulator of angiogenesis.
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22
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Steinkraus BR, Toegel M, Fulga TA. Tiny giants of gene regulation: experimental strategies for microRNA functional studies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2016; 5:311-62. [PMID: 26950183 PMCID: PMC4949569 DOI: 10.1002/wdev.223] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/19/2015] [Accepted: 11/28/2015] [Indexed: 12/11/2022]
Abstract
The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high-throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA-target binding events in vivo drove the emergence of a slew of high-throughput multiplex strategies, which now provide a viable prospect for elucidating genome-wide miRNA-target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post-transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high-precision interference with their direct, endogenous targets. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Toegel
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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23
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A new plasmid-based microRNA inhibitor system that inhibits microRNA families in transgenic mice and cells: a potential new therapeutic reagent. Gene Ther 2016; 23:527-42. [PMID: 26934100 PMCID: PMC4891277 DOI: 10.1038/gt.2016.22] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/19/2016] [Accepted: 02/25/2016] [Indexed: 12/19/2022]
Abstract
Current tools for the inhibition of microRNA (miR) function are limited to modified antisense oligonucleotides, sponges and decoy RNA molecules and none have been used to understand miR function during development. CRISPR/Cas-mediated deletion of miR sequences within the genome requires multiple chromosomal deletions to remove all functional miR family members because of duplications. Here, we report a novel plasmid-based miR inhibitor system (PMIS) that expresses a new RNA molecule, which inhibits miR family members in cells and mice. The PMIS engineered RNA optimal secondary structure, flanking sequences and specific antisense miR oligonucleotide sequence bind the miR in a stable complex to inhibit miR activity. In cells, one PMIS can effectively inhibit miR family members that share the same seed sequence. The PMIS shows no off-target effects or toxicity and is highly specific for miRs sharing identical seed sequences. Transgenic mice expressing both PMIS-miR-17-18 and PMIS-miR-19-92 show similar phenotypes of miR-17-92-knockout mice. Interestingly, mice only expressing PMIS-miR-17-18 have developmental defects distinct from mice only expressing PMIS-miR-19-92 demonstrating usefulness of the PMIS system to dissect different functions of miRs within clusters. Different PMIS miR inhibitors can be linked together to knock down multiple miRs expressed from different chromosomes. Inhibition of the miR-17-92, miR-106a-363 and miR-106b-25 clusters reveals new mechanisms and developmental defects for these miRs. We report a new tool to dissect the role of miRs in development without genome editing, inhibit miR function in cells and as a potential new therapeutic reagent.
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24
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Dynamics and plasticity of the epithelial to mesenchymal transition induced by miR-200 family inhibition. Sci Rep 2016; 6:21117. [PMID: 26887353 PMCID: PMC4758077 DOI: 10.1038/srep21117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/18/2016] [Indexed: 01/19/2023] Open
Abstract
Whereas miR-200 family is known to be involved in the epithelial-to-mesenchymal transition (EMT), a crucial biological process observed in normal and pathological contexts, it has been largely unclear how far the functional levels of these tiny RNAs alone can propagate the molecular events to accomplish this process within several days. By developing a potent inhibitor of miR-200 family members (TuD-141/200c), the expression of which is strictly regulatable by the Tet (tetracycline)-On system, we found using a human colorectal cell line, HCT116, that several direct gene target mRNAs (Zeb1/Zeb2, ESRP1, FN1and FHOD1) of miR-200 family were elevated with distinct kinetics. Prompt induction of the transcriptional suppressors, Zeb1/Zeb2 in turn reduced the expression levels of miR-200c/-141 locus, EpCAM, ESRP1 and E-Cad. The loss of ESRP1 subsequently switched the splicing isoforms of CD44 and p120 catenin mRNAs to mesenchymal type. Importantly, within 9 days after the release from the inhibition of miR-200 family, all of the expression changes in the 14 genes observed in this study returned to their original levels in the epithelial cells. This suggests that the inherent epithelial plasticity is supported by a weak retention of key regulatory gene expression in either the epithelial or mesenchymal states through epigenetic regulation.
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25
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A PCR-Based Method to Construct Lentiviral Vector Expressing Double Tough Decoy for miRNA Inhibition. PLoS One 2015; 10:e0143864. [PMID: 26624995 PMCID: PMC4666662 DOI: 10.1371/journal.pone.0143864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/09/2015] [Indexed: 01/12/2023] Open
Abstract
DNA vector-encoded Tough Decoy (TuD) miRNA inhibitor is attracting increased attention due to its high efficiency in miRNA suppression. The current methods used to construct TuD vectors are based on synthesizing long oligonucleotides (~90 mer), which have been costly and problematic because of mutations during synthesis. In this study, we report a PCR-based method for the generation of double Tough Decoy (dTuD) vector in which only two sets of shorter oligonucleotides (< 60 mer) were used. Different approaches were employed to test the inhibitory potency of dTuDs. We demonstrated that dTuD is the most efficient method in miRNA inhibition in vitro and in vivo. Using this method, a mini dTuD library against 88 human miRNAs was constructed and used for a high-throughput screening (HTS) of AP-1 pathway-related miRNAs. Seven miRNAs (miR-18b-5p, -101-3p, -148b-3p, -130b-3p, -186-3p, -187-3p and -1324) were identified as candidates involved in AP-1 pathway regulation. This novel method allows for an accurate and cost-effective generation of dTuD miRNA inhibitor, providing a powerful tool for efficient miRNA suppression in vitro and in vivo.
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26
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Tsuyama J, Bunt J, Richards LJ, Iwanari H, Mochizuki Y, Hamakubo T, Shimazaki T, Okano H. MicroRNA-153 Regulates the Acquisition of Gliogenic Competence by Neural Stem Cells. Stem Cell Reports 2015. [PMID: 26212661 PMCID: PMC4618452 DOI: 10.1016/j.stemcr.2015.06.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Mammalian neural stem/progenitor cells (NSPCs) sequentially generate neurons and glia during CNS development. Here we identified miRNA-153 (miR-153) as a modulator of the temporal regulation of NSPC differentiation. Overexpression (OE) of miR-153 delayed the onset of astrogliogenesis and maintained NSPCs in an undifferentiated state in vitro and in the developing cortex. The transcription factors nuclear factor I (NFI) A and B, essential regulators of the initiation of gliogenesis, were found to be targets of miR-153. Inhibition of miR-153 in early neurogenic NSPCs induced precocious gliogenesis, whereas NFIA/B overexpression rescued the anti-gliogenic phenotypes induced by miR-153 OE. Our results indicate that miR-mediated fine control of NFIA/B expression is important in the molecular networks that regulate the acquisition of gliogenic competence by NSPCs in the developing CNS. We identify miR-153 as a regulator for the acquisition of gliogenic competence NFIA and NFIB are physiological targets of miR-153 Inhibition of miR-153 confers gliogenic competence on early neurogenic NSPCs Fine-tuning of NFIA/B expressions by miR-153 is involved in the timing of gliogenesis
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Affiliation(s)
- Jun Tsuyama
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-Ku, Tokyo 160-8582, Japan
| | - Jens Bunt
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Linda J Richards
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4067, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Hiroko Iwanari
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Yasuhiro Mochizuki
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Takao Hamakubo
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Takuya Shimazaki
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-Ku, Tokyo 160-8582, Japan.
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-Ku, Tokyo 160-8582, Japan.
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27
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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: 28] [Impact Index Per Article: 3.1] [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.
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28
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Yonemoto H, Asai K, Hamada M. A semi-supervised learning approach for RNA secondary structure prediction. Comput Biol Chem 2015; 57:72-9. [PMID: 25748534 DOI: 10.1016/j.compbiolchem.2015.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 02/03/2015] [Indexed: 12/25/2022]
Abstract
RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited.
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Affiliation(s)
- Haruka Yonemoto
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan
| | - Kiyoshi Asai
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan; Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan; Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7, Aomi, Koto-ku, Tokyo 135-0064, Japan.
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29
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Laganà A, Shasha D, Croce CM. Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools. Front Bioeng Biotechnol 2014; 2:65. [PMID: 25566532 PMCID: PMC4263176 DOI: 10.3389/fbioe.2014.00065] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/23/2014] [Indexed: 01/08/2023] Open
Abstract
The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.
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Affiliation(s)
- Alessandro Laganà
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University , Columbus, OH , USA
| | - Dennis Shasha
- Courant Institute of Mathematical Sciences, New York University , New York, NY , USA
| | - Carlo Maria Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University , Columbus, OH , USA
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30
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Le MTN, Hamar P, Guo C, Basar E, Perdigão-Henriques R, Balaj L, Lieberman J. miR-200-containing extracellular vesicles promote breast cancer cell metastasis. J Clin Invest 2014; 124:5109-28. [PMID: 25401471 DOI: 10.1172/jci75695] [Citation(s) in RCA: 341] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 10/03/2014] [Indexed: 12/21/2022] Open
Abstract
Metastasis is associated with poor prognosis in breast cancer patients. Not all cancer cells within a tumor are capable of metastasizing. The microRNA-200 (miR-200) family, which regulates the mesenchymal-to-epithelial transition, is enriched in the serum of patients with metastatic cancers. Ectopic expression of miR-200 can confer metastatic ability to poorly metastatic tumor cells in some settings. Here, we investigated whether metastatic capability could be transferred between metastatic and nonmetastatic cancer cells via extracellular vesicles. miR-200 was secreted in extracellular vesicles from metastatic murine and human breast cancer cell lines, and miR-200 levels were increased in sera of mice bearing metastatic tumors. In culture, murine and human metastatic breast cancer cell extracellular vesicles transferred miR-200 microRNAs to nonmetastatic cells, altering gene expression and promoting mesenchymal-to-epithelial transition. In murine cancer and human xenograft models, miR-200-expressing tumors and extracellular vesicles from these tumors promoted metastasis of otherwise weakly metastatic cells either nearby or at distant sites and conferred to these cells the ability to colonize distant tissues in a miR-200-dependent manner. Together, our results demonstrate that metastatic capability can be transferred by the uptake of extracellular vesicles.
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31
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Avitabile C, Cimmino A, Romanelli A. Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications. J Med Chem 2014; 57:10220-40. [PMID: 25280271 DOI: 10.1021/jm5006594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
ncRNAs are emerging as key regulators of physiological and pathological processes and therefore have been identified as pharmacological targets and as markers for some diseases. Oligonucleotide analogues represent so far the most widely employed tool for the modulation of the expression of ncRNAs. In this perspective we briefly describe most of the known classes of ncRNAs and then we discuss the design and the applications of oligonucleotide analogues for their targeting. The effects of modifications of the chemical structure of the oligonucleotides on properties such as the binding affinity toward targets and off targets, and the stability to degradation and their biological effects (when known) are discussed. Examples of molecules currently used in clinical trials are also reported.
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Affiliation(s)
- Concetta Avitabile
- Università di Napoli "Federico II" , Dipartimento di Farmacia, via Mezzocannone 16, 80134 Napoli, Italy
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32
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Picardi E, Veneziano D, Russo F, Pulvirenti A, Giugno R, Croce CM, Ferro A. Computational design of artificial RNA molecules for gene regulation. Methods Mol Biol 2014; 1269:393-412. [PMID: 25577393 PMCID: PMC4425273 DOI: 10.1007/978-1-4939-2291-8_25] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA interference (RNAi) is a powerful tool for the regulation of gene expression. Small exogenous noncoding RNAs (ncRNAs) such as siRNA and shRNA are the active silencing agents, intended to target and cleave complementary mRNAs in a specific way. They are widely and successfully employed in functional studies, and several ongoing and already completed siRNA-based clinical trials suggest encouraging results in the regulation of overexpressed genes in disease. siRNAs share many aspects of their biogenesis and function with miRNAs, small ncRNA molecules transcribed from endogenous genes which are able to repress the expression of target mRNAs by either inhibiting their translation or promoting their degradation. Although siRNA and artificial miRNA molecules can significantly reduce the expression of overexpressed target genes, cancer and other diseases can also be triggered or sustained by upregulated miRNAs. Thus, in the past recent years, molecular tools for miRNA silencing, such as antagomiRs and miRNA sponges, have been developed. These molecules have shown their efficacy in the derepression of genes downregulated by overexpressed miRNAs. In particular, while a single antagomiR is able to inhibit a single complementary miRNA, an artificial sponge construct usually contains one or more binding sites for one or more miRNAs and functions by competing with the natural targets of these miRNAs. As a consequence, natural miRNA targets are reexpressed at their physiological level. In this chapter we review the most successful methods for the computational design of siRNAs, antagomiRs, and miRNA sponges and describe the most popular tools that implement them.
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Affiliation(s)
- Ernesto Picardi
- grid.419691.20000000417583396Department of Biosciences, Biotechnology and Biopharmaceutics, and National Research Council, University of Bari; Institute of Biomembranes and Bioenergetics, Bari, Italy, and National Institute of Biostructures and Biosystems (INBB), Rome, Italy
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Fujiwara T, Katsuda T, Hagiwara K, Kosaka N, Yoshioka Y, Takahashi RU, Takeshita F, Kubota D, Kondo T, Ichikawa H, Yoshida A, Kobayashi E, Kawai A, Ozaki T, Ochiya T. Clinical Relevance and Therapeutic Significance of MicroRNA-133a Expression Profiles and Functions in Malignant Osteosarcoma-Initiating Cells. Stem Cells 2014; 32:959-73. [DOI: 10.1002/stem.1618] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 11/20/2013] [Accepted: 11/22/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Tomohiro Fujiwara
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
- Department of Musculoskeletal Oncology; National Cancer Center Hospital; Tokyo Japan
- Department of Orthopedic Surgery; Okayama University Graduate School of Medicine; Dentistry, and Pharmaceutical Sciences Okayama Japan
| | - Takeshi Katsuda
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Keitaro Hagiwara
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Nobuyoshi Kosaka
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Yusuke Yoshioka
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Ryou-U Takahashi
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Fumitaka Takeshita
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Daisuke Kubota
- Division of Pharmacoproteomics; National Cancer Center Research Institute; Tokyo Japan
| | - Tadashi Kondo
- Division of Pharmacoproteomics; National Cancer Center Research Institute; Tokyo Japan
| | - Hitoshi Ichikawa
- Division of Genetics; National Cancer Center Research Institute; Tokyo Japan
| | - Akihiko Yoshida
- Division of Pathology and Clinical Laboratories; National Cancer Center Hospital; Tokyo Japan
| | - Eisuke Kobayashi
- Department of Musculoskeletal Oncology; National Cancer Center Hospital; Tokyo Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology; National Cancer Center Hospital; Tokyo Japan
| | - Toshifumi Ozaki
- Department of Orthopedic Surgery; Okayama University Graduate School of Medicine; Dentistry, and Pharmaceutical Sciences Okayama Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
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Blechinger J, Pieper H, Marzenell P, Kovbasyuk L, Serva A, Starkuviene V, Erfle H, Mokhir A. Short, terminally modified 2'-OMe RNAs as inhibitors of microRNA. Chem Commun (Camb) 2014; 49:7397-9. [PMID: 23863995 DOI: 10.1039/c3cc43174f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We applied 14-mer 2'-OMe RNAs as inhibitors of selected micro RNAs. To improve their properties, we introduced a trimethoxystilbene residue at the 5'-terminus and three 2'-fluoro-2'-deoxynucleotides at the 3'-terminus to obtain potent inhibitors, whose mismatch discrimination is substantially better than that of typically applied >18-mers.
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Affiliation(s)
- Jenny Blechinger
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Henkestr. 42, 91054 Erlangen, Germany
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Bak RO, Hollensen AK, Mikkelsen JG. Managing microRNAs with vector-encoded decoy-type inhibitors. Mol Ther 2013; 21:1478-85. [PMID: 23752312 DOI: 10.1038/mt.2013.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 04/26/2013] [Indexed: 01/16/2023] Open
Abstract
A rapidly growing understanding of the complex circuitry of microRNA (miRNA)-mediated gene regulation is attracting attention to miRNAs as new drug targets. Targeted miRNA suppression is achieved in a sequence-specific manner by antisense RNA "decoy" molecules. Such synthetic miRNA inhibitors have reached the clinic with remarkable pace and may soon appear as new therapeutic modalities in several diseases. Shortcomings, however, include high production costs, the requirement for repeated administration, and difficulty achieving tissue-specific delivery. With the many recent landmark achievements in clinical gene therapy, new and refined vector-encoded miRNA suppression technologies are attractive for many applications, not least as tools in innumerable daily studies of miRNA biology in laboratories worldwide. Here, we provide an overview of the strategies that have been used to adapt vector-encoded inhibitors for miRNA suppression and discuss advantages related to spatiotemporal and long-term miRNA attenuation. With the remarkable new discovery of miRNA management by naturally occurring circular RNAs, RNA circles generated by trans-splicing mechanisms may prove to be well-suited carriers of decoy-type miRNA inhibitors. The community will aspire to combine circles with high-affinity miRNA decoy methodologies, and such "vectorized" RNA circles may represent new solid ways to deliver miRNA inhibitors, perhaps even with therapeutic applications.
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Affiliation(s)
- Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
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Sun K, Deng HJ, Lei ST, Dong JQ, Li GX. miRNA-338-3p suppresses cell growth of human colorectal carcinoma by targeting smoothened. World J Gastroenterol 2013; 19:2197-2207. [PMID: 23599646 PMCID: PMC3627884 DOI: 10.3748/wjg.v19.i14.2197] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 01/13/2013] [Accepted: 02/08/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the regulative effect of miRNA-338-3p (miR-338-3p) on cell growth in colorectal carcinoma (CRC).
METHODS: The lentiviral vector pLV-THM-miR-338-3p and pLV-THM-miR-338-3p-inhibitor were constructed. The recombinant viral vector encoding the pre-miR-338-3p or miR-338-3p-inhibitor and the two packaging plasmids psPAX2 and pMD2.G were cotransfected into human embryonic kidney 293T cells to package lentivirus. The supernatant containing the lentivirus particles was harvested to determine the viral titer, and this supernatant was then used to transduce CRC-derived cell line, SW-620. Flow cytometry was utilized for sorting the green fluorescent protein (GFP)+ cells to establish the SW-620 cell line stably expressing pre-miR-338-3p or miR-338-3p-inhibitor. Moreover, the expression of miR-338-3p was determined by real-time reverse transcriptase polymerase chain reaction, and Western blotting was used to detect the expression of the smoothened (SMO, the possible target of miR-338-3p) protein in SW-620 cells. Furthermore, the status of CRC cell proliferation and apoptosis were detected by 3-(4,5-dimethyl-2 thiazoyl)-2,5-diphenyl-2H-tetrazolium bromide assay and flow cytometry, respectively.
RESULTS: Restriction enzyme digestion and DNA sequencing demonstrated that the lentiviral vector pLV-THM-miR-338-3p and pLV-THM-miR-338-3p-inhibitor were constructed successfully. GFP was expressed after the SW-620 cells were transduced by the lentivirus. Expression of miR-338-3p in SW-620 cells transduced with the lentivirus pLV-THM-miR-338-3p was significantly increased (relative expression 3.91 ± 0.51 vs 2.36 ± 0.44, P < 0.01). Furthermore, overexpression of miR-338-3p inhibited the expression of SMO protein in SW-620 cells, which showed obviously suppressed proliferation ability [cellular proliferation inhibition rate (CPIR) 61.9% ± 5.2% vs 41.6% ± 4.8%, P < 0.01]. Expression of miR-338-3p in SW-620 cells transduced with the lentivirus pLV-THM-miR-338-3p-inhibitor was significantly decreased (relative expression 0.92 ± 0.29 vs 2.36 ± 0.44, P < 0.01). Moreover, the downregulated expression of miR-338-3p caused upregulated expression of the SMO protein in SW-620 cells, which showed significantly enhanced proliferation ability (CPIR 19.2% ± 3.8% vs 41.6% ± 4.8%, P < 0.01). However, anti-SMO-siRNA largely, but not completely, reversed the effects induced by blockage of miR-338-3p, suggesting that the regulative effect of miR-338-3p on CRC cell growth was indeed mediated by SMO.
CONCLUSION: miR-338-3p could suppress CRC growth by inhibiting SMO protein expression.
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Chistiakov DA, Sobenin IA, Orekhov AN. Strategies to deliver microRNAs as potential therapeutics in the treatment of cardiovascular pathology. Drug Deliv 2013; 19:392-405. [PMID: 23173580 DOI: 10.3109/10717544.2012.738436] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CONTEXT MicroRNAs (miRNAs) are important and powerful mediators in a variety of diseases including cardiovascular pathology. Thus, they emerged as interesting new drug targets. However, it is important to develop efficient transfer tools to successfully deliver miRNAs or antisense oligonucleotides (antagomirs) to the target tissue. OBJECTIVE The aim of this study was to review the scientific literature on delivery techniques currently used for transfer of miRNAs and antagomirs to animal models of cardiovascular disease and those that are likely to be used for therapeutic miRNA transport in the nearest future. METHODS The research was carried out by consulting the following medical websites: Medicus Medline Index, PubMed (National Library of Medicine), and a registry database of clinical trials conducted in USA ( www.clinicaltrials.gov). The selection gathers articles written in English, published from January 2012. RESULTS A current delivery technique includes chemical modification of antagomirs with 2-O-methyl-group or 2-O-methyoxyethyl or using locked nucleic acids to increase drug stability and affinity. Development of miRNA sponges/decoys aims to target all members of a miRNA seed family of interest. A further strategy to augment miRNA levels is to use miRNA delivery through viral-based vectors including adenoviruses, adeno-associated viruses, and lentiviruses. To date, a variety of nanocarriers is available for efficient delivery of miRNAs. Microvesicles, and apoptotic bodies that contain circulating miRNAs could be also used as therapeutic transport systems in the nearest future. CONCLUSION Development of new miRNA carrier systems with advanced properties and large animal data in the cardiovascular field is highly recommended.
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Affiliation(s)
- Dimitry A Chistiakov
- Department of Medical Nanobiotechnology, Pirogov Russian State Medical University, Moscow, Russia.
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Bak RO, Hollensen AK, Primo MN, Sørensen CD, Mikkelsen JG. Potent microRNA suppression by RNA Pol II-transcribed 'Tough Decoy' inhibitors. RNA (NEW YORK, N.Y.) 2013; 19:280-93. [PMID: 23249752 PMCID: PMC3543086 DOI: 10.1261/rna.034850.112] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/09/2012] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression and modulators of diverse biological pathways. Analyses of miRNA function as well as therapeutic managing of miRNAs rely on cellular administration of miRNA inhibitors which may be achieved by the use of viral vehicles. This study explores the miRNA-suppressive capacity of inhibitors expressed intracellularly from lentivirus-derived gene vectors. Superior activity of two decoy-type inhibitors, a "Bulged Sponge" with eight miRNA recognition sites and a hairpin-shaped "Tough Decoy" containing two miRNA recognition sites, is demonstrated in a side-by-side comparison of seven types of miRNA inhibitors transcribed as short RNAs from an RNA Pol III promoter. We find that lentiviral vectors expressing Tough Decoy inhibitors are less vulnerable than Bulged Sponge-encoding vectors to targeting by the cognate miRNA and less prone, therefore, to reductions in transfer efficiency. Importantly, it is demonstrated that Tough Decoy inhibitors retain their miRNA suppression capacity in the context of longer RNA transcripts expressed from an RNA Pol II promoter. Such RNA Pol II-transcribed Tough Decoy inhibitors are new tools in managing of miRNAs and may have potential for temporal and spatial regulation of miRNA activity as well as for therapeutic targeting of miRNAs that are aberrantly expressed in human disease.
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Hollensen AK, Bak RO, Haslund D, Mikkelsen JG. Suppression of microRNAs by dual-targeting and clustered Tough Decoy inhibitors. RNA Biol 2013; 10:406-14. [PMID: 23324610 DOI: 10.4161/rna.23543] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are ubiquitous regulators of gene expression that contribute to almost any cellular process. Methods for managing of miRNA activity are attracting increasing attention in relation to diverse experimental and therapeutic applications. DNA-encoded miRNA inhibitors expressed from plasmid or virus-based vectors provide persistent miRNA suppression and options of tissue-directed micromanaging. In this report, we explore the potential of exploiting short, hairpin-shaped RNAs for simultaneous suppression of two or more miRNAs. Based on the "Tough Decoy" (TuD) design, we create dual-targeting hairpins carrying two miRNA recognition sites and demonstrate potent co-suppression of different pairs of unrelated miRNAs by a single DNA-encoded inhibitor RNA. In addition, enhanced miRNA suppression is achieved by expression of RNA polymerase II-transcribed inhibitors carrying clustered TuD hairpins with up to a total of eight miRNA recognition sites. Notably, by expressing clustered TuD inhibitors harboring a single recognition site for each of a total of six miRNAs, we document robust parallel suppression of multiple miRNAs by inhibitor RNA molecules encoded by a single expression cassette. These findings unveil a new potential of TuD-based miRNA inhibitors and pave the way for standardizing synchronized suppression of families or clusters of miRNAs.
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Lucas K, Raikhel AS. Insect microRNAs: biogenesis, expression profiling and biological functions. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:24-38. [PMID: 23165178 PMCID: PMC3534889 DOI: 10.1016/j.ibmb.2012.10.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/24/2012] [Accepted: 10/28/2012] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNA) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that modulate gene expression at the post-transcriptional level via base pairing to target sites within messenger RNAs (mRNA). Typically, the miRNA "seed sequence" (nucleotides 2-8 at the 5' end) binds complementary seed match sites within the 3' untranslated region of mRNAs, resulting in either translational inhibition or mRNA degradation. MicroRNAs were first discovered in Caenorhabditis elegans and were shown to be involved in the timed regulation of developmental events. Since their discovery in the 1990s, thousands of potential miRNAs have since been identified in various organisms through small RNA cloning methods and/or computational prediction, and have been shown to play functionally important roles of gene regulation in invertebrates, vertebrates, plants, fungi and viruses. Numerous functions of miRNAs identified in Drosophila melanogaster have demonstrated a great significance of these regulatory molecules. However, elucidation of miRNA roles in non-drosophilid insects presents a challenging and important task.
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Affiliation(s)
- Keira Lucas
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, CA 92521, U.S.A
| | - Alexander S. Raikhel
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Corresponding author. Department of Entomology, University of California, Riverside, Riverside, CA 92521, U.S.A. Tel. +1 951 827 2129. (Keira Lucas); (Alexander S. Raikhel)
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Construction of lentivirus-based inhibitor of hsa-microRNA-338-3p with specific secondary structure. Acta Pharmacol Sin 2013. [PMID: 23202799 DOI: 10.1038/aps.2012.172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM To construct a lentivirus-based inhibitor with specific secondary structure that could exert long-term suppression on microRNA-338-3p (miR-338-3p), thus elucidating its molecular function in colorectal carcinoma cells. METHODS The miR-338-3p inhibitor sequence was synthesized and inserted into pLV-THM plasmid. HEK-293T cells were co-transfected with the lentiviral vectors pLV-THM-miR-338-3p-inhibitor, psPAX2, and pMD2.G. The supernatant containing the lentivirus particles was harvested to determine the viral titer, and then used to infect colorectal carcinoma-derived SW-620 cells. eGFP(+) cells were sorted using flow cytometry. The expression of miR-338-3p in SW-620 cells was determined with real-time RT-PCR, and the expression of the smoothened (SMO) protein was detected using Western blot analysis. The migration ability of the transfected SW-620 cells was assessed with transwell assay. RESULTS Restriction endonuclease analysis and DNA sequencing demonstrated that the lentiviral vector pLV-THM-miR-338-3p-inhibitor was successfully constructed. The expression of miR-338-3p in SW-620 cells was significantly decreased by infection with the lentivirus pLV-THM-miR-338-3p-inhibitor. Moreover, the down-regulated expression of miR-338-3p caused up-regulated expression of the SMO protein in SW-620 cells, which showed significantly enhanced migration in transwell assay. CONCLUSION The construction of the lentiviral vector pLV-THM-miR-338-3p-inhibitor with specific secondary structure provides a basis for further studies the molecular function of miR-338-3p in colorectal carcinoma. miR-338-3p may suppress SMO gene expression and thereby inhibit colorectal carcinoma migration.
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Fajardo T, Rosas MF, Sobrino F, Martinez-Salas E. Exploring IRES region accessibility by interference of foot-and-mouth disease virus infectivity. PLoS One 2012; 7:e41382. [PMID: 22815996 PMCID: PMC3399821 DOI: 10.1371/journal.pone.0041382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/20/2012] [Indexed: 11/22/2022] Open
Abstract
Translation initiation of picornavirus RNA is driven by an internal ribosome entry site (IRES) element located upstream of the initiator codon. RNA structure organization as well as RNA-protein interaction plays a fundamental role in internal initiation. IRES activity has been mainly analyzed in the context of reporter genes, lacking regions of the viral genome potentially affecting translation efficiency. With the aim to understand the vulnerability of the IRES and translation start region to small molecules in the context of the viral genome, we designed a set of customized RNase-resistant 2'O-methyl antisense oligoribonucleotides (2'OMe AONs) based on RNA structure data. These AONs were then used to monitor their capacity to interfere viral RNA translation, and thus, to inhibit virus yield. Foot-and-mouth disease virus (FMDV) RNA translation can be initiated at two in-frame AUG codons. We show here that a 2'OMe AON complementary to AUG2 inhibited viral multiplication more efficiently than the one that targeted AUG1. Furthermore, the response of the viral RNA to AONs targeting the IRES region denoted important differences between tissue culture cells and cell-free systems, reinforcing the need to analyze viral RNA response in living cells. Importantly, we have identified four specific motifs within the IRES element that are targets for viral inhibitors both in tissue culture cells and in cell-free systems. The identified targets define accessible regions to small molecules, which disturb either the RNA structural organization or the RNA-protein interactions needed to initiate translation in FMDV RNA.
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Affiliation(s)
- Teodoro Fajardo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, Madrid, Spain
| | - Maria Flora Rosas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, Madrid, Spain
| | - Francisco Sobrino
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, Madrid, Spain
| | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, Madrid, Spain
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Chistiakov DA, Chekhonin VP. Contribution of microRNAs to radio- and chemoresistance of brain tumors and their therapeutic potential. Eur J Pharmacol 2012; 684:8-18. [PMID: 22484336 DOI: 10.1016/j.ejphar.2012.03.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/09/2012] [Accepted: 03/22/2012] [Indexed: 12/17/2022]
Abstract
Glioblastomas, particularly high grade brain tumors such as glioblastoma multiforme, are characterized by increased anaplasy, malignancy, proliferation, and invasion. These tumors exhibit high resistance to radiation therapy and treatment with anti-cancer drugs. The radio- and chemoresistance of gliomas is attributed to cancer stem cells (CSCs) that are considered as major contributors for maintenance and propagation of tumor cell mass, cancer malignancy and invasiveness, and tumor cell survival after courses of radiotherapy and medical interventions. MicroRNAs (miRNAs), key post-transcriptional gene regulators, have altered expression profiles in gliomas. Some of miRNAs whose expression is markedly up-regulated in brain tumors are likely to have a pro-oncogenic role through supporting growth, proliferation, migration, and survival of cancer stem and non-stem cells. In contrast, a population of miRNA possessing anti-tumor effects is suppressed in gliomas. In this review, we will consider miRNAs and their influence on radio- and chemoresistance of gliomas. These miRNAs harbor a great therapeutic significance as potent agents in future targeted anti-cancer therapy to sensitize glioma tumor cells and CSCs to cytotoxic effects of radiation exposure and treatment with anti-cancer drugs.
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Affiliation(s)
- Dimitry A Chistiakov
- Department of Medical Nanobiotechnology, Pirogov Russian State Medical University, Moscow, Russia.
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