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MicroRNAs Regulating Autophagy in Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1208:191-264. [PMID: 34260028 DOI: 10.1007/978-981-16-2830-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Social and economic impacts of neurodegenerative diseases (NDs) become more prominent in our constantly aging population. Currently, due to the lack of knowledge about the aetiology of most NDs, only symptomatic treatment is available for patients. Hence, researchers and clinicians are in need of solid studies on pathological mechanisms of NDs. Autophagy promotes degradation of pathogenic proteins in NDs, while microRNAs post-transcriptionally regulate multiple signalling networks including autophagy. This chapter will critically discuss current research advancements in the area of microRNAs regulating autophagy in NDs. Moreover, we will introduce basic strategies and techniques used in microRNA research. Delineation of the mechanisms contributing to NDs will result in development of better approaches for their early diagnosis and effective treatment.
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Koehler C, Estrada Girona G, Reinkemeier CD, Lemke EA. Inducible Genetic Code Expansion in Eukaryotes. Chembiochem 2020; 21:3216-3219. [PMID: 32598534 PMCID: PMC7754456 DOI: 10.1002/cbic.202000338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/25/2020] [Indexed: 11/07/2022]
Abstract
Genetic code expansion (GCE) is a versatile tool to site-specifically incorporate a noncanonical amino acid (ncAA) into a protein, for example, to perform fluorescent labeling inside living cells. To this end, an orthogonal aminoacyl-tRNA-synthetase/tRNA (RS/tRNA) pair is used to insert the ncAA in response to an amber stop codon in the protein of interest. One of the drawbacks of this system is that, in order to achieve maximum efficiency, high levels of the orthogonal tRNA are required, and this could interfere with host cell functionality. To minimize the adverse effects on the host, we have developed an inducible GCE system that enables us to switch on tRNA or RS expression when needed. In particular, we tested different promotors in the context of the T-REx or Tet-On systems to control expression of the desired orthogonal tRNA and/or RS. We discuss our result with respect to the control of GCE components as well as efficiency. We found that only the T-REx system enables simultaneous control of tRNA and RS expression.
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Affiliation(s)
- Christine Koehler
- BiocentreJohannes-Gutenberg University Mainz55128MainzGermany
- Institute of Molecular Biology gGmbH55128MainzGermany
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
| | - Christopher D. Reinkemeier
- BiocentreJohannes-Gutenberg University Mainz55128MainzGermany
- Institute of Molecular Biology gGmbH55128MainzGermany
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
| | - Edward A. Lemke
- BiocentreJohannes-Gutenberg University Mainz55128MainzGermany
- Institute of Molecular Biology gGmbH55128MainzGermany
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
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Chen E, Chen Z, Li S, Xing D, Guo H, Liu J, Ji X, Lin Y, Liu S, Xia Q. MicroRNAs bmo-miR-2739 and novel-miR-167 coordinately regulate the expression of the vitellogenin receptor in Bombyx mori oogenesis. Development 2020; 147:dev.183723. [DOI: 10.1242/dev.183723] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
Vitellogenin receptors (VgRs) play critical roles in oogenesis by mediating endocytosis of vitellogenin and other nutrients in ovipara. We conducted small RNA sequencing and screening with a luciferase reporter system, and found that bmo-miR-2739 and a novel miRNA (novel-miR-167) coordinately regulate the expression of VgR in Bombyx mori (BmVgR). Further analyses suggested that these two miRNAs direct target repression by binding directly to the BmVgR 3ʹ untranslated region. Forced expression of either miRNA using the piggyBac system blocked vitellogenin (Vg) transport and retarded ovariole development. Antagomir silencing of bmo-miR-2739 or novel-miR-167 resulted in increased amounts of BmVgR protein in the ovaries and BmVgR mRNA in the fat body. This evidence combined with spatiotemporal expression profiles revealed that these two miRNAs function together to fine-tune the amount of BmVgR protein for ovarian development. Additionally, novel-miR-167 mainly switched on the posttranscriptional repression of BmVgR in non-ovarian tissues. The results of this study contribute to a better understanding of the function of miRNA during ovarian development of a lepidopteran and suggest a new strategy for controlling insect reproduction.
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Affiliation(s)
- Enxiang Chen
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
| | - Zhiwei Chen
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
| | - Shenglong Li
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
| | - Dongxu Xing
- Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510610, China
| | - Huizhen Guo
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
| | - Jianqiu Liu
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
| | - Xiaocun Ji
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Ying Lin
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
| | - Shiping Liu
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing 400716, PR China
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Beibei, Chongqing 400716, PR China
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Li B, Wang L, Li Z, Wang W, Zhi X, Huang X, Zhang Q, Chen Z, Zhang X, He Z, Xu J, Zhang L, Xu H, Zhang D, Xu Z. miR-3174 Contributes to Apoptosis and Autophagic Cell Death Defects in Gastric Cancer Cells by Targeting ARHGAP10. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:294-311. [PMID: 29246308 PMCID: PMC5684471 DOI: 10.1016/j.omtn.2017.10.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 01/04/2023]
Abstract
Gastric cancer (GC) is a major health problem worldwide because of its high morbidity and mortality. Considering the well-established roles of miRNA in the regulation of GC carcinogenesis and progression, we screened differentially expressed microRNAs (miRNAs) by using The Cancer Genome Atlas (TCGA) and the GEO databases. We found that miR-3174 was the most significantly differentially expressed miRNA in GC. Ectopic miR-3174 expression was also detected in clinical GC patient samples and cell lines and associated with poor patient prognosis. Apoptosis and autophagic cell death are two types of programmed cell death, whereas both are deficient in gastric cancer. Our functional analyses demonstrated that miR-3174 inhibited mitochondria-dependent apoptosis and autophagic cell death in GC. Moreover, high expression of miR-3174 also resulted in Cisplatin resistance in GC cells. Using bioinformatics analyses combined with in vitro and in vivo experiments, we determined that miR-3174 directly targets ARHGAP10. Notably, ARHGAP10 promoted mitochondria-dependent apoptosis by enhancing p53 expression, which was followed by Bax trans-activation and caspase cleavage. ARHGAP10 also facilitated autophagic cell death by suppressing mammalian target of rapamycin complex 1 (mTOC1) activity. Our results reveal a potential miRNA-based clinical therapeutic target that may also serve as a predictive marker for GC.
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Affiliation(s)
- Bowen Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Lu Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Zheng Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Weizhi Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Xiaofei Zhi
- Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Xiaoxu Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Qiang Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Zheng Chen
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xuan Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Zhongyuan He
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Jianghao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Lu Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Diancai Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.
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Fischer S, Marquart KF, Pieper LA, Fieder J, Gamer M, Gorr I, Schulz P, Bradl H. miRNA engineering of CHO cells facilitates production of difficult-to-express proteins and increases success in cell line development. Biotechnol Bioeng 2017; 114:1495-1510. [PMID: 28262952 PMCID: PMC6084326 DOI: 10.1002/bit.26280] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/25/2017] [Accepted: 03/01/2017] [Indexed: 01/05/2023]
Abstract
In recent years, coherent with growing biologics portfolios also the number of complex and thus difficult-to-express (DTE) therapeutic proteins has increased considerably. DTE proteins challenge bioprocess development and can include various therapeutic protein formats such as monoclonal antibodies (mAbs), multi-specific affinity scaffolds (e.g., bispecific antibodies), cytokines, or fusion proteins. Hence, the availability of robust and versatile Chinese hamster ovary (CHO) host cell factories is fundamental for high-yielding bioprocesses. MicroRNAs (miRNAs) have emerged as potent cell engineering tools to improve process performance of CHO manufacturing cell lines. However, there has not been any report demonstrating the impact of beneficial miRNAs on industrial cell line development (CLD) yet. To address this question, we established novel CHO host cells constitutively expressing a pro-productive miRNA: miR-557. Novel host cells were tested in two independent CLD campaigns using two different mAb candidates including a normal as well as a DTE antibody. Presence of miR-557 significantly enhanced each process step during CLD in a product independent manner. Stable expression of miR-557 increased the probability to identify high-producing cell clones. Furthermore, production cell lines derived from miR-557 expressing host cells exhibited significantly increased final product yields in fed-batch cultivation processes without compromising product quality. Strikingly, cells co-expressing miR-557 and a DTE antibody achieved a twofold increase in product titer compared to clones co-expressing a negative control miRNA. Thus, host cell engineering using miRNAs represents a promising tool to overcome limitations in industrial CLD especially with regard to DTE proteins. Biotechnol. Bioeng. 2017;114: 1495-1510. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Simon Fischer
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany.,Cell Culture Development CMB, Boehringer Ingelheim GmbH & Co. KG, Biberach, Germany
| | - Kim F Marquart
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Lisa A Pieper
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Juergen Fieder
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Martin Gamer
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Ingo Gorr
- Early Stage Bioprocess Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Patrick Schulz
- Cell Culture Development CMB, Boehringer Ingelheim GmbH & Co. KG, Biberach, Germany
| | - Harald Bradl
- Cell Culture Development CMB, Boehringer Ingelheim GmbH & Co. KG, Biberach, Germany
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Mileshina D, Niazi AK, Wyszko E, Szymanski M, Val R, Valentin C, Barciszewski J, Dietrich A. Mitochondrial targeting of catalytic RNAs. Methods Mol Biol 2015; 1265:227-54. [PMID: 25634279 DOI: 10.1007/978-1-4939-2288-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Genetic transformation of mitochondria in multicellular eukaryotes has remained inaccessible, hindering fundamental investigations and applications to gene therapy or biotechnology. In this context, we have developed a strategy to target nuclear transgene-encoded RNAs into mitochondria in plants. We describe here mitochondrial targeting of trans-cleaving ribozymes destined to knockdown organelle RNAs for regulation studies and inverse genetics and biotechnological purposes. The design and functional assessment of chimeric RNAs combining the ribozyme and the mitochondrial shuttle are detailed, followed by all procedures to prepare constructs for in vivo expression, generate stable plant transformants, and establish target RNA knockdown in mitochondria.
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Affiliation(s)
- Daria Mileshina
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
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7
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Human RNAi pathway: crosstalk with organelles and cells. Funct Integr Genomics 2013; 14:31-46. [PMID: 24197738 DOI: 10.1007/s10142-013-0344-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 12/12/2022]
Abstract
Understanding gene regulation mechanisms has been a serious challenge in biology. As a novel mechanism, small non-coding RNAs are an alternative means of gene regulation in a specific and efficient manner. There are growing reports on regulatory roles of these RNAs including transcriptional gene silencing/activation and post-transcriptional gene silencing events. Also, there are several known small non-coding RNAs which all work through RNA interference pathway. Interestingly, these small RNAs are secreted from cells toward targeted cells presenting new communication approach in cell-cell or cell-organ signal transduction. In fact, understanding cellular and molecular basis of these pathways will strongly improve developing targeted therapies and potent and specific regulatory tools. This study will review some of the most recent findings in this subject and will introduce a super-pathway RNA interference-based small RNA silencing network.
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Wang PY, Sun YX, Zhang S, Pang M, Zhang HH, Gao SY, Zhang C, Lv CJ, Xie SY. Let-7c inhibits A549 cell proliferation through oncogenic TRIB2 related factors. FEBS Lett 2013; 587:2675-81. [PMID: 23850892 DOI: 10.1016/j.febslet.2013.07.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/01/2013] [Accepted: 07/01/2013] [Indexed: 01/15/2023]
Abstract
MicroRNAs have tumor suppressive or oncogenic roles in carcinogenesis. This study aimed to investigate the mechanism of let-7c in suppressing lung cancer cell proliferation. First, let-7c was revealed to be able to inhibit lung adenocarcinoma cell proliferation significantly. TRIB2 was further demonstrated to be a novel target and negatively regulated by let-7c. As downstream signals of TRIB2, the activities of C/EBP-α and phosphorylated p38MAPK were increased obviously in let-7c-treated cells compared with controls. Our results demonstrate that, through regulating the expression of TRIB2 and its downstream factors, let-7c can effectively inhibit A549 cell proliferation in vitro and in vivo.
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Affiliation(s)
- Ping-Yu Wang
- Key Laboratory of Tumor Molecular Biology in Binzhou Medical University, Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China
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Somanna NK, Pandey AC, Arise KK, Nguyen V, Pandey KN. Functional silencing of guanylyl cyclase/natriuretic peptide receptor-A by microRNA interference: analysis of receptor endocytosis. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 4:41-53. [PMID: 23638320 PMCID: PMC3627067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 01/15/2013] [Indexed: 06/02/2023]
Abstract
Guanylyl cyclase/natriuretic peptide receptor-A (GC-A/NPRA) is the principal receptor for the regulatory action of atrial and brain natriuretic peptides (ANP and BNP) and an important effector molecule in controlling of extracellular fluid volume and blood pressure homeostasis. We have utilized RNA interference to silence the expression of GC-A/NPRA gene (Npr1), providing a novel system to study the internalization and trafficking of NPRA in intact cells. MicroRNA (miRNA)-mediated small interfering RNA (siRNA) elicited functional gene-knockdown of NPRA in stably transfected human embryonic kidney 293 (HEK-293) cells expressing a high density of recombinant NPRA. We artificially expressed three RNA polymerase II-driven miRNAs that specifically targeted the Npr1 gene, but shared no significant sequence homology with any other known mouse genes. Reverse transcription-PCR (RT-PCR) and Northern blot analyses identified two highly efficient Npr1 miRNA sequences to knockdown the expression of NPRA. The Npr1 miRNA in chains or clusters decreased NPRA expression more than 90% as compared with control cells. ANP-dependent stimulation of intracellular accumulation of cGMP and guanylyl cyclase activity of NPRA were significantly reduced in Npr1 miRNA-expressing cells by 90-95% as compared with control cells. Treatment with Npr1 miRNA caused a drastic reduction in the receptor density subsequently a deceased internalization of radiolabeled (125)I-ANP-NPRA ligand-receptor complexes. Only 12%-15% of receptor population was localized in the intracellular compartments of microRNA silenced cells as compared to 70%-80% in control cells.
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Affiliation(s)
- Naveen K Somanna
- Department of Physiology, Tulane University Health Sciences Center School of Medicine New Orleans, LA 70112, USA
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Maczuga P, Koornneef A, Borel F, Petry H, van Deventer S, Ritsema T, Konstantinova P. Optimization and comparison of knockdown efficacy between polymerase II expressed shRNA and artificial miRNA targeting luciferase and Apolipoprotein B100. BMC Biotechnol 2012; 12:42. [PMID: 22827812 PMCID: PMC3424168 DOI: 10.1186/1472-6750-12-42] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 07/03/2012] [Indexed: 11/30/2022] Open
Abstract
Background Controlling and limiting the expression of short hairpin RNA (shRNA) by using constitutive or tissue-specific polymerase II (pol II) expression can be a promising strategy to avoid RNAi toxicity. However, to date detailed studies on requirements for effective pol II shRNA expression and processing are not available. We investigated the optimal structural configuration of shRNA molecules, namely: hairpin location, stem length and termination signal required for effective pol II expression and compared it with an alternative strategy of avoiding toxicity by using artificial microRNA (miRNA) scaffolds. Results Highly effective shRNAs targeting luciferase (shLuc) or Apolipoprotein B100 (shApoB1 and shApoB2) were placed under the control of the pol II CMV promoter and expressed at +5 or +6 nucleotides (nt) with reference to the transcription start site (TSS). Different transcription termination signals (TTS), namely minimal polyadenylation (pA), poly T (T5) and U1 were also used. All pol II- expressed shRNA variants induced mild inhibition of Luciferase reporters carrying specific targets and none of them showed comparable efficacy to their polymerase III-expressed H1-shRNA controls, regardless of hairpin position and termination signal used. Extending hairpin stem length from 20 basepairs (bp) to 21, 25 or 29 bp yielded only slight improvement in the overall efficacy. When shLuc, shApoB1 and shApoB2 were placed in an artificial miRNA scaffold, two out of three were as potent as the H1-shRNA controls. Quantification of small interfering RNA (siRNA) molecules showed that the artificial miRNA constructs expressed less molecules than H1-shRNAs and that CMV-shRNA expressed the lowest amount of siRNA molecules suggesting that RNAi processing in this case is least effective. Furthermore, CMV-miApoB1 and CMV-miApoB2 were as effective as the corresponding H1-shApoB1 and H1-shApoB2 in inhibiting endogenous ApoB mRNA. Conclusion Our results demonstrate that artificial miRNA have a better efficacy profile than shRNA expressed either from H1 or CMV promoter and will be used in the future for RNAi therapeutic development.
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Affiliation(s)
- Piotr Maczuga
- Department of Research & Development, uniQure biopharma b.v., Meibergdreef 61, Amsterdam, BA 1105, The Netherlands
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11
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Schanen BC, Li X. Transcriptional regulation of mammalian miRNA genes. Genomics 2010; 97:1-6. [PMID: 20977933 DOI: 10.1016/j.ygeno.2010.10.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 09/12/2010] [Accepted: 10/16/2010] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are members of a growing family of non-coding transcripts, 21-23 nucleotides long, which regulate a diverse collection of biological processes and various diseases by RNA-mediated gene-silencing mechanisms. While currently many studies focus on defining the regulatory functions of miRNAs, few are directed towards how miRNA genes are themselves transcriptionally regulated. Recent studies of miRNA transcription have elucidated RNA polymerase II as the major polymerase of miRNAs, however, little is known of the structural features of miRNA promoters, especially those of mammalian miRNAs. Here, we review the current literature regarding features conserved among miRNA promoters useful for their detection and the current novel methodologies available to enable researchers to advance our understanding of the transcriptional regulation of miRNA genes.
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Affiliation(s)
- Brian C Schanen
- Burnet School of Biomedical Science, University of Central Florida, Orlando, FL 32826, USA
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12
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Lambeth LS, Van Hateren NJ, Wilson SA, Nair V. A direct comparison of strategies for combinatorial RNA interference. BMC Mol Biol 2010; 11:77. [PMID: 20937117 PMCID: PMC2958852 DOI: 10.1186/1471-2199-11-77] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 10/11/2010] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Combinatorial RNA interference (co-RNAi) is a valuable tool for highly effective gene suppression of single and multiple-genes targets, and can be used to prevent the escape of mutation-prone transcripts. There are currently three main approaches used to achieve co-RNAi in animal cells; multiple promoter/shRNA cassettes, long hairpin RNAs (lhRNA) and miRNA-embedded shRNAs, however, the relative effectiveness of each is not known. The current study directly compares the ability of each co-RNAi method to deliver pre-validated siRNA molecules to the same gene targets. RESULTS Double-shRNA expression vectors were generated for each co-RNAi platform and their ability to suppress both single and double-gene reporter targets were compared. The most reliable and effective gene silencing was achieved from the multiple promoter/shRNA approach, as this method induced additive suppression of single-gene targets and equally effective knockdown of double-gene targets. Although both lhRNA and microRNA-embedded strategies provided efficient gene knockdown, suppression levels were inconsistent and activity varied greatly for different siRNAs tested. Furthermore, it appeared that not only the position of siRNAs within these multi-shRNA constructs impacted upon silencing activity, but also local properties of each individual molecule. In addition, it was also found that the insertion of up to five promoter/shRNA cassettes into a single construct did not negatively affect the efficacy of each individual shRNA. CONCLUSIONS By directly comparing the ability of shRNAs delivered from different co-RNA platforms to initiate knockdown of the same gene targets, we found that multiple U6/shRNA cassettes offered the most reliable and predictable suppression of both single and multiple-gene targets. These results highlight some important strengths and pitfalls of the currently used methods for multiple shRNA delivery, and provide valuable insights for the design and application of reliable co-RNAi.
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Affiliation(s)
- Luke S Lambeth
- Institute for Animal Health, Compton, Berkshire, UK
- Tumour Suppression Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Australia
| | - Nick J Van Hateren
- Department of Molecular Biology & Biotechnology, University of Sheffield, Western Bank, Sheffield, UK
| | - Stuart A Wilson
- Department of Molecular Biology & Biotechnology, University of Sheffield, Western Bank, Sheffield, UK
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Saayman S, Arbuthnot P, Weinberg MS. Deriving four functional anti-HIV siRNAs from a single Pol III-generated transcript comprising two adjacent long hairpin RNA precursors. Nucleic Acids Res 2010; 38:6652-63. [PMID: 20525791 PMCID: PMC2965221 DOI: 10.1093/nar/gkq460] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Revised: 05/07/2010] [Accepted: 05/11/2010] [Indexed: 11/19/2022] Open
Abstract
Several different approaches exist to generate expressed RNA interference (RNAi) precursors for multiple target inhibition, a strategy referred to as combinatorial (co)RNAi. One such approach makes use of RNA Pol III-expressed long hairpin RNAs (lhRNAs), which are processed by Dicer to generate multiple unique short interfering siRNA effectors. However, because of inefficient intracellular Dicer processing, lhRNA duplexes have been limited to generating two independent effective siRNA species. In this study, we describe a novel strategy whereby four separate anti-HIV siRNAs were generated from a single RNA Pol III-expressed transcript. Two optimized lhRNAs, each comprising two active anti-HIV siRNAs, were placed in tandem to form a double long hairpin (dlhRNA) expression cassette, which encodes four unique and effective siRNA sequences. Processing of the 3' position lhRNA was more variable but effective multiple processing was possible by manipulating the order of the siRNA-encoding sequences. Importantly, unlike shRNAs, Pol III-expressed dlhRNAs did not compete with endogenous and exogenous microRNAs to disrupt the RNAi pathway. The versatility of expressed lhRNAs is greatly expanded and we provide a mechanism for generating transcripts with modular lhRNAs motifs that contribute to improved coRNAi.
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Affiliation(s)
| | | | - Marc S. Weinberg
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
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Hu T, Chen P, Fu Q, Liu Y, Ishaq M, Li J, Ma L, Guo D. Comparative Studies of Various Artificial microRNA Expression Vectors for RNAi in Mammalian Cells. Mol Biotechnol 2010; 46:34-40. [DOI: 10.1007/s12033-010-9264-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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15
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Wang SL, Yao HH, Qin ZH. Strategies for short hairpin RNA delivery in cancer gene therapy. Expert Opin Biol Ther 2009; 9:1357-68. [DOI: 10.1517/14712590903236843] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Hu T, Fu Q, Chen P, Ma L, Sin O, Guo D. Construction of an artificial MicroRNA expression vector for simultaneous inhibition of multiple genes in mammalian cells. Int J Mol Sci 2009; 10:2158-2168. [PMID: 19564946 PMCID: PMC2695274 DOI: 10.3390/ijms10052158] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 04/16/2009] [Accepted: 05/14/2009] [Indexed: 12/20/2022] Open
Abstract
Recently, artificial microRNA (amiRNA) has become a promising RNA interference (RNAi) technology. Here, we describe a flexible and reliable method for constructing both single- and multi-amiRNA expression vectors. Two universal primers, together with two specific primers carrying the encoding sequence of amiRNA were designed and utilized to synthesize the functional amiRNA cassette through a one-step PCR. With appropriate restriction sites, the synthesized amiRNA cassettes can be cloned into any site of different destination vectors. Using the method, we constructed both single- and multi-amiRNA expression vectors to target three reporter genes, which code firefly luciferase (Fluc), enhanced green fluorescent protein (EGFP) and β-galactosidase (LacZ), respectively. The expressions of three genes were all specifically inhibited by either the corresponding single- or the multi-amiRNA expression vector in 293T cells. And the RNAi efficiency of each amiRNA produced by both single- and multi-amiRNA expression vectors was comparable.
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Affiliation(s)
- Tao Hu
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Qiong Fu
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Ping Chen
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China; E-Mail:
(P.C.)
| | - Li Ma
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Onsam Sin
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Deyin Guo
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +86-27-6875-2506; Fax: +86-27-6875-2897
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Turner MJ, Slack FJ. Transcriptional control of microRNA expression in C. elegans: promoting better understanding. RNA Biol 2009; 6:49-53. [PMID: 19106630 DOI: 10.4161/rna.6.1.7574] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcriptional regulation of microRNA (miRNA) expression is one of the least understood aspects of miRNA biogenesis. In C. elegans the list of miRNAs whose transcriptional control has been described in some detail is currently limited to four: let-7, lin-4, lsy-6, and mir-61. Each of these genes has been shown experimentally to be transcriptionaly regulated by cis- and/or trans-acting factors that either promote or inhibit expression. Additionally, computational methods based on conservation among miRNA genes have yielded predicted regulatory sequences in C. elegans that may function to regulate miRNA expression on a genome-wide scale.
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Affiliation(s)
- Michael J Turner
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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Abstract
MicroRNAs (miRNAs) are a family of endogenous small noncoding RNA molecules, of 19–28 nucleotides in length. In humans, up to 3% of all genes are estimated to encode these evolutionarily conserved sequences. miRNAs are thought to control expression of thousands of target mRNAs. Mammalian miRNAs generally negatively regulate gene expression by repressing translation, possibly through effects on mRNA stability and compartmentalisation, and/or the translation process itself. An extensive range of in silico and experimental techniques have been applied to our understanding of the occurrence and functional relevance of such sequences, and antisense technologies have been successfully used to control miRNA expression in vitro and in vivo. Interestingly, miRNAs have been identified in both normal and pathological conditions, including differentiation and development, metabolism, proliferation, cell death, viral infection and cancer. Of specific relevance and excitement to the area of diabetes research, miRNA regulation has been implicated in insulin secretion from pancreatic β-cells, diabetic heart conditions and nephropathy. Further analyses of miRNAs in vitro and in vivo will, undoubtedly, enable us determine their potential to be exploited as therapeutic targets in diabetes.
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