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Buccheri V, Pasulka J, Malik R, Loubalova Z, Taborska E, Horvat F, Roos Kulmann MI, Jenickova I, Prochazka J, Sedlacek R, Svoboda P. Functional canonical RNAi in mice expressing a truncated Dicer isoform and long dsRNA. EMBO Rep 2024:10.1038/s44319-024-00148-z. [PMID: 38769420 DOI: 10.1038/s44319-024-00148-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Canonical RNA interference (RNAi) is sequence-specific mRNA degradation guided by small interfering RNAs (siRNAs) made by RNase III Dicer from long double-stranded RNA (dsRNA). RNAi roles include gene regulation, antiviral immunity or defense against transposable elements. In mammals, RNAi is constrained by Dicer's adaptation to produce another small RNA class-microRNAs. However, a truncated Dicer isoform (ΔHEL1) supporting RNAi exists in mouse oocytes. A homozygous mutation to express only the truncated ΔHEL1 variant causes dysregulation of microRNAs and perinatal lethality in mice. Here, we report the phenotype and canonical RNAi activity in DicerΔHEL1/wt mice, which are viable, show minimal miRNome changes, but their endogenous siRNA levels are an order of magnitude higher. We show that siRNA production in vivo is limited by available dsRNA, but not by Protein kinase R, a dsRNA sensor of innate immunity. dsRNA expression from a transgene yields sufficient siRNA levels to induce efficient RNAi in heart and muscle. DicerΔHEL1/wt mice with enhanced canonical RNAi offer a platform for examining potential and limits of mammalian RNAi in vivo.
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Grants
- 20-03950X Czech Science Foundation
- 647403 EC | European Research Council (ERC)
- LO1419 Ministry of Education, Youth, and Sports of the Czech Republic
- LM2018126 Ministry of Education, Youth, and Sports of the Czech Republic
- LM2023036 Ministry of Education, Youth, and Sports of the Czech Republic
- LM2023050 Ministry of Education, Youth, and Sports of the Czech Republic
- 90254 Ministry of Education, Youth, and Sports of the Czech Republic
- 90255 Ministry of Education, Youth, and Sports of the Czech Republic
- PhD fellowship Charles University
- RVO 68378050 Czech Academy of Sciences
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Affiliation(s)
- Valeria Buccheri
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Josef Pasulka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Zuzana Loubalova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eliska Taborska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Marcos Iuri Roos Kulmann
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Irena Jenickova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic.
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Braun M, Shoshani S, Teixeira J, Mellul Shtern A, Miller M, Granot Z, Fischer SE, Garcia SMA, Tabach Y. Asymmetric inheritance of RNA toxicity in C. elegans expressing CTG repeats. iScience 2022; 25:104246. [PMID: 35494247 PMCID: PMC9051633 DOI: 10.1016/j.isci.2022.104246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 11/18/2022] Open
Abstract
Nucleotide repeat expansions are a hallmark of over 40 neurodegenerative diseases and cause RNA toxicity and multisystemic symptoms that worsen with age. Through an unclear mechanism, RNA toxicity can trigger severe disease manifestation in infants if the repeats are inherited from their mother. Here we use Caenorhabditis elegans bearing expanded CUG repeats to show that this asymmetric intergenerational inheritance of toxicity contributes to disease pathogenesis. In addition, we show that this mechanism is dependent on small RNA pathways with maternal repeat-derived small RNAs causing transcriptomic changes in the offspring, reduced motility, and shortened lifespan. We rescued the toxicity phenotypes in the offspring by perturbing the RNAi machinery in the affected hermaphrodites. This points to a novel mechanism linking maternal bias and the RNAi machinery and suggests that toxic RNA is transmitted to offspring, causing disease phenotypes through intergenerational epigenetic inheritance. Maternal origin of expanded CUG repeats induces RNA toxicity in Caenorhabditis elegans offspring Offspring of affected hermaphrodites show molecular and phenotypic disease phenotypes The RNAi machinery is directly related to the maternal inheritance of RNA toxicity Altering the RNAi machinery in affected hermaphrodites rescues toxicity in offspring
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Affiliation(s)
- Maya Braun
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shachar Shoshani
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Joana Teixeira
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790 Finland
| | - Anna Mellul Shtern
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Maya Miller
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Zvi Granot
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sylvia E.J. Fischer
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Susana M.D. A. Garcia
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790 Finland
- Corresponding author
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Corresponding author
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3
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Demeter T, Vaskovicova M, Malik R, Horvat F, Pasulka J, Svobodova E, Flemr M, Svoboda P. Main constraints for RNAi induced by expressed long dsRNA in mouse cells. Life Sci Alliance 2019; 2:2/1/e201800289. [PMID: 30808654 PMCID: PMC6391682 DOI: 10.26508/lsa.201800289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
A systematic survey of dsRNA expression in mouse fibroblasts and embryonic stem cells shows main constraints for RNAi. RNAi activity depends on the initial Dicer cleavage of dsRNA, having implications for the evolution of mammalian RNAi functions. RNAi is the sequence-specific mRNA degradation guided by siRNAs produced from long dsRNA by RNase Dicer. Proteins executing RNAi are present in mammalian cells but rather sustain the microRNA pathway. Aiming for a systematic analysis of mammalian RNAi, we report here that the main bottleneck for RNAi efficiency is the production of functional siRNAs, which integrates Dicer activity, dsRNA structure, and siRNA targeting efficiency. Unexpectedly, increased expression of Dicer cofactors TARBP2 or PACT reduces RNAi but not microRNA function. Elimination of protein kinase R, a key dsRNA sensor in the interferon response, had minimal positive effects on RNAi activity in fibroblasts. Without high Dicer activity, RNAi can still occur when the initial Dicer cleavage of the substrate yields an efficient siRNA. Efficient mammalian RNAi may use substrates with some features of microRNA precursors, merging both pathways even more than previously suggested. Although optimized endogenous Dicer substrates mimicking miRNA features could evolve for endogenous regulations, the same principles would make antiviral RNAi inefficient as viruses would adapt to avoid efficacy.
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Affiliation(s)
- Tomas Demeter
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Michaela Vaskovicova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Filip Horvat
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Josef Pasulka
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Matyas Flemr
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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4
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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5
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Coutinho MF, Santos JI, Matos L, Alves S. Genetic Substrate Reduction Therapy: A Promising Approach for Lysosomal Storage Disorders. Diseases 2016; 4:diseases4040033. [PMID: 28933412 PMCID: PMC5456330 DOI: 10.3390/diseases4040033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 01/10/2023] Open
Abstract
Lysosomal storage diseases are a group of rare genetic disorders characterized by the accumulation of storage molecules in late endosomes/lysosomes. Most of them result from mutations in genes encoding for the catabolic enzymes that ensure intralysosomal digestion. Conventional therapeutic options include enzyme replacement therapy, an approach targeting the functional loss of the enzyme by injection of a recombinant one. Even though this is successful for some diseases, it is mostly effective for peripheral manifestations and has no impact on neuropathology. The development of alternative therapeutic approaches is, therefore, mandatory, and striking innovations including the clinical development of pharmacological chaperones and gene therapy are currently under evaluation. Most of them, however, have the same underlying rationale: an attempt to provide or enhance the activity of the missing enzyme to re-establish substrate metabolism to a level that is consistent with a lack of progression and/or return to health. Here, we will focus on the one approach which has a different underlying principle: substrate reduction therapy (SRT), whose uniqueness relies on the fact that it acts upstream of the enzymatic defect, decreasing storage by downregulating its biosynthetic pathway. Special attention will be given to the most recent advances in the field, introducing the concept of genetic SRT (gSRT), which is based on the use of RNA-degrading technologies (RNA interference and single stranded antisense oligonucleotides) to promote efficient substrate reduction by decreasing its synthesis rate.
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Affiliation(s)
- Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, INSA, National Health Institute Doutor Ricardo Jorge, Rua Alexandre Herculano, 321 4000-055 Porto, Portugal.
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, INSA, National Health Institute Doutor Ricardo Jorge, Rua Alexandre Herculano, 321 4000-055 Porto, Portugal.
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, INSA, National Health Institute Doutor Ricardo Jorge, Rua Alexandre Herculano, 321 4000-055 Porto, Portugal.
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, INSA, National Health Institute Doutor Ricardo Jorge, Rua Alexandre Herculano, 321 4000-055 Porto, Portugal.
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6
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Coutinho MF, Santos JI, Alves S. Less Is More: Substrate Reduction Therapy for Lysosomal Storage Disorders. Int J Mol Sci 2016; 17:ijms17071065. [PMID: 27384562 PMCID: PMC4964441 DOI: 10.3390/ijms17071065] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 12/11/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a group of rare, life-threatening genetic disorders, usually caused by a dysfunction in one of the many enzymes responsible for intralysosomal digestion. Even though no cure is available for any LSD, a few treatment strategies do exist. Traditionally, efforts have been mainly targeting the functional loss of the enzyme, by injection of a recombinant formulation, in a process called enzyme replacement therapy (ERT), with no impact on neuropathology. This ineffectiveness, together with its high cost and lifelong dependence is amongst the main reasons why additional therapeutic approaches are being (and have to be) investigated: chaperone therapy; gene enhancement; gene therapy; and, alternatively, substrate reduction therapy (SRT), whose aim is to prevent storage not by correcting the original enzymatic defect but, instead, by decreasing the levels of biosynthesis of the accumulating substrate(s). Here we review the concept of substrate reduction, highlighting the major breakthroughs in the field and discussing the future of SRT, not only as a monotherapy but also, especially, as complementary approach for LSDs.
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Affiliation(s)
- Maria Francisca Coutinho
- Department of Human Genetics, Research and Development Unit, National Health Institute Doutor Ricardo Jorge, Rua Alexandre Herculano, 321 4000-055 Porto, Portugal.
| | - Juliana Inês Santos
- Department of Human Genetics, Research and Development Unit, National Health Institute Doutor Ricardo Jorge, Rua Alexandre Herculano, 321 4000-055 Porto, Portugal.
| | - Sandra Alves
- Department of Human Genetics, Research and Development Unit, National Health Institute Doutor Ricardo Jorge, Rua Alexandre Herculano, 321 4000-055 Porto, Portugal.
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7
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Svoboda P. Renaissance of mammalian endogenous RNAi. FEBS Lett 2014; 588:2550-6. [DOI: 10.1016/j.febslet.2014.05.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 01/03/2023]
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8
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Nejepinska J, Malik R, Filkowski J, Flemr M, Filipowicz W, Svoboda P. dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells. Nucleic Acids Res 2011; 40:399-413. [PMID: 21908396 PMCID: PMC3245926 DOI: 10.1093/nar/gkr702] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, including sequence-specific RNA interference (RNAi), sequence-independent interferon (IFN) response and editing by adenosine deaminases. To study the routing of dsRNA to these pathways in vivo, we used transgenic mice ubiquitously expressing from a strong promoter, an mRNA with a long hairpin in its 3′-UTR. The expressed dsRNA neither caused any developmental defects nor activated the IFN response, which was inducible only at high expression levels in cultured cells. The dsRNA was poorly processed into siRNAs in somatic cells, whereas, robust RNAi effects were found in oocytes, suggesting that somatic cells lack some factor(s) facilitating siRNA biogenesis. Expressed dsRNA did not cause transcriptional silencing in trans. Analysis of RNA editing revealed that a small fraction of long dsRNA is edited. RNA editing neither prevented the cytoplasmic localization nor processing into siRNAs. Thus, a long dsRNA structure is well tolerated in mammalian cells and is mainly causing a robust RNAi response in oocytes.
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Affiliation(s)
- Jana Nejepinska
- Institute of Molecular Genetics AS CR, Videnska 1083, 14220 Prague 4, Czech Republic
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9
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Krulko I, Ustyanenko D, Polischuk V. Role of siRNAs and miRNAs in the processes of RNA-mediated gene silencing during viral infections. CYTOL GENET+ 2009; 43:63-72. [PMID: 32214541 PMCID: PMC7089099 DOI: 10.3103/s0095452709010113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/1995] [Indexed: 11/30/2022]
Abstract
Phenomenon of RNA-induced gene silencing is a highly conservative mechanism among eukaryotic organisms. Several classes of small RNAs (siRNAs and miRNAs) 21-25 nt in length, which play a significant role in the processes of development of an organism, occurred important components of antiviral defence in animals and plants. This review shortly describes the main stages of gene silencing mechanism, features of antiviral RNA silencing in plants, invertebrates, mammals, ways of suppression of RNA-interference by viruses, as well as possible approaches of utilization of abovementioned phenomenon for struggling against viral infections.
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Affiliation(s)
- I. Krulko
- Taras Shevchenko Kyiv National University, ul. Volodymyrska 64, Kyiv, 01033 Ukraine
| | - D. Ustyanenko
- Taras Shevchenko Kyiv National University, ul. Volodymyrska 64, Kyiv, 01033 Ukraine
| | - V. Polischuk
- Taras Shevchenko Kyiv National University, ul. Volodymyrska 64, Kyiv, 01033 Ukraine
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10
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Saayman S, Barichievy S, Capovilla A, Morris KV, Arbuthnot P, Weinberg MS. The efficacy of generating three independent anti-HIV-1 siRNAs from a single U6 RNA Pol III-expressed long hairpin RNA. PLoS One 2008; 3:e2602. [PMID: 18596982 PMCID: PMC2434202 DOI: 10.1371/journal.pone.0002602] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2007] [Accepted: 06/06/2008] [Indexed: 11/24/2022] Open
Abstract
RNA Interference (RNAi) effectors have been used to inhibit rogue RNAs in mammalian cells. However, rapidly evolving sequences such as the human immunodeficiency virus type 1 (HIV-1) require multiple targeting approaches to prevent the emergence of escape variants. Expressed long hairpin RNAs (lhRNAs) have recently been used as a strategy to produce multiple short interfering RNAs (siRNAs) targeted to highly variant sequences. We aimed to characterize the ability of expressed lhRNAs to generate independent siRNAs that silence three non-contiguous HIV-1 sites by designing lhRNAs comprising different combinations of siRNA-encoding sequences. All lhRNAs were capable of silencing individual target sequences. However, silencing efficiency together with concentrations of individual lhRNA-derived siRNAs diminished from the stem base (first position) towards the loop side of the hairpin. Silencing efficacy against HIV-1 was primarily mediated by siRNA sequences located at the base of the stem. Improvements could be made to first and second position siRNAs by adjusting spacing arrangements at their junction, but silencing of third position siRNAs remained largely ineffective. Although lhRNAs offer advantages for combinatorial RNAi, we show that good silencing efficacy across the span of the lhRNA duplex is difficult to achieve with sequences that encode more than two adjacent independent siRNAs.
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Affiliation(s)
- Sheena Saayman
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Samantha Barichievy
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Alexio Capovilla
- HIV Pathogenesis Lab, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Kevin V. Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patrick Arbuthnot
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Marc S. Weinberg
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
- * E-mail:
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11
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Groux-Degroote S, van Dijk SM, Wolthoorn J, Neumann S, Theos AC, De Mazière AM, Klumperman J, van Meer G, Sprong H. Glycolipid-dependent sorting of melanosomal from lysosomal membrane proteins by lumenal determinants. Traffic 2008; 9:951-63. [PMID: 18373728 DOI: 10.1111/j.1600-0854.2008.00740.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Melanosomes are lysosome-related organelles that coexist with lysosomes in mammalian pigment cells. Melanosomal and lysosomal membrane proteins share similar sorting signals in their cytoplasmic tail, raising the question how they are segregated. We show that in control melanocytes, the melanosomal enzymes tyrosinase-related protein 1 (Tyrp1) and tyrosinase follow an intracellular Golgi to melanosome pathway, whereas in the absence of glycosphingolipids, they are observed to pass over the cell surface. Unexpectedly, the lysosome-associated membrane protein 1 (LAMP-1) and 2 behaved exactly opposite: they were found to travel through the cell surface in control melanocytes but followed an intracellular pathway in the absence of glycosphingolipids. Chimeric proteins having the cytoplasmic tail of Tyrp1 or tyrosinase were transported like lysosomal proteins, whereas a LAMP-1 construct containing the lumenal domain of Tyrp1 localized to melanosomes. In conclusion, the lumenal domain contains sorting information that guides Tyrp1 and probably tyrosinase to melanosomes by an intracellular route that excludes lysosomal proteins and requires glucosylceramide.
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Affiliation(s)
- Sophie Groux-Degroote
- Membrane Enzymology, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584CH Utrecht, The Netherlands
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12
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Barichievy S, Saayman S, von Eije KJ, Morris KV, Arbuthnot P, Weinberg MS. The inhibitory efficacy of RNA POL III-expressed long hairpin RNAs targeted to untranslated regions of the HIV-1 5' long terminal repeat. Oligonucleotides 2008; 17:419-31. [PMID: 17896874 DOI: 10.1089/oli.2007.0095] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) is a lentivirus that causes persistent infection resulting in the demise of immune regulatory cells, and ensuing diseases associated with acquired immune deficiency syndrome (AIDS). Although current therapeutic modalities have had a significant impact on mortality rates, novel therapies are constantly needed to prevent the emergence of resistant viral variants that escape the effects of antivirals. RNA Interference (RNAi) is a promising therapeutic modality for the inhibition of HIV-1 RNAs. Traditionally, RNAi effector sequences include expressed short hairpin RNAs (shRNAs) or short interfering RNAs (siRNAs). Recently, expressed long hairpin RNAs (lhRNAs) have been used with the aim of generating multiple independent siRNAs, which simultaneously target different susceptible sites on HIV-1. Here, modified lhRNAs expressed from U6 RNA Pol III promoters were targeted to sites within the first transcribed sequences of the HIV-1 5' long terminal repeat (LTR) region. Both Tat-dependent and independent suppressive efficacy was demonstrated against subtype B and C reporter sequences; however, lhRNAs complementary to the TAR stem-loop were refractory to silencing. None of the lhRNAs induced an unwanted interferon response as measured by interferon beta levels. Silencing by the lhRNAs was not equal across the extent of its cognate sequence, with the greatest efficacy observed for sequences located at the base of the stem. Nevertheless, direct antireplicative activity was seen when targeting lhRNAs to a subtype B HIV clone pNL4-3 Luc and a subtype C wild-type HIV-1 strain, FV5. These data highlight distinct target loci within the 5' LTR of HIV-1 that are susceptible to lhRNA targeting, and may prove to have an important advantage over other RNAi target sites within HIV-1. Although lhRNAs themselves require further manipulation to improve their overall efficacy in generating multiple functioning siRNAs, they may prove useful in any combinatorial-based approach to treating HIV-1 infection.
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Affiliation(s)
- Samantha Barichievy
- Antiviral Gene Therapy Unit, Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
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13
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Sano M, Li H, Nakanishi M, Rossi JJ. Expression of Long Anti-HIV-1 Hairpin RNAs for the Generation of Multiple siRNAs: Advantages and Limitations. Mol Ther 2008; 16:170-7. [PMID: 17726454 DOI: 10.1038/sj.mt.6300298] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Promoter expressed long-hairpin RNAs (lhRNAs) that can be processed into multiple small interfering RNA (siRNAs) are being considered as effective agents for treating rapidly mutating viruses such as human immunodeficiency virus (HIV). In the present study, we have generated human U6 promoter-driven lhRNAs of 50, 53, and 80 base pairs (bp) targeting contiguous sequences within the tat and rev genes of HIV-1 and evaluated the efficacy of these lhRNAs as well as their processing in cells. By using multiple G:U mismatches in the stems, we have been able to readily incorporate the long-hairpin structures into a lentiviral vector transduction system. Here we show that such long hairpins can be stably and functionally expressed for a long term in HIV-1 susceptible T cells, where they provide potent inhibition of HIV replication against both non-mutant and mutant variants of HIV-1. Our studies provide strong support for the use of the G:U wobble pair containing lhRNAs to generate multiple siRNAs from a single transcript, but we also show that lhRNAs of 80 bp may be the upper size limit for effectively producing multiple, functional siRNAs.
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Affiliation(s)
- Masayuki Sano
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, California, USA
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14
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Gantier MP, Baugh JA, Donnelly SC. Nuclear transcription of long hairpin RNA triggers innate immune responses. J Interferon Cytokine Res 2007; 27:789-97. [PMID: 17892400 DOI: 10.1089/jir.2006.0152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
RNA interference (RNAi) is one of the most promising tools for deciphering the human genome and has great therapeutic potential. However, its high target specificity limits its efficiency for therapeutic protection from viruses with high rates of genetic mutation. This limitation may be overcome by the expression of long hairpin RNAs (lhRNAs). Indeed, lhRNAs have been shown recently to have increased efficacy over short interfering RNAs (siRNAs) as protective antiviral agents. Here, we investigate the expression of lhRNAs and demonstrate unintended effects. We show that overexpressed lhRNAs are exported to the cytoplasm. As a consequence, we detect activation of innate immune signaling pathways by lhRNAs. With growing concerns about the complexity of cytoplasmic detection of dsRNAs by the innate immune machinery, this work highlights the need for closer scrutiny when using lhRNAs as potential antiviral agents.
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Affiliation(s)
- Michael P Gantier
- School of Medicine and Medical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, and St. Vincent's University Hospital, Dublin, Ireland
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15
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Abstract
MicroRNAs (miRNAs) are emerging as potent regulators of many biological processes, including cellular differentiation and disease. Recently, miRNA has been directly involved in innate immunity and transduction signalling by Toll-like receptors and the ensuing cytokine response. In this review, we present an overview of what is currently known of the involvement of miRNA and RNA interference components in the fine-tuning of innate immune responses.
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Affiliation(s)
- Michael P Gantier
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia
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16
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Diaz-Font A, Chabás A, Grinberg D, Vilageliu L. RNAi-mediated inhibition of the glucosylceramide synthase (GCS) gene: A preliminary study towards a therapeutic strategy for Gaucher disease and other glycosphingolipid storage diseases. Blood Cells Mol Dis 2006; 37:197-203. [PMID: 16959503 DOI: 10.1016/j.bcmd.2006.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 07/17/2006] [Accepted: 07/17/2006] [Indexed: 12/24/2022]
Abstract
Small interference RNAs (siRNAs) have recently been used in various experimental settings to silence gene expression. In some of them, chemically synthesized or in vitro transcribed siRNAs have been transfected into cells. In others, siRNAs have been expressed endogenously from siRNA expression vectors. Enzyme replacement and substrate deprivation therapies are currently used to treat Gaucher disease. Although good results have been reported, there are several limitations and side effects that make necessary to search for new alternatives. We present a new approach based on the inhibition of the GCS gene using siRNAs as a potential therapeutic strategy for Gaucher disease. We have designed four siRNAs for the human GCS gene and transfected them into HeLa cells. A clear reduction of GCS RNA levels and enzyme activity was obtained using two of the four siRNAs. Furthermore, a reduction in glucosylceramide synthesis was also observed. Similar results were obtained when plasmids expressing shRNAs (targeting the same sequences) were transfected into the cells. The inhibition of the mouse homolog Ugcg gene was also achieved, using a siRNA that targeted both human and mouse sequences.
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Affiliation(s)
- Anna Diaz-Font
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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17
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Strat A, Gao L, Utsuki T, Cheng B, Nuthalapaty S, Mathis JM, Odaka Y, Giordano T. Specific and nontoxic silencing in mammalian cells with expressed long dsRNAs. Nucleic Acids Res 2006; 34:3803-10. [PMID: 16916791 PMCID: PMC1540741 DOI: 10.1093/nar/gkl532] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A number of groups have developed libraries of siRNAs to identify genes through functional genomics. While these studies have validated the approach of making functional RNAi libraries to understand fundamental cellular mechanisms, they require information and knowledge of existing sequences since the RNAi sequences are generated synthetically. An alternative strategy would be to create an RNAi library from cDNA. Unfortunately, the complexity of such a library of siRNAs would make screening difficult. To reduce the complexity, longer dsRNAs could be used; however, concerns of induction of the interferon response and off-target effects of long dsRNAs have prevented their use. As a first step in creating such libraries, long dsRNA was expressed in mammalian cells. The 250 nt dsRNAs were capable of efficiently silencing a luciferase reporter gene that was stably transfected in MDA-MB-231 cells without inducing the interferon response or off-target effects any more than reported for siRNAs. In addition, a long dsRNA expressed in the same cell line was capable of silencing endogenous c-met expression and inhibited cell migration, whereas the dsRNA against luciferase had no effect on c-met or cell migration. The studies suggest that large dsRNA libraries are feasible and that functional selection of genes will be possible.
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Affiliation(s)
- Aurel Strat
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences CenterShreveport, LA, USA
| | - Lu Gao
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences CenterShreveport, LA, USA
| | - Tada Utsuki
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences CenterShreveport, LA, USA
| | - Bing Cheng
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences CenterShreveport, LA, USA
| | - Sam Nuthalapaty
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences CenterShreveport, LA, USA
| | - J. Mike Mathis
- Department of Cell Biology and Anatomy, Louisiana State University Health Sciences CenterShreveport, LA, USA
| | - Yoshinobu Odaka
- Department of Cell Biology and Anatomy, Louisiana State University Health Sciences CenterShreveport, LA, USA
| | - Tony Giordano
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences CenterShreveport, LA, USA
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences CenterShreveport, LA, USA
- To whom correspondence should be addressed. Tel: +1 318 675 7791; Fax: +1 318 675 5180;
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18
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Konstantinova P, de Vries W, Haasnoot J, ter Brake O, de Haan P, Berkhout B. Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA. Gene Ther 2006; 13:1403-13. [PMID: 16708080 PMCID: PMC7091653 DOI: 10.1038/sj.gt.3302786] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Inhibition of virus replication by means of RNA interference has been reported for several important human pathogens, including human immunodeficiency virus type 1 (HIV-1). RNA interference against these pathogens has been accomplished by introduction of virus-specific synthetic small interfering RNAs (siRNAs) or DNA constructs encoding short-hairpin RNAs (shRNAs). Their use as therapeutic antiviral against HIV-1 is limited, because of the emergence of viral escape mutants. In order to solve this durability problem, we tested DNA constructs encoding virus-specific long-hairpin RNAs (lhRNAs) for their ability to inhibit HIV-1 production. Expression of lhRNAs in mammalian cells may result in the synthesis of many siRNAs targeting different viral sequences, thus providing more potent inhibition and reducing the chance of viral escape. The lhRNA constructs were compared with in vitro diced double-stranded RNA and a DNA construct encoding an effective nef-specific shRNA for their ability to inhibit HIV-1 production in cells. Our results show that DNA constructs encoding virus-specific lhRNAs are capable of inhibiting HIV-1 production in a sequence-specific manner, without inducing the class I interferon genes.
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Affiliation(s)
- P Konstantinova
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - W de Vries
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Viruvation BV Wassenaarseweg 72, Leiden, The Netherlands
| | - J Haasnoot
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - O ter Brake
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - P de Haan
- Viruvation BV Wassenaarseweg 72, Leiden, The Netherlands
| | - B Berkhout
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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