Viral Vectors Applied for RNAi-Based Antiviral Therapy
Abstract
:1. Introduction
2. RNAi and Gene Silencing
3. RNAi and Bioinformatics
4. Delivery of RNAi
5. Virus-Based RNAi Antiviral Therapy
6. RNAi-Based Antiviral Therapy Using Non-Viral Delivery
7. Conclusions
Funding
Conflicts of Interest
References
- De Clercq, E.; Li, G. Approved antiviral drugs over the past 50 years. Clin. Microbiol. Rev. 2016, 29, 695–747. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lundstrom, K. Coronavirus pandemic—Therapy and vaccines. Biomedicines 2020, 8, 109. [Google Scholar] [CrossRef]
- Warren, T.K.; Jordan, R.; Lo, M.K.; Ray, A.S.; Mackman, R.L.; Soloveva, V.; Siegel, D.; Perron, M.; Bannister, R.; Hui, H.C.; et al. Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys. Nature 2016, 531, 381–385. [Google Scholar] [CrossRef] [PubMed]
- Ben-Zvi, I.; Kivity, S.; Langevitz, P.; Schoenfeld, Y. Hydroxychloroquine: From malaria to autoimmunity. Clin. Rev. Allergy Immunol. 2012, 42, 145–153. [Google Scholar] [CrossRef] [PubMed]
- Chandwani, A.; Shuter, J. Lopinavir/ritonavir in the treatment of HIV-infection: A review. Ther. Clin. Risk Manag. 2008, 4, 1023–1033. [Google Scholar] [PubMed] [Green Version]
- Das, S.; Bhowmick, S.; Tiwari, S.; Sen, S. An updated systematic review of the therapeutic role of hydroxychloroquine in Coronavirus Disease-19 (COVID-19). Clin. Drug Investig. 2020, 40, 591–601. [Google Scholar] [CrossRef]
- Gordon, D.E.; Jang, G.M.; Bouhaddou, M.; Xu, J.; Obernier, K.; White, K.M.; O’Meara, M.J.; Rezelj, V.V.; Guo, J.Z.; Swaney, D.L.; et al. A SARS-CoV-2 protein interaction map reveals target for drug repurposing. Nature 2020. [Google Scholar] [CrossRef]
- Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complimentary to lin-14. Cell 1993, 75, 843–854. [Google Scholar] [CrossRef]
- Pasquinelli, A.E.; Reinhart, B.J.; Slack, F.; Martindale, M.Q.; Kuroda, M.I.; Maller, B.; Hayward, D.C.; Ball, E.E.; Degnan, B.; Müller, P.; et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408, 86–89. [Google Scholar] [CrossRef]
- Lee, R.C.; Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001, 294, 862–864. [Google Scholar] [CrossRef] [Green Version]
- Griffiths-Jones, S.; Grocock, R.J.; van Dongen, S.; Bateman, A.; Enright, A.J. miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006, 34, D140–D144. [Google Scholar] [CrossRef] [PubMed]
- Krek, A.; Grun, D.; Poy, M.N.; Wolf, R.; Rosenberg, L.; Epstein, E.J.; MacMenamin, P.; da Piedade, I.; Gunsalus, K.C.; Stoffel, M.; et al. Combinatorial microRNA target predictions. Nat. Genet. 2005, 37, 495–500. [Google Scholar] [CrossRef] [PubMed]
- Kozomara, A.; Birgaoanu, M.; Griffiths-Jones, S. miRbase: From miRNA sequences to function. Nucleic Acids Res. 2019, 47, D155–D162. [Google Scholar] [CrossRef] [PubMed]
- Dana, H.; Chalbatani, G.M.; Mahmoodzadeh, H.; Karimloo, R.; Rezaiean, O.; Moradzhadeh, A.; Mehmandoost, N.; Moazzen, F.; Mazraeh, A.; Marmari, V.; et al. Molecular mechanisms and biological functions of siRNA. Int. J. Biomed. Sci. 2017, 13, 48–57. [Google Scholar] [PubMed]
- Moore, C.B.; Guthrie, E.H.; Huang, T.-Z.; Taxman, D.J. Short hairpin RNA (shRNA): Design, delivery and assessment of gene knockdown. Methods Mol. Biol. 2010, 629, 141–158. [Google Scholar] [PubMed] [Green Version]
- Kutter, C.; Svoboda, P. miRNA, siRNA, piRNA: Knowns of the unknown. RNA Biol. 2008, 5, 181–188. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pillai, R. MicroRNA functions: Multiple mechanisms for a tiny RNA. RNA J. 2005, 11, 1753–1756. [Google Scholar] [CrossRef] [Green Version]
- Herrea-Carrillo, E.; Berkhout, B. Dicer-independent processing of small RNA duplexes: Mechanistic insights and applications. Nucl. Acids Res. 2017, 45, 10369–10379. [Google Scholar] [CrossRef] [Green Version]
- Chen, X.; Mangala, L.S.; Rodriguez-Aguayo, C.; Kong, X.; Lopez-Berestein, G.; Sood, A.K. RNA interference-based therapy and delivery systems. Cancer Metastasis Rev. 2018, 37, 107–124. [Google Scholar] [CrossRef]
- Arkin, M.R.; Tang, Y.; Wells, J.A. Small-molecule inhibitors of protein-protein interactions: Progressing toward the reality. Chem. Biol. 2014, 21, 1102–1114. [Google Scholar] [CrossRef] [Green Version]
- Mohr, S.E.; Perrimon, N. RNAi screening: New approaches, understandings, and organisms. Wiley Interdiscip. Rev. RNA 2012, 3, 145–158. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rupaimoole, R.; Han, H.D.; Lopez-Berestein, G.; Sood, A.K. MicroRNA therapeutics: Principles, expectations, and challenges. Chin. J. Cancer 2011, 30, 368–370. [Google Scholar] [CrossRef] [PubMed]
- Colagrossi, L.; Hermans, L.E.; Salpini, R.; Di Carlo, D.; Pas, S.D.; Alvarez, M.; Ben-Ari, Z.; Boland, G.; Bruzzone, B.; Coppola, N.; et al. Immune-escape mutations and stop-codons in HBsAg develop in a large proportion of patients with chronic HBV infection exposed to anti-HBV drugs in Europe. BMC Infect. Dis. 2018, 18, 251. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Choi, J.-G.; Bharaj, P.; Abraham, S.; Ma, H.; Yi, G.; Ye, C.; Dang, Y.; Manjunath, N.; Wu, H.; Shankar, P. Multiplexing seven miRNA-Based shRNAs to suppress HIV replication. Mol. Ther. 2015, 23, 310–320. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Leonard, J.N.; Schaffer, D.V. Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape. J. Virol. 2005, 79, 1645–1654. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Quereshi, A.; Tantray, V.G.; Kirmani, A.R.; Ahangar, A.G. A review on current status on antiviral siRNA. Rev. Med. Virol. 2018, 28, e1976. [Google Scholar] [CrossRef]
- VIRsiRNAdb. Available online: http://crdd.osdd.net/servers/virsirnadb (accessed on 26 May 2020).
- Thakur, N.; Quereshi, A.; Kumar, M. VIRsiRNAdb: A curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res. 2012, 40, D230–D236. [Google Scholar] [CrossRef] [Green Version]
- HIVsirDB. Available online: http://crdd.osdd.net/raghava/hivsir (accessed on 26 May 2020).
- Database of HIV inhibiting siRNAs. Available online: http://crdd.osdd.net/raghava/hivsir/hiv-esc-seq.php (accessed on 26 May 2020).
- Tyagi, A.; Ahmed, F.; Thakur, N.; Sharma, A.; Raghave, G.P.; Kumar, M. HIVsiRDB: A database of HIV inhibiting siRNAs. PLoS ONE 2011, 6, e25917. [Google Scholar] [CrossRef] [Green Version]
- Amarzguioui, M.; Prydz, H. An algorhitm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun. 2004, 316, 1050–1058. [Google Scholar] [CrossRef]
- Naito, Y.; Ui-Tei, K.; Nishikawa, T.; Takebe, Y.; Saigo, K. siVirus: Web-based anti-viral siRNA design software for highly divergent viral sequences. Nucleic Acids Res. 2006, 34, W448–W450. [Google Scholar] [CrossRef] [Green Version]
- Nur, S.M.; Hasan, A.; Al Amin, M.; Hossain, M.; Sharmin, T. Design of potential RNAi (miRNA and siRNA) molecules for middle east respiratory syndrome coronavirus (MERS-CoV) gene silencing by computational method. Interdiscip. Sci. 2015, 7, 257–265. [Google Scholar] [CrossRef] [PubMed]
- Gomez, J.; Nadal, A.; Sabariegos, R.; Beguiristain, N.; Martell, M.; Piron, M. Three properties of the hepatitis C virus RNA genome related to antiviral strategies based on RNA-therapeutics: Variability, structural conformation and tRNA mimicry. Curr. Pharm. Des. 2004, 10, 3741–3756. [Google Scholar] [CrossRef] [PubMed]
- Herrera-Carillo, E.; Liu, Y.P.; Brekhout, B. Improving miRNA expression cassettes in diverse virus vectors. Hum. Gene Ther. Meth. 2017, 28, 177–190. [Google Scholar] [CrossRef] [PubMed]
- Raouane, M.; Desmaele, D.; Urbinati, G.; Massaad-Massade, L.; Couvreur, P. Lipid conjugated oligonucleotides: A useful strategy for delivery. Bioconjug. Chem. 2012, 23, 1091–1104. [Google Scholar] [CrossRef]
- Layek, B.; Lipp, L.; Singh, J. Cell Penetrating peptide conjugated chitosan for enhanced delivery of nucleic acid. Int. J. Mol. Sci. 2015, 16, 28912–28930. [Google Scholar] [CrossRef] [Green Version]
- O’Loughlin, A.J.; Mager, I.; de Jong, O.G.; Varela, M.A.; Schiffelers, R.M.; El Andaloussi, S.; Wood, M.J.A.; Vader, P. Functional delivery of lipid-conjugated siRNA by extracellular vesicles. Mol. Ther. 2017, 25, 1580–1587. [Google Scholar] [CrossRef] [Green Version]
- Wang, Y.; Chen, X.; Tian, B.; Liu, J.; Yang, L.; Zeng, L.; Chen, T.; Hong, A.; Wang, X. Nucleolin-targeted extracellular vesicles as a versatile platform for biologics delivery to breast cancer. Theranostics 2017, 7, 1360–1372. [Google Scholar] [CrossRef]
- Powell, D.; Chandra, S.; Dodson, K.; Shaheen, F.; Wiltz, K.; Ireland, S.; Syed, M.; Dash, S.; Wiese, T.; Mandal, T.; et al. Aptamer-functionalized hybrid nanoparticle for the treatment of breast cancer. Eur. J. Pharm. Biopharm. 2017, 114, 108–118. [Google Scholar] [CrossRef] [Green Version]
- Brück, J.; Pascolo, S.; Fuchs, K.; Kellerer, C.; Glocova, I.; Geisel, J.; Dengler, K.; Yazdi, A.S.; Röcken, M.; Ghoreschi, K. Cholesterol modification of p40-specific small interfering RNA enables therapeutic targeting of dendritic cells. J. Immunol. 2015, 195, 2216–2223. [Google Scholar] [CrossRef] [Green Version]
- Wang, H.; Feng, Q.; Wei, L.; Zhuo, L.; Chen, H.; Diao, Y.; Tang, Y. Significant inhibition of Tembusu virus envelope and NS5 gene using an adenovirus-mediated short hairpin RNA delivery system. Infect. Genet. Evol. 2017, 54, 387–396. [Google Scholar] [CrossRef]
- Schaar, K.; Geisler, A.; Kraus, M.; Pinkert, S.; Pryshkliak, M.; Spencer, J.F.; Tollefson, A.E.; Ying, B.; Kurreck, J.; Wold, W.S.; et al. Anti-adenoviral artificial MicroRNAs expressed from AAV9 vectors inhibit human adenovirus infection in immunosuppressed Syrian Hamsters. Mol. Ther. Nucleic Acids 2017, 8, 300–316. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Devroe, E.; Silver, P.A. Therapeutic potential of retroviral RNAi vectors. Expert Opin. Biol. Ther. 2004, 4, 319–321. [Google Scholar] [CrossRef] [PubMed]
- Westerhout, E.M.; Vink, M.; Hasnoot, P.C.J.; Das, A.T.; Berkhout, B. A conditionally replicating HIV-based vector that stably expresses an antiviral shRNA against HIV-1 replication. Mol. Ther. 2006, 14, 268–275. [Google Scholar] [CrossRef] [PubMed]
- Bastin, D.; Aitken, A.S.; Pelin, A.; Pikor, L.A.; Crupi, M.J.F.; Huh, M.S.; Bourgeois-Daigneault, M.C.; Bell, J.C.; Ilkow, C.S. Enhanced susceptibility of cancer cells to oncolytic rhabdo-virotherapy by expression of Nodamura virus protein B2 as a suppressor of RNA interference. J. Immunother. Cancer 2018, 6, 62. [Google Scholar] [CrossRef] [PubMed]
- Ylosmaki, E.; Martikainen, M.; Hinkkanen, A.; Saksela, K. Attenuation of Semliki Forest virus neurovirulence by microRNA-mediated detargeting. J. Virol. 2013, 87, 335–344. [Google Scholar] [CrossRef] [Green Version]
- Baltusnikas, J.; Satkauskas, S.; Lundstrom, K. Constructing RNA viruses for long-term transcriptional gene silencing. Trends Biotechnol. 2019, 37, 20–28. [Google Scholar] [CrossRef]
- Bagasra, O. RNAi as an antiviral therapy. Expert Opin. Biol. Ther. 2005, 5, 1463–1474. [Google Scholar] [CrossRef]
- Ibrisimovic, M.; Kneidinger, D.; Lion, T.; Klein, R. An adenoviral vector-based expression and delivery system for the inhibition of wild-type adenovirus replication by artificial miRNAs. Antivir. Res. 2013, 97, 10–23. [Google Scholar] [CrossRef] [Green Version]
- Mowa, M.B.; Crowther, C.; Ely, A.; Arbuthnot, P. Efficient silencing of hepatis B by helper-dependent adenovirus vector-mediated delivery of artificial antiviral primary micro RNAs. Microrna 2012, 1, 19–25. [Google Scholar] [CrossRef]
- Mowa, M.B.; Crowther, C.; Ely, A.; Arbuthnot, P. Inhibition of hepatitis B virus replication by helper dependent adenoviral vectors expressing artificial anti-HBV pri-mRs from a liver-specific promoter. Biomed Res. Int. 2014, 2014, 718743. [Google Scholar] [CrossRef] [Green Version]
- Chen, C.-C.; Sun, C.-P.; Ma, H.-I.; Fang, C.-C.; Wu, P.-Y.; Xiao, X.; Tao, M.-H. Comparative study of anti-hepatitis B virus RNA interference by double-stranded adeno-associated virus Serotypes 7, 8, and 9. Mol. Ther. 2009, 17, 352–359. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chen, C.-C.; Chang, C.-M.; Sun, C.-P.; Yu, C.-P.; Wu, P.-Y.; Jeng, K.-S.; Hu, C.-P.; Chen, P.-J.; Wu, J.C.; Shih, C.-H.; et al. Use of RNA interference to modulate liver adenoma development in a murine model transgenic for hepatitis B virus. Gene Ther. 2012, 19, 25–33. [Google Scholar] [CrossRef] [PubMed]
- Maepa, M.B.; Ely, A.; Grayson, W.; Arbuthnot, P. Sustained inhibition of HBV replication in vivo after systemic injection of AAVs encoding artificial antiviral primary microRNAs. Mol. Ther. Nucleic Acids 2017, 7, 190–199. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Macpherson, J.L.; Boyd, M.P.; Arndt, A.J.; Todd, A.V.; Fanning, G.C.; Ely, J.A.; Elliott, F.; Knop, A.; Raponi, M.; Murray, J.; et al. Long term survival and concomitant gene expression of ribozyme-transduced CD4+ T-lymphocytes in HIV infected patients. J. Gene Med. 2005, 7, 552–564. [Google Scholar] [CrossRef] [PubMed]
- Amado, R.G.; Mitsuyasu, R.T.; Rosenblatt, J.D.; Ngok, F.K.; Bakker, A.; Cole, S.; Chorn, N.; Lin, L.S.; Bristol, G.; Boyd, M.P.; et al. Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a Phase I study: Myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients. Hum. Gene Ther. 2004, 15, 251–262. [Google Scholar] [CrossRef] [Green Version]
- Mitsuyasu, R.T.; Merigan, T.C.; Carr, A.; Zack, J.A.; Winters, M.A.; Workman, C.; Bloch, M.; Lalezari, J.; Becker, S.; Thornton, L.; et al. Phase 2 gene therapy trial of an anti-HIV ribozyme in autologous CD34(+) cells. Nat. Med. 2009, 15, 285–292. [Google Scholar] [CrossRef] [Green Version]
- Kumar, M.; Follenzi, A.; Garforth, S.; Gupta, S. Control of HBV replication by antiviral microRNAs transferred by lentiviral vectors for potential cell and gene therapy approaches. Antivir. Ther. 2012, 17, 519–528. [Google Scholar] [CrossRef] [Green Version]
- Li, M.J.; Kim, J.; Li, S.; Zaia, J.; Yee, J.-K.; Anderson, J.; Akkina, R.; Ross, J.J. Long-term inhibition of HIV-1 infection in primary hematopoietic cells by lentiviral vector delivery of a triple combination of anti-HIV shRNA, anti-CCR5 ribozyme, and a nucleolar-localizing TAR decoy. Mol. Ther. 2005, 12, 900–909. [Google Scholar] [CrossRef]
- DiGiusto, D.L.; Krishnan, A.; Li, L.; Li, H.; Li, S.; Rao, A.; Mi, S.; Yam, P.; Stinson, S.; Kalos, M.; et al. RNA-based gene therapy for HIV with lentiviral vector modified CD34(+) cells in patients undergoing transplantation for AIDS-related lymphoma. Sci. Transl. Med. 2010, 2, 36–43. [Google Scholar] [CrossRef] [Green Version]
- Herrera-Carrillo, E.; Berkhout, B. Novel AgoshRNA molecules for silencing of the CCR5 co-receptor for HIV-1 infection. PLoS ONE 2017, 12, e0177935. [Google Scholar] [CrossRef]
- McCarthy, D.M. Self-complementary AAV vectors; advances and applications. Mol. Ther. 2008, 16, 1648–1656. [Google Scholar] [CrossRef] [PubMed]
- Mnyandu, N.; Arbuthnot, P.; Maepa, M.B. In vivo delivery of cassettes encoding anti-HBV primary microRNAs using an ancestral adeno-associated viral vector. Methods Mol. Biol. 2020, 2115, 171–183. [Google Scholar] [PubMed]
- Howe, S.J.; Mansour, M.R.; Schwarzwaelder, K.; Bartholomae, C.; Hubank, M.; Kempski, H.; Brugman, M.H.; Pike-Overzet, K.; Chatters, S.J.; de Ridder, D.; et al. Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients. J. Clin. Investig. 2008, 118, 3143–3150. [Google Scholar] [CrossRef] [PubMed]
- Yu, S.F.; von Ruden, T.; Kantoff, P.W.; Garber, C.; Seiberg, M.; Rüther, U.; Anderson, W.F.; Wagner, E.F.; Gilboa, E. Self-inactivating retroviral vectors designed for transfer of whole genes into mammalian cells. Proc. Natl. Acad. Sci. USA 1986, 83, 3194–3198. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ter Brake, O.; Berkhout, B. Lentiviral vectors that carry anti-HIV shRNAs: Problems and solutions. J. Gene Med. 2007, 9, 743–750. [Google Scholar] [CrossRef]
- Kotsopoulou, E.; Kim, V.N.; Kingsman, A.J.; Kingsman, S.M.; Mitrophanous, K.A. A rev-independent human immunodeficiency virus type 1 (HIV-1)-based vector that exploits a codon-optimized HIV-1 gag-pol gene. J. Virol. 2000, 74, 4839–4852. [Google Scholar] [CrossRef] [Green Version]
- Berkhout, B.; Liu, Y.P. Towards improved shRNA and miRNA reagents as inhibitors of HIV-1 replication. Future Microbiol. 2014, 9, 561–571. [Google Scholar] [CrossRef]
- Martikainen, M.; Niittykoski, M.; von und zu Frauenberg, M.; Immonen, A.; Koponen, S. MicroRNA-attenuated clone of virulent Semliki Forest virus overcomes antiviral type I interferon in resistant mouse CT-2A glioma. J. Virol. 2015, 89, 10637–10647. [Google Scholar] [CrossRef] [Green Version]
- Ramachandran, M.; Yu, D.; Dyczynski, M.; Baskaran, S.; Zhang, L.; Lulla, A.; Lulla, V.; Saul, S.; Nelander, S.; Dimberg, A.; et al. Safe and effective treatment of experimental neuroblastoma and glioblastoma using systemically delivered triple microRNA-detargeted Oncolytic Semliki forest virus. Clin. Cancer Res. 2017, 23, 1519–1530. [Google Scholar] [CrossRef] [Green Version]
- Kong, W.H.; Bae, K.H.; Jo, S.D.; Kim, J.S.; Park, T.G. Cationic lipid-coated gold nanoparticles as efficient and non-cytotoxic intracellular siRNA delivery vehicles. Pharm. Res. 2012, 29, 362–374. [Google Scholar] [CrossRef]
- Saulnier, A.; Pelletier, I.; Labadie, K.; Colbère-Garapin, F. Complete cure of persistant virus infections by antiviral siRNAs. Mol. Ther. 2006, 13, 142–150. [Google Scholar] [CrossRef] [PubMed]
- Thi, E.P.; Mire, C.E.; Lee, A.C.; Geisbert, J.B.; Ursic-Bedoya, R.; Agans, K.N.; Robbins, M.; Deer, D.J.; Cross, R.W.; Kondratowicz, A.S.; et al. siRNA rescues nonhuman primates from advanced Marburg and Ravn virus disease. J. Clin. Investig. 2017, 127, 4437–4448. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Villegas, P.M.; Ortega, E.; Villa-Tanaca, L.; Barron, B.L.; Torres-Flores, J. Inhibition of Dengue virus infection by small interfering RNAs that target highly conservative sequences in the NS4B or NS5 coding regions. Arch. Virol. 2018, 163, 1331–1335. [Google Scholar] [CrossRef] [PubMed]
- Dash, P.K.; Tiwari, M.; Santhosh, S.R.; Parida, M.; Rao, P.V.L. RNA interference mediated inhibition of Chikungunya virus replication in mammalian cells. Biochem. Biophys. Res. Commun. 2008, 376, 718–722. [Google Scholar] [CrossRef] [PubMed]
- Saha, A.; Bhagyawant, S.; Parida, M.; Dash, P.K. Vector-delivered artificial miRNA effectively inhibited replication of Chikungunya virus. Antivir. Res. 2016, 134, 42–49. [Google Scholar] [CrossRef] [PubMed]
- Ma, H.; Dallas, A.; Ilves, H.; Shorenstein, J.; MacLachlan, I.; Klumpp, K.; Johnston, B.H. Formulated minimal-length synthetic small hairpin RNAs are potent inhibitors of hepatitis C virus in mice with humanized livers. Gastroenterology 2014, 146, 63–66. [Google Scholar] [CrossRef] [Green Version]
- Idrees, S.; Ashfaq, U.A. RNAi: Antiviral therapy against dengue virus. Asian Pac. J. Trop. Biomed. 2013, 3, 232–236. [Google Scholar] [CrossRef] [Green Version]
- Zhang, Y.; Li, T.; Fu, L.; Yu, C.; Li, Y.; Xu, X.; Wang, Y.; Ning, H.; Zhang, S.; Chen, W.; et al. Silencing SARS-CoV Spike protein expression in cultured cells by RNA interference. FEBS Lett. 2004, 560, 141–146. [Google Scholar] [CrossRef] [Green Version]
- Zheng, B.J.; Guan, Y.; Tang, Q.; Du, C.; Xie, F.Y.; He, M.L.; Chan, K.W.; Wong, K.L.; Lader, E.; Woodle, M.C.; et al. Prophylactic and therapeutic effects of small interfering RNA targeting SARS-coronavirus. Antivir. Res. 2004, 9, 365–374. [Google Scholar]
- Li, B.-J.; Tang, Q.; Cheng, D.; Qin, C.; Xie, F.Y.; Wei, Q.; Xu, J.; Liu, Y.; Zhen, B.-J.; Woodle, M.C.; et al. Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaques. Nat. Med. 2005, 11, 944–951. [Google Scholar] [CrossRef]
- Lu, C.Y.; Huang, H.-Y.; Yang, T.H.; Chang, L.Y.; Lee, C.Y.; Huang, L.M. siRNA silencing of angiotensin-converting enzyme 2 reduced severe acute respiratory syndrome-associated coronavirus replications in Vero cells. Eur. J. Clin. Microbiol. Infect. Dis. 2008, 27, 709–715. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Millet, J.K.; Nal, B. Investigation of the functional roles of host cell proteins involved in coronavirus infection using highly specific and scalable RNA interference (RNAi) approach. Methods Mol. Biol. 2015, 1282, 231–240. [Google Scholar] [PubMed]
- Sohrab, S.S.; El-Kafrawy, S.A.; Mirza, Z.; Kamal, M.A.; Azhar, E.I. Design and delivery of therapeutic siRNAs: Application of MERS-Coronavirus. Curr. Pharm. Des. 2018, 24, 62–77. [Google Scholar] [CrossRef] [PubMed]
- Gu, W.Y.; Li, Y.; Liu, B.J.; Wang, J.; Yuan, G.F.; Chen, S.J.; Zuo, Y.Z.; Fan, J.H. Short hairpin RNAs targeting M and N genes reduce replication of porcine deltacoronavirus in ST cells. Virus Genes 2019, 55, 795–801. [Google Scholar] [CrossRef] [Green Version]
- Li, K.; Li, H.; Bi, Z.; Song, D.; Zhang, F.; Lei, D.; Luo, S.; Li, Z.; Gong, W.; Huang, D.; et al. Significant inhibition of re-emerged and emerging swine enteric coronavirus in vitro using the multiple shRNA expression vector. Antivir. Res. 2019, 166, 11–18. [Google Scholar] [CrossRef]
- Chen, W.; Feng, P.; Liu, K.; Wu, M.; Lin, H. Computational identification of small RNA targets in SARS-CoV-2. Virol. Sin. 2020, 1–3. [Google Scholar] [CrossRef] [Green Version]
- Zhao, W.M.; Song, S.H.; Chen, M.L.; Zou, D.; Ma, L.N.; Ma, Y.K.; Li, R.J.; Hao, L.L.; Li, C.P.; Tian, D.M.; et al. The 2019 novel coronavirus resource. Yi Chuan 2020, 42, 212–222. [Google Scholar]
- Taroncher-Oldenburg, G.; Marshall, A. Trends in biotech literature 2006. Nat. Biotechnol. 2007, 25, 961. [Google Scholar] [CrossRef]
- Seyhan, A.A.; Rya, T.E. RNAi screening for the discovery of novel modulators of human disease. Curr. Pharm. Biotechnol. 2010, 11, 735–756. [Google Scholar] [CrossRef]
- Houseley, J.; Tollervey, D. The many pathways of RNA degradation. Cell 2009, 136, 763–776. [Google Scholar] [CrossRef] [Green Version]
- Lundstrom, K. Latest development on RNA-based drugs and vaccines. Future Sci. OA 2018, 4, FSO300. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hadinoto, K.; Sundaresan, A.; Cheow, W.S. Lipid-polymer hybrid nanoparticles as a new generation therapeutic delivery platform: A review. Eur. J. Pharm. Biopharm. 2013, 85, 427–443. [Google Scholar] [CrossRef] [PubMed]
- Lundstrom, K. Self-amplifying RNA viruses as RNA vaccines. Int. J. Mol. Sci. 2020, 21, 5130. [Google Scholar] [CrossRef] [PubMed]
- Tiemann, K.; Rosso, J.J. RNAi-based therapeutics-current status, challenges and prospects. EMBO Mol. Med. 2009, 1, 142–151. [Google Scholar] [CrossRef]
- Jackson, A.L.; Burchard, J.; Schelter, J.; Chau, B.N.; Cleary, M.; Lim, L.; Linsley, P.S. Widespread siRNA ‘off-target’ transcript silencing mediated by seed region sequence complementarity. RNA 2006, 12, 1179–1187. [Google Scholar] [CrossRef] [Green Version]
- Grimm, D.; Streetz, K.L.; Jopling, C.L.; Storm, T.A.; Pandey, K.; Davis, C.R.; Marion, P.; Salazar, F.; Kay, M.A. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006, 441, 537–541. [Google Scholar] [CrossRef]
- Robbins, M.; Judge, A.; Ambegia, E.; Choi, C.; Yaworski, E.; Palmer, L.; McClintock, K.; Maclachlan, I. Misinterpreting the therapeutic effects of siRNA caused by immune stimulation. Hum. Gene Ther. 2008, 19, 991–999. [Google Scholar] [CrossRef] [Green Version]
- Judge, A.; MacLachlan, I. Overcoming the innate immune response to small interfering RNA. Hum. Gene Ther. 2008, 19, 111–124. [Google Scholar] [CrossRef] [Green Version]
- Kaiser, P.K.; Symons, R.C.A.; Shah, S.M.; Quinlan, E.J.; Tabandeb, H.; Do, D.V.; Reisen, G.; Lockridge, J.A.; Short, B.; Guerciolini, R.; et al. RNAi-based treatment for neurovascular age-related macular degeneration by Sirna-027. Am. J. Ophthalmol. 2010, 150, 33–39. [Google Scholar] [CrossRef]
- AMD Book. Available online: https://amdbook.org/content/agn-745-sirna-027-wet-amd-development-was-halted (accessed on 28 May 2020).
- Setten, R.L.; Rossi, J.J.; Han, S.-P. The current state and future directions of RNAi-based therapeutics. Nat. Rev. Drug Discov. 2019, 18, 421–446. [Google Scholar] [CrossRef]
- Weng, Y.; Xiao, H.; Zhang, J.; Liang, X.-J.; Huang, Y. RNAi Therapeutic and Its Innovative Biotechnological Evolution. Biotechnol. Adv. 2019, 37, 801–825. [Google Scholar] [CrossRef] [PubMed]
Indication | Vector/RNAi | Response | Ref |
---|---|---|---|
TMUV | Ad5/E and NS5 shRNAs | Inhibition of TMUV in Vero cells | [43] |
Ad wt | Ad5/E1A/pTP amiRs | Decrease in Ad wt infection | [44] |
HBV | HD Ad/HBV pri-miRs | Inhibition of HBV replication | [52] |
HBV | HD Ad MTTR/pri-miRs | Long-term inhibition of HBV replication | [53] |
Ad5 | scAAV9/pT/E1A amiRs | Inhibition of Ad5 replication in vitro | [44] |
Ad5 | scAAV9/pT/E1A amiRs | Inhibition of Ad5 replication in hamsters | [44] |
HBV | AAV7,8,9/HBV shRNA | Reduced HBV titers, mRNA and DNA levels | [54] |
HBV | AAV7,8,9/HBV shRNA | Prevention of HBV hepatocellular adenoma | [55] |
HBV | scAAV8/pri-miR-31 | HBV suppression for 32 weeks in mice | [56] |
HIV | MMLV/tat Ribozyme | Safe delivery in HIV patients in phase I trial | [57] |
HIV | MMLV/anti-HIV Ribozyme | MMLV-containing vector in HIV patients | [58] |
HIV | MMLV/anti-HIV Ribozyme | Phase II safety, but no efficacy | [59] |
HIV | HIV-1/shRNAs | Shutdown of HIV-1 replication | [46] |
HBV | HIV/siRNA HBV pol, core | Decrease in HBV DNA and RNA levels | [60] |
HIV | HIV/shRNA combination | Suppression of HIV replication | [61] |
HIV | HIV/shRNA combination | Persistent expression up to 24 months | [62] |
HIV | HIV/AgoshRNAs | Protection against CCR5-tropic HIV-1 strains | [63] |
HIV | HIV/shRNA-miRs | Suppression of HIV-1 replication in mice | [24] |
Disease | Vector/Target | Effect | Ref |
---|---|---|---|
HBV | NP-Gold/siRNA | Inhibition of HBV replication in HepG cells | [73] |
Poliovirus | siRNAs | Complete cure in HEp-2 cells | [74] |
MARV | LNPs/siRNA | 100% survival of MARV infected macaques | [75] |
RAVV | LNPs/siRNA | 100% survival of RAVV infected macaques | [75] |
DENV | NS4B/NS5 siRNAs | Inhibition of DENV replication in cell lines | [76] |
CHIKV | nsP3/E1 siRNAs | Titer reduction (99.6%) in Vero cells | [77] |
CHIKV | amiRNAs | Inhibition of CHIKV replication in Vero cells | [78] |
HCV | LNP/IRES sshRNA | Inhibition of HCV infection | [79] |
Disease | Vector/Target | Effect | Ref |
---|---|---|---|
SARS | Hairpin cDNA/S1S2 siRNAs | Inhibition of replication in Vero E6 cells | [81] |
S, nsP-12/13/16 siRNAs | 90% inhibition of replication in FRhK4 cells | [82] | |
S, nsP-12 siRNAs | Suppression of SARS symptoms in macaques | [83] | |
ACE2 shRNAs | Reduced infection in ACE2-silenced cells | [84] | |
Ezrin siRNAs | Knock-down of ezrin | [85] | |
MERS | ORF1ab siRNAs | Computational predictions for MERS control | [86] |
ORF1ab miRNAs | Computational predictions for MERS control | [86] | |
PDCoV | M/N shRNAs | Reduced titers and viral RNA in ST cells | [87] |
PEDV | M shRNAs | Inhibition of viral RNA and replication | [88] |
SADS | M shRNAs | Inhibition of viral RNA and replication | [89] |
COVID-19 | ORF1b/3a/S,M/N siRNAs | Computational design of siRNAs | [90] |
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Lundstrom, K. Viral Vectors Applied for RNAi-Based Antiviral Therapy. Viruses 2020, 12, 924. https://doi.org/10.3390/v12090924
Lundstrom K. Viral Vectors Applied for RNAi-Based Antiviral Therapy. Viruses. 2020; 12(9):924. https://doi.org/10.3390/v12090924
Chicago/Turabian StyleLundstrom, Kenneth. 2020. "Viral Vectors Applied for RNAi-Based Antiviral Therapy" Viruses 12, no. 9: 924. https://doi.org/10.3390/v12090924