Inhibition of hepatitis C virus in mice by a small interfering RNA targeting a highly conserved sequence in viral IRES pseudoknot

Jae Su Moon, Seung Hoon Lee, Eun Jung Kim, Hee Cho, Wooseong Lee, Geon Woo Kim, Hyun Ji Park, Seung Woo Cho, Choongho Lee, Jong Won Oh

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

The hepatitis C virus (HCV) internal ribosome entry site (IRES) that directs cap-independent viral translation is a primary target for small interfering RNA (siRNA)-based HCV antiviral therapy. However, identification of potent siRNAs against HCV IRES by bioinformaticsbased siRNA design is a challenging task given the complexity of HCV IRES secondary and tertiary structures and association with multiple proteins, which can also dynamically change the structure of this cis-acting RNA element. In this work, we utilized siRNA tiling approach whereby siRNAs were tiled with overlapping sequences that were shifted by one or two nucleotides over the HCV IRES stem-loop structures III and IV spanning nucleotides (nts) 277-343. Based on their antiviral activity, we mapped a druggable region (nts 313- 343) where the targets of potent siRNAs were enriched. siIE22, which showed the greatest anti-HCV potency, targeted a highly conserved sequence across diverse HCV genotypes, locating within the IRES subdomain IIIf involved in pseudoknot formation. Stepwise target shifting toward the 50 or 30 direction by 1 or 2 nucleotides reduced the antiviral potency of siIE22, demonstrating the importance of siRNA accessibility to this highly structured and sequence-conserved region of HCV IRES for RNA interference. Nanoparticle-mediated systemic delivery of the stability-improved siIE22 derivative gs-PS1 siIE22, which contains a single phosphorothioate linkage on the guide strand, reduced the serum HCV genome titer by more than 4 log10 in a xenograft mouse model for HCV replication without generation of resistant variants. Our results provide a strategy for identifying potent siRNA species against a highly structured RNA target and offer a potential pan-HCV genotypic siRNA therapy that might be beneficial for patients resistant to current treatment regimens.

Original languageEnglish
Article numbere0146710
JournalPloS one
Volume11
Issue number1
DOIs
Publication statusPublished - 2016 Jan 11

Fingerprint

Hepatitis C virus
conserved sequences
Conserved Sequence
small interfering RNA
ribosomes
Viruses
Hepacivirus
Small Interfering RNA
mice
Nucleotides
nucleotides
Antiviral Agents
RNA
Internal Ribosome Entry Sites
therapeutics
nanoparticles
Virus Replication
virus replication
RNA Interference
Viral Load

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Moon, Jae Su ; Lee, Seung Hoon ; Kim, Eun Jung ; Cho, Hee ; Lee, Wooseong ; Kim, Geon Woo ; Park, Hyun Ji ; Cho, Seung Woo ; Lee, Choongho ; Oh, Jong Won. / Inhibition of hepatitis C virus in mice by a small interfering RNA targeting a highly conserved sequence in viral IRES pseudoknot. In: PloS one. 2016 ; Vol. 11, No. 1.
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abstract = "The hepatitis C virus (HCV) internal ribosome entry site (IRES) that directs cap-independent viral translation is a primary target for small interfering RNA (siRNA)-based HCV antiviral therapy. However, identification of potent siRNAs against HCV IRES by bioinformaticsbased siRNA design is a challenging task given the complexity of HCV IRES secondary and tertiary structures and association with multiple proteins, which can also dynamically change the structure of this cis-acting RNA element. In this work, we utilized siRNA tiling approach whereby siRNAs were tiled with overlapping sequences that were shifted by one or two nucleotides over the HCV IRES stem-loop structures III and IV spanning nucleotides (nts) 277-343. Based on their antiviral activity, we mapped a druggable region (nts 313- 343) where the targets of potent siRNAs were enriched. siIE22, which showed the greatest anti-HCV potency, targeted a highly conserved sequence across diverse HCV genotypes, locating within the IRES subdomain IIIf involved in pseudoknot formation. Stepwise target shifting toward the 50 or 30 direction by 1 or 2 nucleotides reduced the antiviral potency of siIE22, demonstrating the importance of siRNA accessibility to this highly structured and sequence-conserved region of HCV IRES for RNA interference. Nanoparticle-mediated systemic delivery of the stability-improved siIE22 derivative gs-PS1 siIE22, which contains a single phosphorothioate linkage on the guide strand, reduced the serum HCV genome titer by more than 4 log10 in a xenograft mouse model for HCV replication without generation of resistant variants. Our results provide a strategy for identifying potent siRNA species against a highly structured RNA target and offer a potential pan-HCV genotypic siRNA therapy that might be beneficial for patients resistant to current treatment regimens.",
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Inhibition of hepatitis C virus in mice by a small interfering RNA targeting a highly conserved sequence in viral IRES pseudoknot. / Moon, Jae Su; Lee, Seung Hoon; Kim, Eun Jung; Cho, Hee; Lee, Wooseong; Kim, Geon Woo; Park, Hyun Ji; Cho, Seung Woo; Lee, Choongho; Oh, Jong Won.

In: PloS one, Vol. 11, No. 1, e0146710, 11.01.2016.

Research output: Contribution to journalArticle

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