Advanced

Quantitative assessment of the antiviral potencies of 21 shRNA vectors targeting conserved, including structured, hepatitis B virus sites

Sun, Dianxing; Roesler, Christine; Kidd-Ljunggren, Karin LU and Nassal, Michael (2010) In Journal of Hepatology 52(6). p.817-826
Abstract
Background & Aims: RNA interference (RNAi) may offer new treatment options for chronic hepatitis B. Replicating via an RNA intermediate, hepatitis B virus (HBV) is known to be principally vulnerable to RNAi. However, beyond delivery, the relevant issues of potential off-target effects, target site conservation in circulating HBV strains, and efficacy of RNAi itself have not systematically been addressed, nor can the different existing data be quantitatively compared. The aim of this study was to provide such information. Methods: To focus on the intracellular RNAi process itself and minimise other variables affecting overall RNAi efficacy, we used a robust co-transfection system to quantitatively assess the relative potencies of 21... (More)
Background & Aims: RNA interference (RNAi) may offer new treatment options for chronic hepatitis B. Replicating via an RNA intermediate, hepatitis B virus (HBV) is known to be principally vulnerable to RNAi. However, beyond delivery, the relevant issues of potential off-target effects, target site conservation in circulating HBV strains, and efficacy of RNAi itself have not systematically been addressed, nor can the different existing data be quantitatively compared. The aim of this study was to provide such information. Methods: To focus on the intracellular RNAi process itself and minimise other variables affecting overall RNAi efficacy, we used a robust co-transfection system to quantitatively assess the relative potencies of 21 small-hairpin (sh) RNA vectors, targeting conserved sites throughout the HBV genome, against viral RNAs, proteins, nucleocapsids, and secreted virions under standardised conditions. Results: The approach enabled a distinct efficacy ranking, with the six most potent shRNAs achieving >= 95% reductions in virion formation, sequence-specifically and without detectable interferon induction, yet by differentially affecting different steps. Efficacy correlated poorly with predictions and was not principally abolished by target structure. Sequence comparisons suggest that truly conserved, RNAi-targetable sequences comprise less than 500 nucleotides of the circulating HBV genomes. Conclusions: The HBV genome can harbour only a finite number of optimal target sites, but current predictions are poorly suited to constrain the number of possible candidates. However, the small size of the highly conserved sequence space suggests experimental identification as a viable option. (c) 2010 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
HBV conservation, Antiviral RNAi, Hepatitis B virus, RNA interference, Structured RNAi targets
in
Journal of Hepatology
volume
52
issue
6
pages
817 - 826
publisher
Elsevier
external identifiers
  • wos:000279705800008
  • scopus:77952425411
ISSN
0168-8278
DOI
10.1016/j.jhep.2009.10.038
language
English
LU publication?
yes
id
8643cf22-fb90-4d49-ac9d-c2c2d81d6b88 (old id 1657419)
date added to LUP
2010-08-31 12:44:20
date last changed
2018-05-29 10:01:01
@article{8643cf22-fb90-4d49-ac9d-c2c2d81d6b88,
  abstract     = {Background & Aims: RNA interference (RNAi) may offer new treatment options for chronic hepatitis B. Replicating via an RNA intermediate, hepatitis B virus (HBV) is known to be principally vulnerable to RNAi. However, beyond delivery, the relevant issues of potential off-target effects, target site conservation in circulating HBV strains, and efficacy of RNAi itself have not systematically been addressed, nor can the different existing data be quantitatively compared. The aim of this study was to provide such information. Methods: To focus on the intracellular RNAi process itself and minimise other variables affecting overall RNAi efficacy, we used a robust co-transfection system to quantitatively assess the relative potencies of 21 small-hairpin (sh) RNA vectors, targeting conserved sites throughout the HBV genome, against viral RNAs, proteins, nucleocapsids, and secreted virions under standardised conditions. Results: The approach enabled a distinct efficacy ranking, with the six most potent shRNAs achieving >= 95% reductions in virion formation, sequence-specifically and without detectable interferon induction, yet by differentially affecting different steps. Efficacy correlated poorly with predictions and was not principally abolished by target structure. Sequence comparisons suggest that truly conserved, RNAi-targetable sequences comprise less than 500 nucleotides of the circulating HBV genomes. Conclusions: The HBV genome can harbour only a finite number of optimal target sites, but current predictions are poorly suited to constrain the number of possible candidates. However, the small size of the highly conserved sequence space suggests experimental identification as a viable option. (c) 2010 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.},
  author       = {Sun, Dianxing and Roesler, Christine and Kidd-Ljunggren, Karin and Nassal, Michael},
  issn         = {0168-8278},
  keyword      = {HBV conservation,Antiviral RNAi,Hepatitis B virus,RNA interference,Structured RNAi targets},
  language     = {eng},
  number       = {6},
  pages        = {817--826},
  publisher    = {Elsevier},
  series       = {Journal of Hepatology},
  title        = {Quantitative assessment of the antiviral potencies of 21 shRNA vectors targeting conserved, including structured, hepatitis B virus sites},
  url          = {http://dx.doi.org/10.1016/j.jhep.2009.10.038},
  volume       = {52},
  year         = {2010},
}