Rational design of therapeutic siRNAs: minimizing off-targeting potential to improve the safety of RNAi therapy for Huntington's disease

Ryan L Boudreau; Ryan M Spengler; Beverly L Davidson

doi:10.1038/mt.2011.185

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Rational design of therapeutic siRNAs: minimizing off-targeting potential to improve the safety of RNAi therapy for Huntington's disease

Journal article

Open access

Peer reviewed

Rational design of therapeutic siRNAs: minimizing off-targeting potential to improve the safety of RNAi therapy for Huntington's disease

Ryan L Boudreau, Ryan M Spengler and Beverly L Davidson

Molecular therapy, Vol.19(12), pp.2169-2177

12/2011

DOI: 10.1038/mt.2011.185

PMCID: PMC3242660

PMID: 21952166

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Abstract

RNA interference (RNAi) provides an approach for the treatment of many human diseases. However, the safety of RNAi-based therapies can be hampered by the ability of small inhibitory RNAs (siRNAs) to bind to unintended mRNAs and reduce their expression, an effect known as off-target gene silencing. Off-targeting primarily occurs when the seed region (nucleotides 2-8 of the small RNA) pairs with sequences in 3'-UTRs of unintended mRNAs and directs translational repression and destabilization of those transcripts. To date, most therapeutic RNAi sequences are selected primarily for gene silencing efficacy, and later evaluated for safety. Here, in designing siRNAs to treat Huntington's disease (HD), a dominant neurodegenerative disorder, we prioritized selection of sequences with minimal off-targeting potentials (i.e., those with a scarcity of seed complements within all known human 3'-UTRs). We identified new promising therapeutic candidate sequences which show potent silencing in cell culture and mouse brain. Furthermore, we present microarray data demonstrating that off-targeting is significantly minimized by using siRNAs that contain "safe" seeds, an important strategy to consider during preclinical development of RNAi-based therapeutics.

Dependovirus - genetics

Gene Targeting

RNA, Small Interfering - genetics

MicroRNAs - administration & dosage

Humans

RNA, Messenger - genetics

Gene Silencing

Corpus Striatum - metabolism

Blotting, Western

Immunoenzyme Techniques

Brain - metabolism

Huntington Disease - therapy

Serotonin Plasma Membrane Transport Proteins - metabolism

Serotonin Plasma Membrane Transport Proteins - chemistry

Serotonin Plasma Membrane Transport Proteins - genetics

Animals

RNA Interference

Drug Design

Brain - pathology

Huntington Disease - genetics

Mice

MicroRNAs - genetics

Corpus Striatum - pathology

Real-Time Polymerase Chain Reaction

Details

Title: Subtitle: Rational design of therapeutic siRNAs: minimizing off-targeting potential to improve the safety of RNAi therapy for Huntington's disease
Creators: Ryan L Boudreau - Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
Ryan M Spengler
Beverly L Davidson
Resource Type: Journal article
Publication Details: Molecular therapy, Vol.19(12), pp.2169-2177
Publisher: United States
DOI: 10.1038/mt.2011.185
PMID: 21952166
PMCID: PMC3242660
ISSN: 1525-0016
eISSN: 1525-0024
Grant note: RC1 NS068099 / NINDS NIH HHS P01 NS050210 / NINDS NIH HHS T32 HL007121 / NHLBI NIH HHS DK-54759 / NIDDK NIH HHS NS-50210 / NINDS NIH HHS NS-068099 / NINDS NIH HHS P30 DK054759 / NIDDK NIH HHS
Language: English
Date published: 12/2011
Academic Unit: Iowa Neuroscience Institute; Cardiovascular Medicine; Fraternal Order of Eagles Diabetes Research Center; Internal Medicine
Record Identifier: 9984065390902771

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