Designing effective siRNAs with off-target control

Snøve, Ola; Nedland, Magnar; Fjeldstad, Ståle; Humberset, Håkon; Birkeland, Olaf René; Grünfeld, Thomas; Sætrom, Pål

doi:10.1016/j.bbrc.2004.10.097

Cited by 22 publications

(7 citation statements)

References 39 publications

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“…High concentrations of siRNA have been known to cause immune reactions, off target effects and saturation of the microRNA pathway (Snove et al, 2004; Grimm and Kay, 2006). …”

Section: Discussionmentioning

confidence: 99%

Mu opioid receptor knockdown in the substantia nigra/ventral tegmental area by synthetic small interfering RNA blocks the rewarding and locomotor effects of heroin

Zhang¹,

Landthaler²,

Schlussman³

et al. 2009

Neuroscience

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Mu opioid receptors (MOP-r) play an important role in the rewarding and locomotor stimulatory effects of heroin. The aim of the current study was to determine whether infusion of small interfering RNAs (siRNA) targeting MOP-r into the midbrain could knock down MOP-r mRNA and affect heroin-induced locomotor activity or heroin-induced conditioned place preference. Ten week old male C57BL/6J mice were surgically implanted bilaterally with guide cannulae directed between the substantia nigra and ventral tegmental area. After 4 days recovery, mice were infused bilaterally with siRNAs that target the MOP-r (2mM × 0.75 μl/side/day for 3 days) or control siRNA. Seven days after the last infusion, a procedure for conditioned place preference was begun with four heroin (3mg/kg i.p.) administration sessions alternating with four saline sessions. While heroin induced an increase in locomotor activity in all groups, siRNAs targeting specific regions of MOP-r significantly attenuated this effect. Of particular interest, mice infused with specific siRNAs targeting the MOP-r failed to develop and express conditioned place preference to heroin, or showed a significantly attenuated preference. These alterations in reward related behaviors are likely due to the reduction in MOP-r mRNA and protein, shown in separate studies by in situ hybridization and autoradiography using the same MOP-r- siRNA infusions. Taken together, these studies demonstrate the utility of siRNA in the neurobiological study of specific components of the reward system and should contribute to the study of other complex behaviors.

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“…High concentrations of siRNA have been known to cause immune reactions, off target effects and saturation of the microRNA pathway (Snove et al, 2004; Grimm and Kay, 2006). …”

Section: Discussionmentioning

confidence: 99%

Mu opioid receptor knockdown in the substantia nigra/ventral tegmental area by synthetic small interfering RNA blocks the rewarding and locomotor effects of heroin

Zhang¹,

Landthaler²,

Schlussman³

et al. 2009

Neuroscience

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“…Some others focus on selection of hyperfunctional siRNAs that work effectively even at low concentrations and thus induce fewer off-target effects [40]. Regardless of which algorithm is used to select effective and specific siRNAs, global gene expression analysis is an inevitable step, especially for siRNAs that will be carried into clinics [31, 41, 42]. …”

Section: Pre-clinical Development Of Sirna-based Therapeuticsmentioning

confidence: 99%

Preclinical and clinical development of siRNA-based therapeutics

Özcan

Özpolat

Coleman

et al. 2015

Advanced Drug Delivery Reviews

400

301

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Discovery of RNA interference, first in plants and C. elegans and later in mammalian cells, led to the emergence of a transformative view in biomedical research. Knowledge of the multiple actions of non-coding RNAs has truly allowed viewing DNA, RNA and proteins in novel ways. Small interfering RNAs (siRNAs) can be used as tools to study single gene function both in vitro and in vivo and are an attractive new class of therapeutics, especially against undruggable targets for the treatment of cancer and other diseases. Despite the potential of siRNAs in cancer therapy, many challenges remain, including rapid degradation, poor cellular uptake and off-target effects. Rational design strategies, selection algorithms, chemical modifications and nanocarriers offer significant opportunities to overcome these challenges. Here, we review the development of siRNAs as therapeutic agents from early design to clinical trial, with special emphasis on the development of EphA2-targeting siRNAs for ovarian cancer treatment.

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“…That is, the siRNAs should have a high potency, meaning that they satisfy the thermodynamic properties required for incorporation of the desired strand (Khvorova et al, 2003;Schwarz et al, 2003), and target sites that are appropriate for silencing Snøve et al, 2004).…”

Section: Introduction R Na Interference (Rnai) By Transfection Of Shortmentioning

confidence: 99%

Conserved MicroRNA Characteristics in Mammals

Sætrom¹,

Snøve

Nedland³

et al. 2006

Oligonucleotides

Self Cite

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Short hairpin RNAs (shRNAs) and short interfering RNAs (siRNAs) probably enter different stages of the microRNA (miRNA) pathway for depletion of mRNA and suppression of protein translation. Primary and secondary structural characteristics that are shared between endogenous primary miRNA transcripts (pri-miRNAs) may contribute toward efficient biogenesis and potent silencing. This study investigates known miRNA transcripts for characteristics that are conserved between miRNAs and that distinguish them from random hairpins with similar lengths. The primary structure is conserved, as demonstrated by a significant presence or absence of certain bases at specific positions in the miRNA precursors and their flanking regions. The secondary structure is also conserved between miRNAs, as internal loops and bulges commonly appear in specific positions in the miRNA stem. The conservation of base-pairing continues past the mature duplex and 13 bases into the primary stem, with no detectable conservation of secondary structure beyond this region. Based on these observations, we have designed a hairpin construct that incorporates the most important characteristics present in endogenous miRNAs. Preliminary experiments suggest that this construct may rescue the efficacy of shRNA triggers that cannot be used with a miR-30-based hairpin, and vice versa.

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Designing effective siRNAs with off-target control

Cited by 22 publications

References 39 publications

Mu opioid receptor knockdown in the substantia nigra/ventral tegmental area by synthetic small interfering RNA blocks the rewarding and locomotor effects of heroin

Mu opioid receptor knockdown in the substantia nigra/ventral tegmental area by synthetic small interfering RNA blocks the rewarding and locomotor effects of heroin

Preclinical and clinical development of siRNA-based therapeutics

Conserved MicroRNA Characteristics in Mammals

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