Cutting down on sense makes sense for gene silencing

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Science Translational Medicine  29 Jul 2015:
Vol. 7, Issue 298, pp. 298ec127
DOI: 10.1126/scitranslmed.aac9738

Because dominant negative genetic disorders remain out of reach for gene therapy, researchers have had high hopes for RNA interference through shRNAs to silence detrimental genes. But initial enthusiasm has been dampened by off-target effects from RNA interference technologies. Now, Mockenhaupt and coworkers propose a versatile way to reduce these off-target effects from vector-encoded shRNAs by simple co-delivery of inhibitory RNA decoys. To this end, they designed modular constructs that deliver the therapeutic shRNA alongside a decoy against shRNA sense strand, the culprit for the off-target effects. The use of decoys that sequester shRNA sense strands can increase specificity in various gene silencing paradigms.

First, the authors studied the sense strand activity of a large set of shRNAs and their counteraction by RNA decoys in a human cell line. They demonstrated the ability of the co-delivered decoy RNAs to suppress the undesired effects of the shRNA sense strand on global gene expression patterns while maintaining the desired antisense efficacy. They then applied this principle to improve the specificity of viral replication inhibition in a cellular model of hepatitis C virus (HCV) infection. Going one step further, they also showed that two decoys—one to counteract shRNA sense strand and an additional one to counteract HCV-related cellular miRNAs involved in viral replication—provide further benefit. Their combinatorial RNAi strategy, delivered via an adeno-associated viral vector, increased both the efficacy and specificity of RNA interference against HSV replication.

The versatility of the design principles described in this study raises hopes for improving existing shRNA constructs for clinical application. If this strategy is adapted for the design of next-generation shRNA silencing technologies, the increased specificity—and thus safety—will widen their use as therapeutics.

S. Mockenhaupt et al., Alleviation of off-target effects from vector-encoded shRNAs via codelivered RNA decoys. Proc. Natl. Acad. Sci. U.S.A.10.1073/pnas.1510476112 (2015). [Abstract]

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