RNA interference against viruses: strike and counterstrike

Abstract

RNA interference (RNAi) is a conserved sequence-specific, gene-silencing mechanism that is induced by double-stranded RNA. RNAi holds great promise as a novel nucleic acid-based therapeutic against a wide variety of diseases, including cancer, infectious diseases and genetic disorders. Antiviral RNAi strategies have received much attention and several compounds are currently being tested in clinical trials. Although induced RNAi is able to trigger profound and specific inhibition of virus replication, it is becoming clear that RNAi therapeutics are not as straightforward as we had initially hoped. Difficulties concerning toxicity and delivery to the right cells that earlier hampered the development of antisense-based therapeutics may also apply to RNAi. In addition, there are indications that viruses have evolved ways to escape from RNAi. Proper consideration of all of these issues will be necessary in the design of RNAi-based therapeutics for successful clinical intervention of human pathogenic viruses.

Figure 1. Nucleic acid–based antiviral strategies.

Antiviral nucleic acids can either be transfected into cells (e.g., siRNA or antisense oligonucleotides) or expressed intracellularly (shRNA, ribozymes or RNA decoys). Viral transcripts complementary to the siRNA/shRNA are cleaved upon assembly of the RISC machinery. RISC is not able to target RNA genomes that are protected within viral capsids or shielded from RNAi attack in subcellular compartments (e.g., the nucleus or virus-induced vesicles). Modified antisense oligonucleotides have a high affinity for their target sequence and inhibit gene expression by steric hindrance of the ribosome, splicing (within the nucleus) or through induction of mRNA cleavage by recruitment of RNase H. Binding of ribozymes to the target sequence should also trigger cleavage of the viral RNA. Decoy RNAs bind and sequester essential viral proteins or host cell factors that support virus replication.

Figure 2. Viral escape strategies from RNAi.

Inhibition of the wild-type viral RNA genome by the siRNA–RISC complex is illustrated in the center, surrounded by different viral escape strategies. Intrinsic viral escape routes (right) include viral replication in compartments that are inaccessible to the RNAi-machinery, RNA-shielding by bound proteins or the double-stranded nature of the RNA genome. Induced viral escape routes (left) include the selection of mutations in the target sequence (point mutations, deletions or insertions, although the latter have not been observed) or mutations outside the actual target that induce a new RNA structure that blocks the RNAi attack. RNA structures may play a role in intrinsic resistance to RNAi as described for viroids. RNAi suppressor factors that inhibit RNAi are shown in a separate box (upper right). Adenovirus virus-associated RNAs inhibit RNAi by competing for Dicer and RISC, suppressor proteins such as HIV-1 Tat inhibit Dicer function, and viral proteins (NS1, E3L or VP35) may sequester siRNAs or siRNA precursors.