Wednesday, October 14, 2009

Aptamer-siRNAs: Another Shot at RNAi Therapeutics Delivery

There has been a trickle of papers lately describing the use of aptamers for the functional delivery of siRNAs such as for cancer and HIV. Aptamers are highly folded, 35-100 nucleotide long RNAs that can bind protein targets with relatively high affinities and specificities. One way of thinking about them is as the RNA equivalent of antibodies. Aptamers already are being tested as a therapeutic class of its own where they are typically designed to neutralize extracellular targets, with already one aptamer (Macugen) approved for wet AMD.


As such, aptamers should lend themselves for targeting associated therapeutic siRNAs to cells of interest, in a sense functioning like antibodies and small molecules that have likewise been recruited for targeted RNAi delivery. What distinguishes an aptamer-siRNA combination, however, is the promise of having to simply use only RNA synthesis to generate a pharmacologically viable siRNA therapeutic, obviating the need for complicated formulation technologies. Furthermore, when it comes to repeat-administration such a system may cause inherently little adaptive immunogenicity.

The reason why I have been somewhat skeptical on this technology is that like with so many siRNA targeting approaches, getting to the cell of interest is just a first step, and it is not obvious to me how after e.g. receptor-mediated endocytosis the rather large aptamer-siRNA conjugate would be able to cross the negatively charged lipid bilayer to get into the cytoplasm for incorporation into the RNAi-induced silencing complex (RiSC).

Nevertheless, a recent study in Nature Biotechnology (Dassie and colleagues: “Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors”) suggests that competitively low mg/kg dosages of intraperitoneally injected prostate-specific membrane antigen- (PSMA) targeted aptamer-siRNAs can efficiently knock down the popular cancer target PLK1 in a mouse xenograft model of prostate cancer. The study is a follow-up of a 2006 paper published in Nature Biotech by the same group from the University of Iowa (McNamara and colleagues: “Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras”) where intratumorally injected- i.e. not systemically administered- PSMA-targeted aptamer-siRNAs showed very efficient inhibition of tumor growth in the same model system.

Since systemic administration is deemed to be necessary for an siRNA therapeutic against prostate cancer, the investigators reasoned that they could achieve such delivery by increasing the potency of the aptamer-siRNA by primarily improving siRNA potency through siRNA design (changing an initially blunt siRNA into a Tuschl-type 3’ overhang type) and then attaching the ubiquitous PEG to increase circulation times so that the aptamer-siRNA would have an increased chance of finding its target. As hoped for, both strategies substantially improved in vivo performance. Impressively, PEG addition increased the half-life of the molecule from less than 35 minutes to over 30 hours (!) and this was accompanied by improved silencing and tumor inhibition. The 3’ overhang siRNA (actually it was a Dicer substrate- more on this later) was also much better than the original blunt-ended version. While most aptamer-siRNAs are bi-molecular which reduces the maximum length of RNA to be synthesized, a unimolecular precursor microRNA mimic performed best. This could due to increased stability of an intramolecular duplex and/or a more “natural” appearance to the RNAi machinery. Practically, however, bimolecular conjugates may be preferable as RNA synthesis becomes exponentially less efficient with size and is also for this reason that the authors further reduced the length of the aptamer from the earlier study.

Overall, all of the many controls that they were probably asked for by the reviewers confirmed the specificity of the results: the therapeutic effect correlated very well with the degree of knockdown, both in vitro and in vivo; binding and silencing was only observed in PSMA-bearing cells; no innate immunostimulation that might explain the anti-cancer effect was detected; 5’ RACE showed that there was in vivo RNAi activity. Finally, only ~21nt siRNAs were detected following administration of the Dicer-substrate RNAi triggers which suggests highly efficient Dicer processing. Generally, it has to be said that while the shorter, traditional siRNAs have many advantages in terms of specificity and immunity, Dicer-substrates may be ideally suited for conjugate approaches such as this, as Dicer-processing would liberate and thereby activate the functional siRNA whereas Argonaute loading, in theory, should be diminished by a direct conjugate to the siRNA (however, strategies such as reversible disulfide bonds might work for such a configuration).

As an aside, the studies are further validation of PLK1 as a very good target for RNAi Therapeutics in oncology. PLK1 is one of the most highly over-expressed genes in cancer, and knockdown studies have shown that cancer cells are very sensitive to the reduction in PLK1 levels while normal/healthy cells, even if transfected with PLK1 siRNA are unaffected. PLK1 is also the target for a SNALP cancer therapeutic candidate developed by Tekmira for solid cancers that is slated for IND next year (Alnylam with a 50:50 opt-in right until start of phase II).

In a sign that there is also commercial interest in aptamer-siRNAs, the leading aptamer company Archemix and Dicer-substrate company Dicerna recently agreed to collaborate on aptamer-siRNA delivery. Archemix, which shares a building with Alnylam, similarly chose to collaborate with heart- and muscle-focussed miRagen on the delivery of microRNA therapeutics. Archemix’ sudden move into small RNA therapeutics is also quite interesting given their failed IPO attempt and speculations of a reverse takeover of Silence Therapeutics.

So where do I think aptamer-siRNA delivery technology stands? I’m still somewhat skeptical and would like to see more of these studies from various laboratories. An important question that was posed by an accompanying News and Views article from Alnylam scientists (which btw makes it very likely that the paper was reviewed by them) is whether the surprising cytosolic uptake of the RNA is a peculiarity of the PSMA antigen or could be a more widely mechanism for presumably endosomal escape that could be exploited. Studies into the precise molecular mechanism of the uptake, as with all RNAi delivery systems, are needed. One could also imagine that to enhance uptake, membrane-active agents may be added to the PEG-aptamer-siRNA, although this would be contrary to the initial concept of a simple design. In summary, the more varied approaches being explored, the better for RNAi Therapeutics. For now, aptamer-siRNAs are just one of those to be watched.

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By Dirk Haussecker. All rights reserved.

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