Oligonucleotide Strategies beyond the Liver

As the first major wave of pivotal trial successes involving gene knockdown in the liver has reached the shores, oligonucleotide therapeutics are quickly establishing themselves as the dominant modality in this important target organ for new drug development.  While the industry is milking this organ for therapeutic applications, my thoughts are directed towards the next tissue opportunities that should further feed this revolution in drug development we are witnessing now.

After not having been part of the conference circus for 2 years, this week’s Oligonucleotide Therapeutics Society annual meeting in Bordeaux, France, was just what the doctor ordered for me to get a clear perspective on this issue.  Importantly, lessons learned from GalNAc-targeted oligonucleotide delivery to hepatocytes, but also LNP delivery to the liver prior to this, now allow the field to take the next step in extending delivery beyond the liver.

Chemical stability

All these efforts essentially share their use of highly modified oligonucleotides which have particularly changed the philosophy around the RNAi modality.  This allows the oligonucleotide to not only reach the target tissue intact, but also to remain trapped in endosomal compartments which serve as slow-release depots for long duration of action.

Chemical modification also has greatly reduced the immunogenicity of RNAi triggers and obviated the need for protective nanoparticle formulations.  These often came with the added liability of amplifying the immunostimulatory potential of these molecules.  Consequently, decade-old approaches are now being revisited with more fully modified RNAi trigger versions (e.g. self-delivering RNAi trigger structures as pursued by RXi Pharmaceuticals and the Khvorova group at UMass).

Ironically, after all the song and dance by RNAi bellwether Alnylam about the utility of exotic modifications in their conference presentations (one can also call it willful misleading of the field- not really the purpose of scientific conferences), the strong trend is towards maximizing 2’-O-methyl content, in addition to some 2’-F and phosphorothioation at the RNAi trigger termini.

PK enhancers

One of the reasons why the liver became the first major oligonucleotide target organ is that it is readily accessible from the blood.  This allows it to soak up oligonucleotides before they get removed by renal filtration.  In an effort to fight this tendency, the use of PK enhancers, in particular lipophilic groups is frequently seen.  Ionis and Alnylam are testing these for example for getting better distribution to the muscle and potentially also better functional uptake.

Receptors

PK enhancers, however, are largely about shifting around biodistribution, but it is hepatocyte ASGPR-type receptors that are the most valuable assets the industry is striving to identify.  My highlight of the conference therefore was a talk on a collaboration by AstraZeneca and Ionis demonstrating strikingly selective and effective targeting of beta cells in pancreatic islets. Think diabetes! 

It is the GLP1-receptor that does the magic here and which can be targeted by GLP1-peptides for effective oligonucleotide uptake.  While the in vivo validation was limited to rodent models, including an elegant GLP1-receptor knockout mouse model, I am convinced that the findings will translate to larger animals and humans.  It is one of those things you just know when seeing such data.

This example illustrates the value of knowing your target cell type really well, as this may allow you to identify additional ASGPR-type receptors which had been thought of elusive.  But even if they are lacking in some tissues, a nice, yet simple strategy to overcome this was illustrated by MPEG LA and Axolabs: by linking more than one RNAi trigger to a small scaffold, they were able to show that cellular oligonucleotide uptake capacity can be increased beyond the limits of receptor amount on the cell surface.

 

While the liver certainly does not need this strategy, it should definitely be applied to new targets like the beta cells.  Let free market competition do its magic and have oligonucleotide therapeutics solve diabetes now that you can effectively reach hepatocytes, adipocytes, and now also beta cells. Yes, I love the free markets, but I digress… 

After beta cells, it was a collaboration between Alnylam and Johnson & Johnson on overcoming the long-held dream of oligonucleotide therapeutics addressing gene regulation in cancer cells.  Here, small and stable ~2nm peptide scaffolds referred to as centyrins were coupled to the RNAi trigger and directed towards different receptors like PSMA and EGFR.  Perhaps the most striking aspect of centyrin-siRNA conjugates was their effective tumor penetration where prior RNAi delivery attempts like LNPs had fallen short.

Endosomal release

Sometimes getting to the endosomes alone is not enough when the rate of cytosolic release therefrom is insufficient.  So despite of the DPC fiasco last year and despite of aborted arginin-based endosomal release attempts prior to this, active endosomal release is still embraced in some delivery efforts.  Most notably, Sarepta has shown dramatic increases in dystrophin exon skipping in non-human primates with new peptide-PMOs (PPMOs) compared to their unconjugated parent molecules.

Of course, everybody now wants to know what the therapeutic window really is.  While the Sarepta representative at OTS was a bit cagey when asked about it, Sarepta’s CEO noted in a recent investor presentation that the filing of an IND by the end of the year would be a major positive signal in that regard.

Finally, all of the above developments are aided by more general progress in technologies interrogating biology such as single cell technologies (cell type isolation from complex tissues like the kidney), reduced chemistry costs allowing for much larger numbers of oligonucleotides to be screened, and ubiquitous low-cost and high-throughput sequencing.

 

Sometimes I pinch myself asking whether all this is real and not just a figment of my imagination, but at least in my mind the stars just keep aligning allowing for RNAi and oligonucleotide therapeutics to take the next step up the value ladder.

Aptamer-Targeted RNAi Trigger Delivery

In honor of 25 years of aptamers, or better the SELEX process which underlies the discovery of aptamers, I thought it might be a good time to revisit aptamers for the delivery of RNAi Therapeutics.

Aptamers are nucleic acids that have been selected to preferentially recognize a target, usually a protein, via their 3-dimensional structure in analogy to how monoclonal antibodies recognize their targets.  Aptamers are showing most promise in therapeutic development for the targeting of extracellular proteins in the eye for applications like wet AMD and diabetic macular edema (see Fovista from Ophthotech). 

Its success for systemic applications has been much more modest, however, with short circulation times and unexpected adverse events in a recent phase III study (likely due to the PEG portion of the aptamer drug) largely accounting for it.

Aptamers have also been considered as cell-targeting agents for RNAi Therapeutics.  Early reports suggested efficacy in HIV and cancer models.  Skepticism around the on-target mechanism in these examples was considerable though largely due to questions around how they were supposed to escape the endosomes.

I also fell into the camp of doubters (and still have some reservations), but have adjusted my view to a more productive one after it became clear that IF you had highly productive endosomal uptake like ASGPR/GalNAc and a highly stabilized RNAi trigger, gene silencing is possible even without explicit endosomal release chemistry.

Time to try the next iteration: Aptamer-DPCs

As there may not be another ASGPR-type receptor in the body and to compensate for lower drug exposure compared to the liver, in the quest to make aptamer-delivered RNAi Therapeutics more robust, the new learnings of RNAi trigger stability are probably best applied within the context of DPC delivery technology by Arrowhead Research.

Accordingly, the perhaps 10x lower uptake in say PSMA-expressing prostate cancer cells will be compensated by adding the RNAi trigger-aptamer complex (as one or separately) to a masked endosomal release polymer.  In case that the target cell receptor is only abundant, but does not support productive endosomal uptake, another aptamer may target a second co-receptor on the same cell (akin to some bispecific antibodies, co-receptors in viral cell uptake).

Following endosomal uptake, the masking groups come off, endosomal permeability increased so that the RNAi trigger may escape into the cytoplasm.  In certain configurations, a Dicer substract-type RNAi trigger structure may simplify design and increase stability.

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.