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.

Ocular Applications Back in the Focus of Oligonucleotide Therapeutics

Following yesterday's disclosure that yet another one of GSK’s target picks for clinical development under their antisense options agreement with ISIS Pharmaceuticals is an ocular one, I thought it worth highlighting that ocular applications are regaining traction in oligonucleotide therapeutics in general.  This follows a temporary lull in the area due to setbacks with older generations of the technologies and funding issues for the industry.

Aptamers still in the lead

It may surprise you, but the eye is the one area in oligonucleotide therapeutics where aptamers, nucleic acids binding protein targets based on their shape not sequence (similar to antibodies), are most advanced.  Despite of the fact that the first approved aptamer, Macugen, is considered a great disappointment as it lost out to the monoclonal antibody competition in the VEGF market for wet AMD and DME, there are at least two new development candidates that are poised to become blockbusters in the same market: Fovista by Ophthotech targeting PDGF which has shown unprecedented activity in a phase II study in combination with anti-VEGF antibody Lucentis, and an earlier-stage, but potentially superior VEGF/PDGF bispecific aptamer approach by privately held SomaLogic.

It is now thought that the Macugen failure was due to it not targeting the relevant VEGF isoforms.  In other words, it was a failure of target selection/biological insight, not a failure of the technology.  Aptamers should work well for trapping extracellular proteins for ocular applications, because unlike their often rapid elimination following systemic administration, they can be maintained at elevated concentrations in the eye for sustained periods of time.  Their limitation, however, is in the number of targets available to them, similar to monoclonal antibodies.  Nevertheless, it should be kept in mind that with even just 2 or 3 commercial successes in a therapeutic area, a platform technology can be considered tremendously valuable there.

Gene-regulatory oligos catching up

Although ocular drug development has also been popular in both the antisense and especially RNAi fields, previous technology generations were inadequate to effect robust gene modulation, especially target gene knockdown.  This holds true for 1^st (à Vitravene) and 2^nd generation (cRaf inhibitor by iCo Therapeutics) antisense and the ‘naked’ RNAi trigger folly of the early days of RNAi Therapeutics (à Acuity Pharmaceuticals, Sylentis, Quark, and Sirna/Allergan to name just some of the worst offenders of sound science).

The reason why antisense and RNAi are both staging a comeback in ophthalmology is due to the use of higher affinity chemistries (e.g. cET by ISIS) and self-delivering RNAi triggers, both in the form of (partially) double-stranded (e.g. sd-rxRNAs by RXi Pharmaceuticals) and single-stranded RNAi triggers (à ISIS Pharmaceuticals).  The increased stability and lipophilicity combined with small molecular size should allow such an RNAi approach to efficiently penetrate the vitreous of the eye following needle injection and reach deep into the retina and other ocular structures.  Similarly, what used to be a mediocre 40% knockdown for ASOs could now be a genetically much more useful 70-80% knockdown with gen2.5 RNaseH.

It is too early to tell whether RNaseH gen2.5, ssRNAi, or sdrxRNAs will win out in the end.  At least in terms of timing, it will be as much a matter of investing in the technologies as it is about their potential.  In particular, I am disappointed by the failure of RXi Pharmaceuticals to recognize the need to further develop their sd-rxRNA chemistry.

So keep your eyes peeled as clinical results from the new wave of gene-modulating Oligo Therapeutics will start to emerge in 2016 and beyond.  It is possible that QPI-1007 by Quark Pharma for ocular neuroprotection for NAION may be earlier than that, although the chemical nature of this ‘2^nd generation’ non-AtuRNAi trigger remains unclear to me and therefore might be, or might not be a 'self-delivering' RNAi trigger.  If not this one, the upcoming clinical development of CTGF-targeting RXI-109 for retinal scarring by RXi Pharmaceuticals should be an interesting one to follow.

Regado Shock Raises Questions for Oligonucleotide Therapeutics Field

Ave biotech investor, morituri te salutant.

Last week, aptamer company Regado Biosciences imploded in a spectacular fashion after it had to permanently terminate a large pivotal phase III trial of its lead therapeutic program, REG1.   It followed notification that an unacceptable rate of serious anaphylactic adverse events had occurred.

Aptamers are oligonucleotides that recognize their protein targets based on their 3-dimensional shape, instead of sequence complementarity as is the case with most other oligo-based mechanisms of action.  

Because REG1 involves oligonucleotides and pegylation chemistry, the event warrants the close attention of the wider oligonucleotide therapeutics field.  This blog tries to summarize what is known about REG1 and the adverse events and aims to pinpoint potential safety landmines as well as suggest strategies to circumvent them for the benefit of ongoing and future oligonucleotide drug candidates.

REG1 a 2-component system for the tight regulation of hemostasis

The bane of anticoagulant drug development is that too much of it and/or inhibiting clotting at the wrong drug targets can lead to great morbidity and death due to uncontrolled bleeding.  REG1 aims to address this catch 22 by providing an oligonucleotide-based aptamer that binds and therefore inhibits a key regulator of the clotting cascade, Factor IXa, but with the twist that the inhibition can in turn be turned off at will by administering an antisense oligonucleotide that has sequence complementary to that of the aptamer.  This disrupts the 3-dimensional shape of the aptamer thus abrogating its ability to bind Factor IXa.

The aptamer (pegnivacogin) itself consists of a heavily modified 31mer oligonucleotide with lots of 2’-O-methyl and 2’-O-fluoro residues (~10kDa molecular weight).  However, the bulk of the drug is made of a 40kDa polyethyleneglycol (PEG) moiety appended to the 5’ end of the oligonucleotide.  

The antisense oligonucleotide functioning as the antidote meanwhile is an unassuming 15mer 2’-O-methylated RNA, hardly something that would catch the eye of an oligonucleotide toxicologist.

The reason why the aptamer had been modified with PEG was to extend its circulation half-life.  What otherwise would likely be a half-life of a few minutes for a simple 2'-O-methyl/fluoro oligonucleotide, obviously of little use for the intended regulation of blood clotting, could thereby be extended to over 24 hours when administered intravenously (à REG1) or an even more impressive ~1 week when injected subcutaneously (àREG2).

Serious allergic events in REGULATE PCI study

The REGULATE-PCI study that has just been terminated aimed to enroll approximately 13000 (!) subjects undergoing percutaneous (through the skin) coronary interventions (PCI) to unclog arteries around the heart.  Because things tend to clot around devices introduced into the human body and in the presence of physical stresses such as clot disruptions, such procedures have to be performed with the concurrent use of anti-clotting agents (anticoagulants).

The study was terminated when after about one quarter of the target enrolment (~3200), an imbalance in what the company described as ‘serious allergic adverse events’ in its press release was noted by the body tasked with ensuring the safety of clinical trial participants (DSMB).

Unfortunately, I was not able to retrieve a replay of the conference call held by the company to discuss the trial termination to gather more information on the nature of the adverse events.

It is, however, logical to assume that the serious allergic events are the same that had already been noted in the phase II RADAR trial.  Specifically, 3 of the ~500 subjects that received REG1 had allergic reactions ‘shortly’ after infusion of the pegnivacogin aptamer, 2 of which were considered ‘serious’ and in fact led to a stopping of the phase II trial after it was deemed that the study already had enough statistical power.  The affected patients were successfully managed with antihistamines and steroids (Povsic et al. 2013).

Immune reactions not foreign to Oligonucleotide Therapeutics

Immune stimulation, of course, is also the main safety risk of Oligonucleotide Therapeutics as a class.  We are all familiar with injection site reactions, alternative complement activations and attendant cytokine elevations, antibody generation to phosphorothioated oligonucleotides etc.  Some of them, e.g. TKM-Ebola most recently, have led to Clinical Holds or the discontinuation of drug candidates.  On the other hand, thousands of subjects have been given oligonucleotide therapeutics, some for years, with apparently acceptable safety profiles.

So is the oligonucleotide component of pegnivacogin the culprit for the ‘serious’ allergic reactions?

After reviewing the data, the safety issue is unlikely due to the aptamer itself.  A naked, in this case 2’-O-methylated, 2’-fluoro oligonucleotide alone is expected to be very safe, at least in terms of acute toxicity.  This conclusion can be drawn for example from the administration of naked, non-phosphorothioated oligonucleotides, including the systemic programs of Quark Pharmaceuticals. 

On the other hand, the reason for the apparent safety of unformulated oligonucleotides could be simply because such an oligonucleotide is rapidly excreted into urine and therefore has little chance to be toxic.  This is, however, unlikely since the allergic reactions were reported to occur shortly after drug administration, at a time when there would still be considerable concentrations of naked oligonucleotides left in circulation, therefore allowing for such a comparison.

It is interesting that only REG1 has been terminated so far, but not REG2.  Although this shoe could yet drop due to an abundance of caution, it suggests that the serious allergic events are dependent on the intravenous route of administration, a route of administration that is more generally plagued by immune-related ‘infusion reactions’ from small molecules to large biologics.

...enter Omontys...

This brings me to the topic of Omontys, aka peginesatide.  Omontys, of course, is a pegylated peptide that had to be withdrawn from the market 18 months ago following similar (rare) allergic events, including fatalities due to anaphylactic shock.  

Like pegnivacogin, the pegylation in Omontys had a molecular weight of 40kDa.

Like pegnivacogin, there were both intravenous and subcutaneous versions of peginesatide, but only the intravenous version was associated with the severe allergies that occurred shortly after drug administration.  

Like pegnivacogin, the allergies only occurred during the first administration of peginesatide (note: for pegnivacogin there is just 1 administration).

So taken together with the well-known hypersensitivity often seen in response to PEG, the evidence strongly points towards PEG as the culprit, not the oligonucleotide.

Pegylation widely used in RNAi Therapeutics

This unfortunately does not entirely exonerate oligonucleotide therapeutics.  The reason is that pegylation is a widely used tool in the biotech industry, and within Oligonucleotide Therapeutics, RNAi Therapeutics has made ample use of it and promises to support advances in delivery, especially beyond the liver. 

This raises the question of whether such problematic compounds can be spotted earlier.  If not, or if the decision is to continue development, can simple allergy tests identify the subjects that should not get the drug, or would anti-histamine and/or steroid pre-treatment be practical and acceptable?  Or is it even just a manufacturing/quality control issue or a matter of the molecular weight of PEG? I’m sure some of these questions sound familiar to the readers of this blog, and I expect that the field will learn over time if and when to use these and other strategies. 

As both fearlessness and fear can be fatal to drug development and investment returns, it is worth reminding ourselves here that numerous pegylated drugs have been approved and are being commercialized.  Also, there are various degrees of allergic events, some more serious than others.  

Finally, as a former Affymax (and Lehman Brothers in case you wanted to know) investor who lost a few feathers, I and Affymax just were incredibly unlucky.  It is my contention that Omontys would be widely used today if it had not been for the conservative market entry strategy by Omontys-distributor Fresenius Medical Care which involved the close monitoring of the first commercial Omontys patients which picked up the very rare events.  

Also, why simple strategies such as the use of anti-histamines or just going with the subcutaneous version were not attempted to salvage Omontys remains a mystery to me.  Blame it on the damaged goods theory.

  

For the sake of Regado investors and medicine, let’s hope that the parallels end here and Regado won’t follow in the footsteps of Affymax to bankruptcy and class action lawyers.  

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.