ISIS Demonstrates Wider Utility of RNaseH ASOs for Nuclear Targets

While research astounds us on a daily basis with unexpected discoveries, sometimes it is what we don’t know and haven’t bothered to ask is what is astounding.  One example of the latter in the field of Oligonucleotide Therapeutics is the poor understanding of which tissues and cell types and therefore disease indications are most appropriate for a particular (delivery) approach based on the ability to engage targets there.   

Antisense Therapeutics, over 30 years in the making, has been the biggest violator of this principle.  Smug in the belief that delivery is not necessary, the approach has been to just apply the oligonucleotide and then pray that it will go to the right place and work its magic, especially in cancers.  Only after decades, the field through much clinical trial and error has come to the realization that the liver and kidney may be pharmacologically favored target organs.

In a long overdue tour-de-force, Hung and colleagues from ISIS Pharmaceuticals recently published in the journal Nucleic Acid Therapeutics a detailed investigation of the global biodistribution and RNaseH knockdown efficacy of phosphorotioate antisense chemistries (PS-ASO) following systemic application: Characterization of target mRNA reduction through in situ RNA hybridization in multiple organ systems following systemic antisense treatment in animals. This parallels a similar study for the direct application of this chemistry to the CNS presented at this year's OTS meeting which has yielded the surprising insight of the broad CNS distribution of PS-ASOs following focal administration. 

As a result of the latest research, a roadmap of target organs was created.  Importantly, through the application of newer RNA immunohistochemistry methods rather than the old harvesting and mashing up organs, the study looked at the specific cell types within an organ that were amenable to RNaseH knockdown.  This is important in at least two ways.  Firstly, it allows us to reject a potential target in organs where bulk knockdowns have shown a rather deep knockdown, but where the detailed organ analysis shows that the particular cell type in which one desired the knockdown does not show such a knockdown (e.g. kidney).  Secondly, it allows one to reconsider targets and cell types within organs for which bulk knockdowns have not been observed (e.g. the small intestines).

Another valuable piece of insight of the study was that it compared the old, second-generation 2’ MOE chemistry with the higher affinity locked nucleic acid chemistry version pioneered by Santaris (in this case the cET ISIS knock-off version of LNAs).  In addition to increasing the knockdown potency in traditional tissues such as liver, kidney, and adipose tissue, the chemistry allows for appreciable knockdowns in some less traditional tissues such as muscles.  Unfortunately, the direct comparison between 2’ MOE and LNAs was only performed in mice and at the very high 50mg/kg dose.  In the non-human primate study, also at a very high (35mg/kg) dose, no such direct comparison was  performed and from this, it seems that the new organs enabled by the higher-affinity chemistries were limited to the muscle and lung.

Why Marina Biotech could be the 2014 high-flyer

Regular readers will notice that I have shifted some of my investment attention to Marina Biotech.  The main reason for this is that this company which is considered by many to be dead, actually owns the rights to a high-affinity ASO chemistry (CRN) of a potency that is equivalent to Santaris’ LNAs and probably superior to ISIS’ cET while the market cap of Marina is just one-thousandth that of ISIS Pharmaceuticals.  Even when one considers that the in vivo safety (especially) and potency evaluations lag behind the others due to the budget constraints of Marina Bio, I believe it is a risk worth taking given the enormous valuation gap and the fact that CRN PS-ASO biodistributions and activities can be assumed to be similar to the competing chemistries.

What is more, Marina Bio is pursuing a program in type I myotonic dystrophy which represents the sweet spot of indications uniquely facilitated by these chemistries: muscle as a new druggable target organ and still shielded from superior RNAi competition; a rare, severe orphan disease; and a toxic nuclear RNA.

Largely depending on the recapitalization strategy (partnering first before capital raise or vice versa), this program together with SMARTICLE RNAi delivery and access to usiRNAi triggers, has made me accumulate 1.5% of the company with the intention of increasing my position.  Of course, financial success can only happen if other investors share my view that we should therefore give Marina Bio another chance.  As always, invest at your own risk and according to your unique financial circumstances.

A shameful title

If you re-read the title of the paper and even the entire publication, you may be forgiven for going away with the impression that it is open season for RNaseH knockdown in muscles and other tissues and organs.  This is far from the truth as the ‘exemplary’ target chosen in the study was the nuclear non-coding RNA MALAT.   This is because a high-profile Nature publication by ISIS Pharmaceuticals itself (Wheeler et al. 2012) has shown that whereas largely cytoplasmic m-e-s-s-e-n-g-e-r RNAs (i.e. RNAs encoding for proteins as even a decent high-school kid will know) expressed in muscles were entirely recalcitrant to RNase H knockdown, the mutated nuclear retained DMPK underlying myotonic dystrophy was susceptible to such action.  Curiously, while Wheeler et al. was cited in the Hung paper, the authors failed to point out this important and very obvious caveat.

This can be no innocuous omission as ISIS Pharmaceuticals in one of their patent applications has expressed the striking difference between mRNA and nuclear RNA druggability by PS-ASOs as follows (highlights are mine):

Reduction of Nuclear-Retained RNA

Data provided herein demonstrates that sensitivity to cleavage by ASOs is dramatically increased for a nuclear-retained RNA making it possible to reduce nuclear-retained targets in tissue that has low uptake of oligonucleotide by a pharmacologically relevant amount. For example, out of the more than 4,000 transcripts that Isis has targeted by antisense, MALAT1, a non-coding, nuclear-retained RNA, is demonstrated to be one of the most sensitive targets for antisense oligonucleotide/RNase H inhibition. The data demonstrate a great number of oligonucleotides targeting over the majority of the transcript that inhibit by more than 50% in vitro. The data also demonstrates very low IC50 values in multiple cell types. Half-life studies have also shown that the MALAT1 is stable over a period of at least 10 hours. Subcutaneous administration of oligonucleotide targeting MALAT1 at doses commensurate with other oligonucleotide drugs (e.g., liver targeting drugs) achieved pharmacologically relevant reduction of MALAT1 in skeletal and cardiac muscle. Dosing at 50 mg/kg biweekly for 3.5 weeks achieved a 89% and 85% reduction in gastrocnemius and quadriceps, respectively, and 54% reduction in heart (as compared to 95% reduction in liver). Pharmacologically relevant reduction of MALAT1 has also been achieved in tumor xenograft models.

As a member of the Oligonucleotide Therapeutics Society, it greatly saddens me that the related journal is letting ISIS Pharmaceuticals get away with the highly misleading, and simply wrong title.  There is no arguing around it.  Followers of the competitive oligonucleotide therapeutics investment arena know that the game here is to make RNaseH antisense appear much more widely applicable than it actually is.  What is more, it was at the 2011 OTS meeting in Boston where the ISIS CEO Stan Crooke in his keynote made the ignonimous statement that ‘mipomersen has no side effects’.  

I strongly suggest to the society and the journal Nucleic Acid Therapeutics which are supposed to foster the development of the technology broadly to keep a watchful eye on the growing corporate influence, especially by 'generous sponsors' ISIS and Alnylam Pharmaceuticals.   

ISIS Pharmaceuticals Next-Gen cET Technology on Shaky Grounds

As I was listening to a presentation by ISIS satellite company Regulus Therapeutics at the Future Leaders in the Biotech Industry Conference last week, I noticed that the fight between ISIS/Regulus and Santaris over intellectual property has increased in bitterness. On the same day, Santaris announced that the USPTO had rebuffed the second patent challenge concerning its conformationally constrained nucleotide technology (LNA).  As ISIS and Regulus have decided on making the LNA-derived cET technology their next-generation antisense technology, the increased aggression (including an ongoing gapmer patent infringement suit brought by ISIS against Santaris) may indicate that also ISIS sees cET technology on shaky IP grounds.

Thanks for the Validation!

Even during the hard-fought Tekmira vs Alnylam battle, the participants largely refrained from making direct snarky comments.  This, however, cannot be said of last week’s presentation by Regulus, when it sarcastically thanked Santaris for being years ahead in their miR-122 HCV program and doing all the clinical validation- for them.  The comment obviously refers to the fact that Stanford University had licensed the seminal Sarnow patent related to miR-122 inhibition for HCV therapy to Regulus, not Santaris.  It is also what made GSK dump Santaris and partner with Regulus on the program instead.  I would agree that Regulus has a strong case in this matter, but the unmitigated sarcasm was remarkable.

Is it all about cET?

When ISISfirst reported on their next-generation (gen 2.5 that is) nucleotide modification, it (cET) was explicitly derived from LNAs.  The rationale was that although LNA is the most potent antisense technology around, it suffered from poor safety (as supported by the premature termination of the PCSK9 and ApoB programs by Santaris).  Consequently, additional moieties were incorporated into the bridge that fixes the conformation of the backbone ribose in place.  As a result, the high affinity of the parent LNA was retained, but the safety issues were apparently overcome.

As a LNA-derived technology, the obvious question is whether Santaris, which controls fundamental LNA patents, has IP rights in cET.  Given the importance of cET to ISIS Pharmaceuticals and Regulus such uncertainty is intolerable.  Hence, it would make sense for ISIS and Regulus to attack Santaris and its LNA patents, which is exactly what ISIS has been doing.  Two such pre-emptive strikes, however, have failed according to last week's news.  And as a pre-emptive reminder on my part, a patent only gives you the right to exclude, not freedom-to-operate.

The gapmer patent infringement suit against Santaris may thus be viewed as an effort to get Santaris to the negotiating table.  The miR-122 situation, albeit unrelated to the LNA issue, would be further ammunition to ISIS and Regulus in that effort.

Expect the confrontation to get heatier still, as Santaris should strike back as the overall strategy by ISIS Pharmaceuticals, which is continuing to closeone deal after the other, seems to be working despite the lost patent re-examination battles last week, and is taking away the financial oxygen from Santaris.

Register for the GTC RNAi Research and Therapeutics meeting in San Francisco today (June 20-21).  Get a free RNAi Therapeutics blog T-shirt and 20% discount on registration by entering discount code 'RNABLG13'.

ISIS-CRP Phase I Results: The Decreasing Competitiveness of RNaseH Antisense for Liver Gene Knockdown

To maintain is positive trajectory of the recent comeback, it is important for RNAi Therapeutics to firmly claim gene knockdown in the liver for itself.  This is because liver gene knockdown is the lowest hanging fruit for the technology, yet RNaseH antisense has proven to be capable of gene knockdown there as well.   If RNaseH were to crystallize as the preferred technology, it would jeopardize a considerable portion of the near to midterm market potential of RNAi Therapeutics.  Just think of Alnylam's 5x15(TM) portfolio of drug candidates.

As I have explained before, dose/tissue oligonucleotide concentrations and, related to that, safety/tolerability will determine which technology will win the competition.  Although the odds seem in favor of RNAi Therapeutics, ISIS Pharmaceuticals keeps promising that improved chemistry and screening methods will improve upon the modest potency (~30-35% ApoB knockdown) of and the safety concerns with mipomersen.  Due to the importance of liver gene knockdown to RNAi Therapeutics, this blog will continue to comment on the respective data points as they come in.

RNaseH Antisense CRP Phase I Data

Today, ISIS Pharmaceuticals announced phase I knockdown data from its c-reactive protein (CRP) program, ISIS-CRPRx.   CRP, a gene expressed by the liver, is believed (by some, not all) to act as a central player in a host of inflammatory diseases such as atrial fibrillation and rheumatoid arthritis.  Phase II studies for these indications are ongoing.

The phase I study tested whether ISIS-CRPRx can blunt CRP induction upon inflammatory stress.  Accordingly, healthy volunteers were dosed 6 times over 3 weeks with either 400mg or 600mg of the phosphorothioate antisense molecule against CRP.  Following that, subjects received endotoxin, a common laboratory reagent that is interpreted by the body as an infection.

Subjects treated with placebo saw an approximately 30-fold increase in CRP levels due to endotoxin.  When pre-treated with 400mg and 600mg, however, the induction was reduced by 36% and 63%, respectively.

 

Although the study succeeded in showing that ISIS-CRPRx could blunt CRP induction, it is much less clear whether ISIS-CRPRx makes for a viable therapeutic.  A 63% knockdown knockdown may be OK for some indications, but intuitively one has to wonder whether to stop an acute inflammation in its tracks you need to step much harder on brakes like CRP.  Indeed, the press release proclaimed, as a testament to the specificity of the drug candidate, that ‘other important immune modulators’ were not changed- somewhat puzzling given that CRP is thought to play such a central role in inflammation.

Be that as it may, what the press release did not mention was the side effect profile seen in the ISIS-CRPRx phase I study; to wit, safety and tolerability is the primary objective of any phase I study.  What concerns me is that mipomersen is 200mg weekly and causes injection side reactions, flu-like symptoms, and indications of chronic inflammation which are likely the result of the elevated steady-state tissue concentrations required for RNaseH antisense efficacy.  In the CRP study, 2- to 3-times more phosphorothioate antisense molecules were given.  Although the side effect profile of an RNaseH antisense molecule is also sequence-dependent, doses of 400mg and higher have historically been associated with toxicity/tolerability considered unacceptable outside of cancer.   

My prediction is that due to the poor efficacy-dose relationship, ISIS-CRPRx will not go into phase III.  We have to see whether the gen2.5 cET chemistry brings any significant increases in clinical potencies as inherent molecular potencies as measured in cell culture studies may not take into consideration other pharmacological rate-limiting factors.  If gen2.5 can lower liver tissue concentrations required to obtain 50% gene silencing into the low single-digit microgram/g range, RNaseH would become more interesting again for the liver.  Otherwise, it seems that more fertile hunting grounds for antisense technologies may be found in the areas of noncoding RNAs (e.g. microRNAs and lincRNAs) and therapeutic splice regulation, especially when the target molecules have a long nuclear residence time.  With ISIS about to present phase I data for its spinal muscular atrophy splice modulation drug candidate at next week’s AAN meeting, a next step into that strategic re-direction may be taken.