Antisense Therapeutics Dressing Up with RNAi Delivery

The boundaries between RNAi Therapeutics and Antisense Therapeutics have become blurrier.  Originally, the basic practical difference between RNAi and antisense was as follows: on the one hand, RNAi is very powerful, but it requires special formulation chemistry which often is the tox-limiting factor and necessitates that the drug be administered intravenously.   On the other hand, antisense can be utilized in unformulated/naked form and be administered subcutaneously, but it is less potent and involves the accumulation of large, problematic levels of phosphorothioate molecules in a range of tissues, primarily the kidney, liver, spleen, and probably the vasulature.

   

Recently, however, some RNAi approaches have become more antisense-like in terms of patient convenience in that conjugate technologies and ‘self-delivering’ RNAi triggers that can be administered subcutaneously have advanced into the clinic.  Over the last two weeks then, two pieces of evidence emerged of the reverse trend of antisense technologies adopting delivery technologies originally developed for RNAi Therapeutics.  The is done for improved potency and could also bring critical safety advantages.

Evidence 1: ISIS and Alnylam Find SNALP Delivery to Increase RNaseH Potency by ~20-fold

In a paper by Prakash et al. in ACS Chemical Biology, scientists from ISIS Pharmaceuticals and Alnylam demonstrate significant potency enhancements for RNaseH antisense and single-strand RNAi to be gained from the use of Tekmira’s SNALP technology.  As a reminder, the two companies once collaborated on single-strand RNAi before Alnylam terminated that relationship with ISIS continuing work on the subject, so the present publication relates to historical work during their partnership, but is relevant to ISIS' continued efforts.

The study simply compared the knockdown potencies of RNase H gapmers (phosphorothioate 2’ MOE chemistry), single-strand RNAi triggers (heavily modified), and dsRNAi triggers (ssRNAi molecule as guide together with complementary unmodified passenger strand), either as unformulated oligonucleotides or when formulated with SNALP containing the DLin-KC2-DMA lipid.  This lipid, developed by Old Tekmira (see Semple et al. 2010, Nature Biotech), was a critical ingredient of the first ‘2^nd-generation’ SNALP showing significantly improved liver knockdown potency over the original DLin-DMA SNALPs. 

When targeting PTEN in mouse livers, none of the oligonucleotides alone exhibited knockdown activity at the 4.5mg/kg dose tested.  Only when increasing the dose up to 100-200mg/kg did the RNaseH gapmer and ssRNAi trigger exhibit marked knockdown.

   

In stark contrast, profound knockdowns were achieved with SNALP-formulated RNaseH gapmer and the ssRNAi trigger at the 4.5mg/kg dose.  Remarkably, for the RNaseH gapmer, the activity was obtained at liver oligonucleotide levels that did not differ much from that of the unformulated oligonucleotide (which did not exhibit PTEN knockdown).  This means that SNALPs not so much increases the delivery to the liver per se, but the functional delivery of RNaseH gapmer, possibly by liberating phosphorothioate oligos along the endosomal cellular uptake pathway.  This finding also makes it difficult to believe some reports that phosphorothioate oligos administered without special formulation accumulate in the nuclei as this is the site where they are supposed to be mostly active.  Where the non-functional oligos actually end up is an important question as this also relates to the safety of these molecules.

Overall, the study shows that formulation with RNAi delivery technologies can greatly enhance knockdown potency.  It should be added here, however, that this single-dose study somewhat underestimated the potency of RNaseH antisense as normally a loading dose schedule would be performed to reach threshold tissue levels required for knockdown activity of unformulated PS-RNaseH gapmers.

The lower dosages and more targeted delivery with RNAi delivery may also reduce the typical toxicities associated with phosphorothioate antisense.  Indeed, one may even be able to do away with the phosphorothioate modification altogether.  Of course, toxicity related to the delivery vehicle also needs to be considered, but the authors noted in their paper that SNALP was ‘well tolerated’ and that no changes in liver enzymes or in body weight loss were seen.

To further gauge the value of SNALP and RNAi delivery in general for gapmer antisense technology, a more detailed time-course analysis of the knockdown and the tissue concentrations would be useful.

Evidence 2: Regulus Therapeutics to Employ Alnylam GalNAc-Conjugation for Mir-122 HCV Program

In another example of the value of delivery technology originally developed for RNAi Therapeutics for single-strand oligonucleotide Therapeutics, Regulus Therapeutics disclosed at last week’s Needham conference that it would use Alnylam’s GalNAc conjugation for the delivery of anti-miR122 in its HCV program which is to enter clinical development in 2014.

With this, Regulus expects to achieve once-monthly-dosing with their single-stranded anti-miR at lower doses (0.3mg/kg) than the weekly LNA-based phase II compound by competitor Santaris (>1mg/kg).  Importantly, Regulus claims that HCV patients go to see their doctors to check their antiviral responses on a monthly basis anyway.  Consequently, these routine visits for patients on anti-HCV therapies could then be combined with the subcutaneous administration of the anti-miR.  This obviously would increase compliance in an era in which oral HCV meds reach high cure rates in clinical trials, but the actual cure rates in the field are significantly lower due to rate-limiting compliance issues (h/t to John Alan Tucker from Zacks Investment Research).   

Without showing the data, it remains to be seen whether and by how much GalNAc conjugation improves anti-miR potency.  The once-monthly dosing, however, indicates that once the single-stranded oligonucleotide is in the cytoplasm (where the target is), it is trapped and stays there for quite some time instead of being washed out again into the interstitial space (outside the cells) which would be the case if extracellular and cellular oligonucleotides were in dynamic equilibrium.     

It will be interesting whether the GalNAc approach will utilize the phosphorothioate backbone which ISIS Pharmaceuticals is using at all.  If not, the decision would indicate that ISIS satellite company Regulus is concerned about the safety implications of that chemistry, especially in patients where the liver is already diseased.