Fundamental Baulcombe RNAi Patents Extend Reach

I just got notice of the September issuances of two additional US patents (US 8258285 and US 8263569) belonging to the Baulcombe IP estate.  As previously reported, a first patent (US 8097710) from this series was issued earlier this year and represented a mini-shock to the RNAi Therapeutics IP landscape as it sat smack on the sweet-spot of the prototypical Tuschl-type siRNAs: siRNAs with guide/passenger strands of 20-24 nucleotides in length.  Consequently, Alnylam obtained a non-exclusive license to ‘710 shortly thereafter.

‘569 extends coverage over Dicer-substrate RNAi triggers

The claims of the two newly issued patents extend the coverage of the Baulcombe patent estate in 2 important ways.  Firstly, the ‘569 patent is almost identical to the original ‘710 methods patent.  This time, however, the lengths of the guide/passenger strands can be up to 30 nucleotides in length (20-30 instead of 20-24).  This means that companies working with Dicer-substrates like Dicerna may want to take a license from PBL.  Similarly, the ~25bp dsRNAs previously reported on by RXi and Silence/Intradigm, which curiously did not function as Dicer-substrates, would also fall under this new patent.  The saving grace: like ’710, ‘569 is a methods patent.  Methods patents are often easier to work around.

‘285 is a solid composition-of-matter patent

Having said that, the new ‘285 patent essentially turns the ‘710 20-24nt methods patent into a composition-of-matter one.  There is one important exception though: 20mers have to be unmodified, leaving, de facto (because clinical synthetic RNAi triggers are modified), open important asymmetric designs like the 19/21 and 20/22 designs which have been reported to be even more efficacious in many cases than the classical Tuschl 21/21 design.  Nevertheless, the ‘710 and ‘285 together could pose significant headaches for those trying to find holes with traditional RNAi triggers designs. 

Another interesting question is whether Alnylam will have to seek an additional license to ‘285, as in the press release on the Baulcombe license, only the ‘710 was noted as the subject of the license.  My sense is that ‘285 will be included and that as a result PBL will get a slightly increased participation.

[Update September 17, 2012: in an email, PBL confirmed that the new patents are part of their non-exclusive agreement with Alnylam.]

Classical ddRNAi also impacted?

All 3 patents share claims directed towards DNA-directed RNAi (ddRNAi).  It is therefore possible that they will impact the freedom-to-operate of Benitec which practices short hairpin RNAs from which short RNAs are generated by enzymatic processing in the cell.  Accordingly, an important question will be whether the DNA-directed guide and passenger strands covered by the Baulcombe claims would have to be directly generated by the described vector or can also be provided for in the form of a shRNA-type precursor.  I would guess 'probably', because in the Hamilton et al. work, the small RNAs that were seen and form the basis of the claims were also only indirectly generated. 

In summary, the Baulcombe patents have, quite unexpectedly (because based on plant work), emerged as the strongest RNAi trigger IP estate.  Stronger than Kreutzer-Limmer and stronger than Tuschl I.  In many ways, very deservedly so.  The main limitation is though that they are rapidly ageing.   


Addendum: I reviewed some of the prosecution history of the Baulcombe patents and it seems that for '285 to be granted it had to overcome a 'Crooke' patent (in this case US 6,107,094).  I've always found it a travesty that the Crookes often get cited during RNAi trigger patent prosecutions- although they have no scientific relationship to the biological RNAi process.  It is thus pleasing to see that the Examiner in this case saw the light that a double-stranded RNA that directly inhibits an enzyme (i.e. a PROTEIN) does not represent prior art for a dsRNA that targets an mRNA.  Duh!

ISIS ssRNAi Challenge to Gold Standard RNAi Delivery Comes up Short

The esteemed editors and reviewers of CELL got it wrong this time.  Usually, when a high-impact journal like CELL decides to publish back-to-back papers on a given topic, it believes that they mark a turning point of some sort that will be cited all over.  In this case (Lima et al.; Yu et al.), the turning point would be nanoparticle, or more precisely SNALP-formulated RNAi delivery ‘out’, and unformulated, single-stranded RNAi ‘in’.

For those new to my blog: it is the double-strand feature that is a defining property of the RNAi mechanism.  While a single-stranded intermediate is generated in the process, numerous studies, including indeed the one by Lima et al., show that these are contrived, and consequently about 100-fold less potent ‘inducers’ of RNAi gene silencing.

It is therefore surprising that CELL would publish a confirmation of this.  What is new though is that the in vivo ssRNAi data involved unformulated ssRNAi application, whereas previous in vivo ssRNAi work by e.g. Merck involved LNP-mediated delivery (Haringsma et al., 2012; also covered on this blog here).  However, as detailed below, the efficacy was not impressive. To me, the main point of interest related to chemistry and how this sheds light on the basic RNAi mechanism, which actually made this paper enjoyable to read.  For example, the metabolically stable 5'-(E)-vinylphosphonate modification and the positive effect of 2’F on Ago binding.  Nevertheless, such biochemical detail is not the groundbreaking stuff that lands you a paper in CELL, but more something for the dedicated aficionado.

Does ISIS feel threatened by SNALP delivery?

The complexity of SNALP delivery, by which actually the difficulty of re-engineering SNALP technology without access to Tekmira’s trade secrets and know-how is meant, is held against the technology also in a commercially competitive sense.  If patient outcomes is the main goal, as long as you master complexity, isn’t that a good thing, especially in terms of the all-important length of market exclusivity (note that the main cost of SNALP delivery is still the siRNA ingredient)?

A common criticism of my writings is that I connect all things to Tekmira’s SNALP technology.  But read the Lima et al. paper and see for yourself how ISIS equates formulated RNAi delivery with liposomal delivery (start of the abstract e.g.): 

‘The therapeutic utility of siRNAs is limited by the requirement for complex formulations to deliver them to tissues. If potent single-stranded RNAs could be identified, they would provide a simpler path to pharmacological agents. Here, we describe single-stranded siRNAs (ss-siRNAs) that silence gene expression in animals absent lipid formulation.’  

Or

'However, in their current state, the therapeutic utility of siRNA is limited by the requirement for complex lipid formulations to deliver siRNA to peripheral tissues (Vaishnaw et al., 2010).'

It looks  like 1-billion market cap ISIS feels threatened by $40M market cap Tekmira’s SNALP technology after all and is a very interested participant in the frivolous patent infringement lawsuit against Tekmira (frivolous for the reason alone that Alnylam expressly congratulated Tekmira on the BMS deal).

SNALP requires 1000-10.000-fold less oligonucleotides

The assessment that the ssRNAi work by ISIS does not mark a turning point in systemic RNAi delivery is based on simple math.  1000 to 10.000-fold higher amounts of oligonucleotides were required to achieve equivalent knockdowns in mice: conservative 50microgram/kg/month for SNALP vs 50mg/kg/twice a week for ISIS ssRNAi.    

As with any drug, large doses increase the risk of causing toxicities.  In this case, it is particularly the accumulations of large amounts of phosphorothioated oligonucleotides in the liver and kidney that causes such concern.  Of course, SNALP LNP delivery is not entirely without its safety issues.  For example, in the clinic it still involves the use of transient immune suppression which may e.g. be prohibitive to their use in millions of patients with less severe forms of hypercholesterolemia.

Although assuming for a moment that the amount of required oligonucleotides should be irrelevant as long as it was safe, antisense technologies still suffer from poor cost of goods.  Last week for example, the CEO of another antisense company, Sarepta Therapeutics (formerly known as AVI Biopharma), wrote in an unsettling Open Letter to the Duchenne Muscular Dystrophy community that the company essentially cannot afford the large, almost nutritional amounts of oligonucleotides that are required for attempting a therapeutic splice correction.  Closer to home, instead of acknowledging their current cost of goods, ISIS Pharmaceuticals is only providing estimates for their future oligo manufacturing cost goals.

Extrahepatic tissues, which ones please?

Another claim by ISIS related to their ssRNAi tech was that it would be applicable beyond the liver ('broadly distributed and active in multiple organs'), also following systemic administration.  However, once again, this was directly contradicted by their own data which showed a maximally 35% knockdown (the type of from 100 to 65, not from 100 to 35 mind you) for such a tissue (the kidney) when administering…100mg/kg of oligonucleotides in mice. 

The accompanying Huntington’s Disease paper achieved ssRNAi-mediated knockdown in the brain.  This, however, was observed following non-systemic, intraventricular infusion of large amounts of oligonucleotides in small mice brains.

Alnylam was right in  terminating ssRNAi collaboration

Taken together, the publications explain why Alnylam decided two years ago to terminate their ssRNAi collaboration with ISIS.  In addition to using Tekmira’s intravenously infused SNALP LNPs, Alnylam has been working on GalNAc-siRNA conjugates as a subcutaneously deliverable alternative for gene knockdown in the liver.  Although the gene knockdown achievable with that technology still pales in comparison to SNALP LNP, it is about 10-fold more potent than ISIS’ ssRNAi, which goes to show that despite the disadvantages in cellular delivery of unformulated, rigid dsRNAs, their dramatically increased potency more than compensates for it.

At least Lima and colleagues and I agree on this point (opening statement of the introduction): 'RNA interference (RNAi) is a mechanism by which double-stranded RNA triggers the loss of homologous sequence (Fire et al., 1998).' [Emphasis mine]

Big Agriculture Bankrolling RNAi Therapeutics

After years of pouring millions, if not billions into RNAi-related intellectual property (IP) and the development of double-strand RNA delivery, the RNAi Therapeutics industry is now harvesting returns from an unlikely source: agricultural companies.

Most notably, Alnylam reported yesterday an IP license and collaboration agreement with Monsanto which is widely known for its transgenic seed business.  Particularly eye-catching was the $29.2M in upfront monies, an amount not seen in RNAi Therapeutics for a long time.

However, Alnylam is not the only RNAi company that has been approached by Big Ag.  Admittedly somewhat flying under my radar, Devgenclosed a similarly upfronted RNAi collaboration with Syngenta in May of this year.  Interestingly, that deal came after Devgen’s 4-5 year RNAi partnership with Monsanto had ended in 2011, earning the Belgian (ag) company tens of millions.  This suggests that there is an RNAi scramble in the Ag space reminiscent of what happened in RNAi Therapeutics in 2006-8.  Moreover, Marina Biotech, also in May, exclusively licensed RNAi IP to Monsanto, and Tekmira mentioned in their last two conference calls that it was undertaking evaluative work with a large agricultural company: Monsanto or Syngenta?

The fact that Tekmira is involved in this business development opportunity for RNAi Therapeutics companies suggest that general RNAi IP is only one reason for Big Ag’s approach.

At first, this left me scratching my head: how would you apply double-strand RNA delivery by LNP in a commercially meaningful way in agriculture?  After some research though, it became obvious that Monsanto, Devgen and Syngenta are interested in using orally ingested dsRNA to fight insect pests such as the Western corn rootworm (WCR).  The need of finding new solutions for WCR has dramatically increased as the long-standing transgenic Bacillus thurigiensis toxin-incorporating crop by Monsanto has been plagued by resistance.

Another compelling reason for using non-transgenic approaches in agriculture is the fact that it should speed up the regulatory process as RNA is Generally Regarded as Safe (GRAS) by the FDA. This much reduces the hurdles compared to transgenic plants which might spread in the environment and further express biologically active proteins.  Moreover, unlike a toxin like Bt, the RNAi trigger can be highly specific to the targeted pest species.

The question, of course, is whether this approach, despite its attractions is technically and financially feasible in the first place.  The seminal work by Devgen and Monsanto (Baum et al., Nature Biotech2007) suggests that this is in fact the case: sub-nanogram per cm2 amounts of relatively cheap T7 in vitro transcribed RNA were sufficient to specifically and effectively silence essential genes in the entire body (!!!).  As a result, the growth inhibition caused by the pest was much reduced after ingesting the RNA.  I guess that the delivery work is aimed at even further reducing the required amount of RNA by a log or two.

The mechanism of this amazingly efficient gene silencing is likely the same as the early finding in nematode worms (another group of agriculturally important pests no less) that feeding them with E. coli bacteria expressing dsRNAs can cause potent and long-lasting silencing.  This phenomenon is referred to as ‘systemic RNAi’ and involves RNA amplification.  Although such systemic RNAi is unlikely to operate at the same high efficiency in all pest species, harnessing it in a species like WCR would already be highly commercially lucrative.  Monsanto apparently is close to commercializing such an RNAi-based insectizide.

Transkingdom RNAi and ddRNAi

When thinking about RNAi in plants, DNA-directed RNAi (ddRNAi) usually comes to mind, the type of RNAi where long hairpin RNAs are expressed from a transgene inserted into the host genome.  Certainly, a ddRNAi approach e.g. in corn against the same transgenes is also possible and indeed this has proven to be equally effective when compared to sprayable RNAi in the 2007 Nature Biotech paper.  It should also be added that unlike in your typical protein-expressing transgenic crop, ddRNAi per se does not involve transgenic protein expression, thereby lowering the regulatory hurdles.

When thinking about oral RNAi, especially in light of the RNAi history of feeding dsRNA-expressing bacteria to nematode worms (the first ‘transkingdom RNAi’ example), one may also consider the ‘Transkingdom’ RNAi technology by Marina Biotech (originally from Cequent).  One can speculate that Monsanto’s interest in Marina Biotech is related to this as part of a wider RNAi initiative by the Ag giant. An issue of feeding pests with such bacteria, however, is that again you release transgenic organisms into the wild.  While this may not be so much an environmental or health problem, you know that there are many out there that are religiously against anything ‘GM’, smashed windows and all.

Has Tekmira vs Alnylam been settled?

If we assume that LNP delivery is part of the package in the Alnylam-Monsanto deal and that Monsanto is the Ag company that has been working with Tekmira (until at least just two weeks ago), one can come up with at least three hypotheses for how the deal reflects on the Alnylam-Tekmira litigation:

1)     Tekmira and Alnylam competed, and Alnylam won;

2)     Monsanto will also tap Tekmira to cover all bases;

3)     There is an understanding that Alnylam will use the $30M to settle the lawsuit, and as part of the settlement/M&A, Monsanto will gain access to Tekmira technology.  Announcing the Monsanto deal before settlement is beneficial as it further bolsters Alnylam’s reputation and balance sheet. In that line of reasoning, the Regulus IPO should come SRTL.

The next weeks will tell.

Eventful Months for Tekmira

Last week, Tekmira reported its quarterly results and provided a corporate update.  With interim phase I results for its lead clinical candidate TKM-PLK1, well received clinical results by its licensee Alnylam, the Stop-Work Order from the Department of Defense, milestone payments from Talon and Alnylam, and the prospect of a jury trial following a key decision by the judge in the litigation with Alnylam, these certainly must have been one of Tekmira’s busiest 4 months ever.

TKM-PLK1 Results

20 months after trial start, Tekmira finally reported first data from its lead clinical program, TKM-PLK1 for advanced solid cancers.  The most informative data from this early-stage trial, as expected, related to safety/tolerability and pharmacokinetics. 

Accordingly, it appears that the maximally tolerated dose using an aggressive once-weekly dosing regime is 0.75mg/kg after encountering dose-limiting toxicities in the form of a case of transient thrombocytopenia and hypoxia/dyspnea each at 0.9mg/kg.  These data are in line with the clinical safety/tolerability data from other DlinDMA-based SNALP formulations (ALN-VSP02, ALN-TTR01) where the maximally tolerated dose was slightly higher, but which were dosed in in less aggressive schedules.  Although there seems to be a trade-off between dosing frequency and safety/tolerability, I would agree that for cancer applications where gene knockdown is targeted in rapidly dividing cells, more frequent dosing vs higher, but less frequent dosing may be desirable.  This is because the duration of gene knockdown is known to be largely inversely correlated with cell division frequency.   

Looking back at the overall DLinDMA results (ALN-VSP02, ALN-TTR01, TKM-PLK1), given the fairly uniform maximally tolerated doses, it is possible that lipid-specific toxicity can be as dose-limiting as siRNA sequence-specific immune stimulations.  It will therefore be interesting to see whether there will be a general shift in the maximally tolerated dose with SNALP formulations comprising different lipids.

While, as in many of these small, dose escalation trials, there were encouraging signs of therapeutic efficacy, here in the form of one partial response by RECIST and one stable disease, what excited me most about the released data was that this particular SNALP formulation achieved ‘several fold’ higher drug exposure levels than previous formulations (aka ALN-VSP02).  High/long exposure levels, of course, are thought to be critical for efficient drug delivery via the EPR effect.  The advance can be attributed to Tekmira’s rational SNALP design approach involving the use of a long-chain lipid-anchored PEG such that the cloak of invisibility is shed only after longer circulation times.  This is unlike in ALN-VSP02 (short chain anchor SNALP formulation) which exhibited short circulation times suitable for RNAi trigger delivery into various hepatic cell types.  Similar to ALN-VSP02 this time, further important pharmacokinetic data showed that the PK profile did not change upon repeat administration.  It is therefore unlikely that neutralizing antibodies are generated to the PEG component.  In certain old preclinical studies this had been shown to be an obstacle to repeat administration.

I look forward to learning about the more detailed clinical results.  In particular, I’d like to see not only the blood PK data, but possibly also the drug accumulations in tumor biopsies which could be compared to the ALN-VSP02 biopsy data.  By this, one would be able to model how exactly the higher blood exposure levels translate into tumor delivery benefits.  

Ebola Stop-Work Order

Earlier this month, Tekmira and competitor Sarepta received Stop-Work Orders from the US Department of Defense relating to their Ebola biodefense programs.  Tekmira has greatly benefitted from the DoD contract- not so much in terms of making a direct profit from the contract, but in that it also provided funding for progressing its technology platform.  A significant number of employees would have to be laid off if the final decision on whether to continue with the program, expected by September 1, were negative.  Although the impact on Tekmira’s science would not be immediate, it would definitely impact the speed of Tekmira’s technology advances if no substitute funding was found soon (see litigation section).  What is particularly frustrating about this Order is that it comes in the middle of an ongoing phase I clinical trial (at least wait for the results before making a final decision) and because budgetary uncertainties, not scientific deficiencies apparently being the reason for it.  Ironically, therehave been two recent outbreaks of Ebola in Africa highlighting that Ebola is not just a bioterrorist, but also persistent public health threat.

Tekmira Partners Celebrate Successes, Company Collects Milestones

The recent past were particularly exciting for Tekmira’s technology licensees Alnylam and Talon Therapeutics.  As discussed on this blog before, the ALN-TTR02 knockdown results, critically enabled by Tekmira’s delivery technology, were very positively received by the biotech community, including investors.  These results also paved the way for the initiation of a phase II trial of ALN-TTR02 triggering a $1M milestone to Tekmira.  As important as the milestone is to Tekmira on the eve of the jury trial, once the company has fully recovered possession of its technology, the liver knockdown results should allow the company to turn many of those companies on the sidelines into willing customers once there is a resolution to the litigation.

A somewhat unexpected $1M milestone came from Talon Therapeutics, a small biotech company that had licensed early Tekmira small molecule liposomal drug candidates.  The milestone was triggered by the FDA approval of one of the licensed product candidates, Marqibo (liposomal vincristine), for the treatment of advanced Ph- ALL.  In addition, the company is entitled to receive sales milestones.   

All Set for a Jury Trial

Despite all the important events above, the most important news regarding the financial viability of the company came when the judge made the important decision to reject the delay and cost-intensifying tactic (here: Motion for Summary Judgment) by Alnylam paving the way for a jury trial at the end of October.  As the case will be tried on all counts and, according to Alnylam’s regulatory disclosure, could cost the company in excess of $1 billion, you would think that Alnylam has no choice but to settle the matter (or buy Tekmira).  The longer Alnylam waits, the more dearly it is likely to cost them.

In that light, the next 2-3 months should be even more exciting for Tekmira shareholders and hard-working employees.

The $28M AstraZeneca-Regulus MicroRNA Therapeutics Deal

Yesterday, it was announced that AstraZeneca is paying microRNA Therapeutics company Regulus $28M for three preclinical-stage microRNA targets.  This is certainly good news not only for the field of microRNA Therapeutics, but also oligonucleotide therapeutics in general which is well on the day to be the third major drug development engine after small molecules and monoclonal antibodies.  

After GSK and Sanofi-Aventis, it is the third of its kind for Regulus and there were similar ones between Miragen and Servier late last year and Santaris and GSK before that.  The number of such deals, each usually involving a number of microRNAs, illustrates how far the field of microRNA biology has come in just 10 years from the discovery of microRNAs in humans to yield promising therapeutic targets that number in the dozens.  In fact, microRNA Therapeutics has been more successful than the more straight-forward RNAi Therapeutics approach in attracting the partnering interests of Big Pharma lately.

On the other hand, it’s been now five years since the founding of Regulus Therapeutics, and still no program has made it into the clinic.  Such a performance is certainly not good enough to support an IPO these days for which the company, based on job postings, appears to have had ambitions for for some time now.  With remaining ~25M in cash and an annual burn rate of around that, the revenues recognized from the AZ deal may well be the substitute for a public offering.  

As it was not disclosed how much of the $28M was for equity in Regulus, other than the cash added to Regulus’ balance sheet it is really difficult to tell whether the dealmakers at Regulus will be all smiles about it.  What’s more, the miR-33 atherosclerosis program which had yielded exciting data (including in non-human primates) in enhancing reverse cholesterol transport with a subsequent reduction in plaque size seems to be spoken for already at this early stage (before the magical phase II value-inflection point).

It is unclear what is causing the apparent delay of Regulus progressing programs into the clinic.  Is it the complexity of microRNA biology where each microRNAs often has dozens of targets, or has it something to do with the concern that the 2'-fluoro modification initially favored by the company may be genotoxic?

AstraZeneca’s Return to ‘Proper’ RNA Therapeutics

When AstraZeneca, in its farewell to Silence Therapeutics in January, said that the Silence effort was ‘part of its overallstrategy to explore this important therapeutic approach [i.e. RNA Therapeutics]’, I took it to mean that the Silence projects may not be their top priority in this regard and that it already had other oligonucleotide technologies and companies in mind.  

Confusingly, half a year before that AstraZeneca entered into a ‘small molecule RNA Therapeutics’alliance with PTC.  Beware of companies, particularly prevalent in the (cancer) stem cell field it seems, which claim to be pursuing new platforms and treatment paradigms, when the innovation actually rests on just tying pre-existing molecules to new biological rationalizations.  

Classic Big Pharma I thought then: advertising innovation, but really sticking to its old, rusty guns; and if AstraZeneca is widely thought to have the industry’s worst productivity, you have to look no further for its causes.

Yesterday’s news was therefore quite encouraging in that AstraZeneca has not given up on developing ‘proper’ RNA Therapeutics by which I mean that nucleic acids are the therapeutic agents.  Whether the stream of positive clinical results in oligonucleotide therapeutics (and vaccines) have provided AZ encouragement to go down this path is unclear, but they certainly did not hurt.  Maybe it will even make AZ re-energize its RNAi Therapeutics efforts (e.g. for oncology or respiratory disease).

Want to learn more about microRNAs?  Register for the 2012 Janssen Award Symposium in New York.

Next post: Tekmira's very busy quarter.

As MicroRNAs Make First Clinical Impact, Janssen Prize 2012 Awarded for Their Discovery

20 years ago, Gary Ruvkun and Victor Ambros made the startling discovery that a tiny noncoding RNA, lin-4, could be a key regulator of C. elegans development by downregulating messenger RNAs through Watson-Crick base-pairing.  What for a number of years seemed like an oddity of worm biology has become the first example for a whole new fundamental class of biological molecules, rivaling in importance messenger RNAs: essentially every biological pathway is regulated by a microRNA.     

Not only have microRNAs fundamentally re-shaped our thinking about molecular biology, they have also made quick inroads into the clinic.  Even before RNAi Therapeutics, microRNA-based diagnostics are already making a clinical impact today.  Half a dozen such tests have been commercially launched.  The currently arguably medically most impactful among them, mirViewMets(2) for the diagnosis of Cancers of Unknown Primary by Rosetta Genomics received Medicare coverage in May of this year.  This in the diagnostics is tantamount to the regulatory approval of a drug candidate in the therapeutics space.

On the microRNA therapeutics front, the miR-122 inhibitor by Santaris for the treatment of HCV infection is the most advanced.  Studies with this antisense inhibitor have yielded intriguingclinical data, including the suppression of viral loads to undetectable levels. A number of other miRNA drug candidates are in late preclinical development.

Considering the general biological importance of microRNAs and their rapid translation into the clinic, it is not all that surprising that Gary Ruvkun and Victor Ambros were recognized with the 2012 Dr. Paul Janssen Award for Biomedical Research.  This prize is one of the premier accolades in biomedical research for inspirational scientists that have undertaken ground-breaking science with great medical impact.  Surely, the discovery of microRNAs and their discoverers fit that bill.  Without lessening the importance of the prize and the contributions of corporate sponsor J&J, many of these prizewinners will go on to win the Nobel Prize.  I fully expect Ambros and Ruvkun to do so, too.

Daring Resesarch on the Cutting Edge

One cannot overestimate the scientific accomplishment of the work by Ambros and Ruvkun.  At the time, the notion of small RNAs as genetic regulators was simply unheard of.  It was thus the accomplishment of the Ambros group to embrace the possibility that their odd genetic mapping results during a worm developmental timing project pointed towards such a class of molecules. 

The lab-books around the world are littered with curious findings that never get followed up on because we think that they are likely caused by some experimental artifact and we would no get anything else done if we chased after each of them.  And even when the evidence is so clear before your eyes (e.g. that band in the low molecular weight range), the conditioned eye will simply ignore it.  In this case, the initial disbelief was only overcome by sequencing and re-sequencing before Ambros and colleagues had to finally accept that the mutation was indeed in a region without a proper open-reading frame (= protein).  Moreover, the recognition that a small RNA was the molecule affected by the mutation required that RNAs of all sizes were considered despite the fact that at the time small RNAs were not meant to be captured by the laboratory gels.  And when they accidentally were, such small RNAs surely were artefactual junk.

Discovering microRNAs as a whole new class of key genetic regulators was just one accomplishment.  Another one was deciphering their mechanism of action.  As long-time fellow researchers of worm development, Ruvkun and Ambros were familiar with the genetic interactions of the lin-4 mutant.  One gene in particular, protein-coding gene lin-14 appeared to be suppressed by lin-4.  A deletion mutant in the 3’ UTR of lin-14 found by the Ruvkun group abolished this genetic interaction.  Noticing that there was sequence complementarity between lin-4 and the missing lin-14 3' UTR fragment, it dawned upon the two scientists almost in unison that lin-4 must be interacting with lin-14 through Watson-Crick base-pairing, thereby silencing it post-transcriptionally.

Award Symposium in New York

If you want to learn more about the discovery of microRNAs, their biology and medical importance, and also meet the scientists, you can register for the Dr. Paul Janssen Award Symposium to be held on September 7, 2012 at the New York Academy of Sciences.  It will be a great opportunity for both academic scientists and the biotech crowd to leave the lab bench and trading desks behind them for a few hours and reflect on the importance of basic research, in model organisms as seemingly obscure as the worm, for advancing medicine.

The RNAi Therapeutics Blog is a proud promotional partner of the Symposium.

Shoppers- Attention Please! Marina Bio High-Affinity Nucleotides On Sale

Why pay tens of millions to ISIS Pharmaceuticals or Santaris for modified nucleic acid chemistry when you can get the same, if not better from Marina Bio for just a million?

This is the question that Novartis probably was answering when they non-exclusively licensed CRN technology (for single and double-strand oligo Rx) from Marina Bio for just $1 million in upfront considerations.  CRN stands for conformationally restricted nucleotides, similar in shape and thermodynamic behavior to Santaris’ LNA technology, a technology that is also being researched by ISIS Pharmaceuticals.

To me, CRN has been the best bet for Marina Bio's corporate survival.  The reason is that selling a nucleotide modification, especially for antisense therapeutics should be fairly straight-forward: there is no formulation involved requiring support by a functioning laboratory, just include it in standard phosphorothioate oligos like everybody else.  This comes in handy when you have become a largely virtual, IP-based biotech company like $3M market cap Marina Bio.   

I had wondered whether the reason why Marina Bio had not been able to capitalize on this opportunity so far was either due to IP uncertainties or manufacturing issues with this novel nucleotide.  The latter issue seemed to have been resolved when Marina in May of this year struck a cGMPsupply agreement with Girindus. The IP issue I have to admit I have not researched in too much detail, but suffice it to say that my understanding of Santaris’ and ISIS’ CRN patents is that they are quite structure-specific which would move the IP issue more to questions surrounding their use in general (e.g. in gapmers and the like).  

Today’s announcement also confirms that Novartis is still in the game of oligonucleotide therapeutics after picking their 30+ targets from Alnylam and a product-specific deal on an RNAi Therapeutics from Quark.  Although $1M is not much to a Big Pharma, nobody wants to part just like that with a million, even if it means being able to rescue old friend Michael French (now for the second time after the 2009 mdRNA cash crunch, Marina Bio’s predecessor).

Today’s deal further fuels the rekindled fire of commercial small RNAs:

1)      impressive clinical results by Alnylam facilitated by Tekmira’s technology;

2)      penny stock investors multiplying their money following the Medicare coverage announcement for Rosetta Genomics' Cancer of Unknown Primary miRNA diagnostics;

3)      Rosetta Genomics gearing up for the commercialization of the test in what is a whopping $>25M offering for the company;

4)      new investors in Silence Therapeutics doubling and tripling their money overnight in a new share offering;

5)      and the Tekmira-Alnylam trade secret theft show-down coming to a widely followed climax.

Big investors may be jeering at such nanocap biotech companies, but it is a fact of life that most small silencing RNA companies have become pennystocks, which also means that their resuscitation could make for some nice investment returns.