Small Molecules and Gene Therapy Muscle Out Oligonucleotide Therapeutics

Over the last two days, breathtaking data were reported for the treatment of two severe, inherited muscle-wasting diseases affecting children.  The investigative agents were a small molecule splicing modulator and a gene therapy both of which appear to achieve superior results compared to approved Oligonucleotide Therapeutics agents. 

The developments highlight the risk that while gain-of-function changes (here by splice modulation) may have proved to be low-hanging fruits for Oligonucleotide Therapeutics, they, unlike gene knockdown approaches, face increased challenges from other technology platforms.

Small molecule splicing modulation for Spinal Muscular Atrophy (SMA)

In 2011, Roche started collaborating with PTC Therapeutics on small molecule splice modulators for the treatment of SMA.  The idea is to screen small molecules for their ability to bring about changes in RNA processing that would hopefully be gene-specific enough so as not to cause widespread off-targeting.

I had always considered this to be a monumental, if not insurmountable task.  This is because a given splicing event brings together a set of proteins that each in turn also function at other genes.  So surely a small molecule that may bias splicing from SMN1 to SMN2, as does antisense oligonucleotide SPINRAZA from Ionis and Biogen through highly specific base pairing, would also affect a range of other genes.

If that were not enough of a challenge, a small molecule carries the extra baggage of being more widely available across tissue types such that off-targeting is a risk to not just the CNS as with SPINRAZA, but many other cell types where there may be no benefit from SMN upregulation.

Accordingly, the first compound in the PTC-Roche collaboration to enter clinical development, RG7800, had to be discarded last year due to retinal tox concerns.  Another small molecule competitor, branaplam from Novartis, had similarly been put on hold due to tox concerns although this compound has resumed development late last year.

It was therefore amazing to see updated results from the FIREFISH study of the follow-on compound RG7916 in type I SMA infants.  They show that 90% of children had an improvement in the CHOP-INTEND measure of physical functioning after 6 months on the drug.  The results are particularly impressive considering that treatment had been initiated relatively late compared to the new standard of care with SPINRAZA and the soon-to-be-approved gene therapy by Novartis (àAvexis).   

Not only that, there had been no treatment discontinuations due to safety issues with RG7916.

Given that SPINRAZA has to be given intrathecally while RG7916 can be given orally, and given that both the gene therapy and the orally available RG7916 appear to be somewhat more efficacious than the oligonucleotide, the focus of Biogen and Ionis should now be on testing combinations of SPINRAZA with both modalities.  Ideally, there is added efficacy from using the agents together either because due to higher achievable SMN protein levels and/or due to complementary biodistribution (note: the value of SMN increases outside motor neurons is debated).  If not, the SPINRAZA franchise may have a limited shelf-life.

Fake-it-‘til-you-make-it Sarepta with gene therapy breakthrough

The other piece of great news for families dealing with neuromuscular disease came yesterday at the Sarepta Therapeutics R&D Day. 

To wit, Sarepta had used dubious data and a lot of political lobbying to get the controversial exon skipper eteplirsen approved under accelerated approval.  While delaying the confirmatory study that is supposed to be part-and-parcel of an accelerated approval, Sarepta has been raking in billions in sales and added market capitalization.  This has allowed the company to build a veritable DMD powerhouse with a number of candidates that look much more promising than ordinary PMO-based eteplirsen.  They include peptide-conjugated PMOs and especially gene therapies.

If you are involved in drug development, better get used to the dubious morals of the industry.  If things go well, you behave like the paragon of virtue, if things don’t go so well you fake it until you get another chance at succeeding.  I digress…

Before the initial gene therapy data were to be presented by Jerry Mendell from Children’s Nationwide of SMA fame, I had dreaded the thought of having a hyped-up R&D Day being about divining the meaning of a biopsy slide or two on the barely-above-background expression of the microdystrophin transgene.

However, what was presented was anything but borderline.  Unlike with eteplirsen where we were dealing with debatable 1%-type absolute expression levels, there was robust microdystrophin expression: ~75% of cells expressed the transgene (by IF) with roughly 30% absolute expression of microdystrophin relative dystrophin from a normal person (by Western blot).

Not only this, the microdystrophin was functional at the molecular level as judged by restoring dystrophin-related protein complexes serving to protect the muscle from damage by acting as shock absorbers.  Accordingly, CK levels in the blood, a marker of muscle damage and elevated in children with DMD, were robustly (9x) and uniformly lowered in all 4 boys between the ages of 4 and 7.  Add to this the obligatory before-and-after videos and there is little doubt already at this relatively early stage already (~1-3 months after gene transfer) that AAVrh74.MHCK7.microdystrophin is a powerful agent applicable to essentially all types of DMD.

On the safety side, there were considerable, but transient and manageable increases in liver enzymes.  This was to be expected, however, considering the very high doses of AAVRh74 needed to achieve widespread transgene expression in muscles throughout the body and treating physicians know to look for it.

If the safety holds up and expression continues to be long-lived, AAVrh74.MHCK7.microdystrophin could render many exon-specific oligonucleotide splice modulators obsolete. The duration of action is the most concerning issue to me at this point given the attendant cell turnover and attendant risk of losing episomal gene therapies in patients with muscle damage.    

Black Box Therapeutics Finds Small Molecule Cure for Spinal Muscular Atrophy

After curing Cystic Fibrosis and Duchenne Muscular Dystrophy with nonsense drug ataluren, PTC Therapeutics is moving on to relieving the sufferings of many more children afflicted with severe genetic diseases.  This time it is spinal muscular atrophy (SMA).  In a publication that recently appeared in SCIENCE, PTC Therapeutics has stumbled upon another orally bioavailable small molecule that is claimed to modulate an RNA processing event for therapeutic purposes.

The reason why I’m interested in the PTC story is that their small molecule approach to RNA modulation is counter-intuitive as it instinctively calls for a nucleic acid-based solution.  On the other hand, an oral alternative to what are usually more invasive routes of administration could have certain advantages such as patient convenience and access.

Naryshkin paper

The paper by Naryshkin and colleagues is on the discovery of RG7800, a compound partnered with the new LNA antisense owner Roche.  It is an illustration of the general strategy taken by PTC Therapeutics of finding RNA sequence-specific small molecule modulators of genes of interest. 

In this example, the company began the panning process by hooking up RNA elements from the SMN2 gene that are involved in the splicing of an exon of interest with a luciferase reporter gene so as to enable large-scale small molecule library screening.  If left untouched, this reporter construct will produce very little light emission due to luciferase expression.  On the other hand, if the small molecule is successful in biasing splicing towards the inclusion of exon 7, the intended outcome of this particular SMA treatment approach, then light is produced.

As one might expect there are numerous ‘hits’ that come out of such primary screens.  In this case, 2000 small molecules from the library increased luciferase expression.  Since such expression changes can be due to a myriad of causes, selected candidates were put through a number of tests such as whether the increase was dependent on the SMN2 sequence elements (reporter constructs without the SMN2 sequences would take care of this), whether the selected small molecules change the expression or splicing of other RNAs (à off-targets; e.g. by RNA seq) etc.

RG7800 apparently survived all these tests and was found to increase the desired SMN2 splice form by about 70% in a number of cell models (including patient-derived cells) and in a mouse model.  It also has entered clinical development.

Comparison with ISIS drug

Since RG7800 is in direct competition with antisense drug candidate ISIS-SMNRx by ISIS and Biogen as both aim to increase SMN2 exon inclusion, a brief comparison is warranted.

While RG7800 has the obvious advantage of being orally bioavailable versus the need for intrathecal administration of ISIS-SMNRx, in terms of molecular outcome, exon inclusion in spinal motor neurons, it appears to be lacking: a ~70% increase compared to ~100-150% increases in the good SMN2 isoform achieved by ISIS-SMNRx in two clinical trials in SMA infants and children, and even more than that in rodent studies before (Passini et al. 2011).    However, RG7800 achieves SMN2 splice modulation not just in the motorneurons of the CNS, but in many other places, in and outside the CNS. 

There is ongoing debate as to whether such body-wide modulation is required, a question also prompted by a study by ISIS and collaborators on the systemic/subQ application of the antisense drug (Hua et al. 2011).  Parenthetically, this also means that if ISIS/Biogen wanted global SMN2 regulation, they have an option with subcutaneous administration in addition to intrathecal administration.  Interestingly, with the subcutaneous administration of ISIS-SMNRx, the mice lived much longer than when the oligo was given intrathecally (days/weeks versus months).  Indeed, consistent with those studies, the PTC small molecule also prolonged the lives of SMA mice considerably.  

I guess it will have to be the clinical trials which will be most informative as to whether this is an artefact of the mouse model or not.  If so, systemic drug exposure would add no benefit and only increase the risk of adverse events from off-targeting.

At the end of the day, what I find remarkable is that it is apparently possible to find small molecules that can modulate gene expression in a fairly sequence-selective manner.  While I don’t doubt that you can change splicing with small molecules, it is the apparent specificity of a simple molecule such as RG7800 that perplexes me.  

PTC Therapeutics did not disclose how many compounds they had to sift through to find RG7800.  If they really just picked one or a few after the initial screen that yielded ~2000 hits and then got lucky, I’d be quite skeptical.  Adding to my skepticism is that drug concentrations in the CNS were reported that greatly (>10x) exceeded those in the plasma (supplementary figure S7).  I’m no small molecule guy, but for an oligo guy who has been following drug development in general, that seems very unique. The blood-brain-barrier apparently does not exist for PTC.  

As a result, and also given the controversy around the discovery of ataluren (artefact or not) and the fact that PTC Therapeutics itself can only remotely speculate on the mechanism of action of RG7800, I acknowledge the publication as interesting, but am not ready to jump on board just yet.

Biotech IPOs Show Wall Street Likes New Toys

The biotech sector is white hot these days, and as a result, the IPO window is wide open.  This is illustrated by the fact that preclinical companies like gene therapy outfit Bluebird Bio and Agios Pharmaceuticals have either just slipped through the window or are about to.   This is also illustrated by the fact that Duchenne Muscular Dystrophy (DMD) exon skipping company Prosensa is aiming at a valuation of $400M at its IPO despite the uncertainties around the approvability of its only product candidate that matters (endpoints and safety issues) and for which it has given away much of the financial potential to a Big Pharma (GSK). And the ticker: RNA.

As it relates to gene therapy and RNA Therapeutics companies IPOeing- in addition to Prosensa, small molecule RNA processing modulation Co. PTC Therapeutics and aptamer company Regado- a gap between the valuations of already public companies and those emerging from the obscurity of the private sector is becoming apparent.  Without meaning to talk down on Bluebird Bio or gene therapy, I am scratching my head as to why this early-stage company sports a $150-200M market cap (it priced above its guided range and popped 50% on the open) whereas a much more proven and clinically advanced lentivirus-based gene therapy company, Oxford Biomedica, is not valued at even a quarter of that.  

Given that Oxford Biomedica is developing drugs for medically important indications, especially for those affecting the eye and can be proud of a remarkable preclinical literature record, just as Bluebird Bio can, the difference cannot be product versus platform focus.  Or take for comparison preclinical microRNA Therapeutics company Regulus Therapeutics (2012 IPO) with a market cap of $350M and clinically slightly more advanced Arrowhead Research with a market cap of around $60M (disclosure: I own Arrowhead).   

Instead, I believe it shows the benefit of being able to stay out of the spotlight when valuations are severely depressed as they were in the wake of the housing crisis when research and having a pipeline were actually assumed to be liabilities, not assets.  Companies like Oxford Biomedica and Arrowhead Research may thus be viewed as damaged goods.  Only supposed best-in-class companies in the RNA Therapeutics space with a halo like Alnylam and ISIS Pharmaceuticals were able to decisively spring back from low valuations as sentiments improved.

By contrast, biotech networks such as the one around Third Rock have understood to wrap up biotech companies as exciting new toys for Wall Street to buy.   Orphan drugs anybody?  Of interest, Alnylam’s CEO John Maraganore has had an involvement with both Agios and Bluebird.  I give these individuals full credit for promoting innovation.   By the same token, the depressed valuations of some of the existing innovators are another example of the inefficiency of the public markets.