China Fast-Follower Competition Reaches Clinical CRISPR

There is panic among Western biotech that Chinese competitors will eat their lunch with their capital-efficient fast-follower strategy which typically involves rapid clinical translation via investigator-initiated trials.  This issue has now reached the CRISPR space in the form of first clinical data announced by YolTech regarding a PCSK9 base editing trial for the treatment of hypercholesterolemia.

Almost identical to pioneer Verve Therapeutics which reported stellar data earlier this month (discussed here), YolTech’s YOLT-101 formulation involved a GalNAc-LNP encapsulating an adenine base editor mRNA and guide RNA targeting a splice site of the PCSK9 pre-mRNA for gene knockout.  The more detailed nature of the LNP formulation was not disclosed in the accompanying medRXiv publication.   

The trial tested 3 dose levels of YOLT-101: 0.2mg/kg (n=1), 0.4mg/kg (n=2), and 0.6mg/kg (n=3) indicating an unusually rapid move up in the dose level by international standards.  Efficacy was only reported for one subject treated with 0.4mg/kg and the three 0.6mg/kg subjects with heterozygous familial hypercholesterolemia.

Similar to Verve Therapeutics, LDL-cholesterol lowering was roughly -50% for 0.6mg/kg.  Unfortunately, the information provided did not allow for an analysis of the relationship of total dose of YOLT-101 and LDLc reduction.  On the PCSK9 front, YolTech seemingly did better than Verve Therapeutics reaching a mean of -76% versus the -60% for VERVE-102 both at 0.6mg/kg.

This, however, is where the similarities ended.  In terms of the critical safety of a potentially very widely applicable therapy, 3 out of the 6 subjects treated with YOLT-101 exhibited ‘transient elevations in ALT and AST’ that ‘almost’ returned to normal within one month.  Furthermore, 5 of 6 subjects experienced infusion-related reactions involving fever, myalgia, and vomiting. And similar to Verve’s ill-fated VERVE-101 formulation, one subject at the 0.4mg/kg dose experienced chest pain shortly after LNP infusion.

Nevertheless, the authors noted that the trial remains ongoing to ‘validate the therapeutic durability and safety profile’.  Considering the ALT/AST elevations for which more detailed values were not disclosed, it seems questionable whether this is an ethical decision.  Add to this the rapid dose escalation and selective data disclosures, it provides fodder to those criticizing China for allowing human experimentation and Big Pharma taking advantage of it by licensing therapeutic candidates built on such strategies on the cheap, not even mentioning the intellectual property issues of ‘Chinese Beam Therapeutics’

The time for genome editing is now

Back from recent CRISPR conferences in Ireland and Denmark, I wanted to share my current thinking about the present and foreseeable future of clinical genome editing.

CRISPR is a clinically mature platform

First of all, genome editing, and in particular CRISPR Therapeutics have arrived big time.  Ignore for a moment the 90%+ declines in the share prices of Intellia, Verve, and Metagenomi, that all, with the exception of perhaps Beam Therapeutics, suggest that the industry will not survive.  Focus instead on the transformational results last week by Verve Therapeutics which will shape the management of chronic metabolic and cardiovascular disease for decades to come, Beam Therapeutics last month announcing that it  for the first time fixed a genetic disease (AATD) by reversing a point mutation, or the three ongoing phase 3 programs by Intellia Therapeutics which promise patients live unintruded by their disease.

So you say that this is only half the truth and many of them will develop cancer?  With hundreds of subjects having been given CRISPR therapeutics, we still have yet to hear about such cases, including for the hematopoietic stem cell applications, probably the most stringent test in that regard given the history of retroviral gene therapy.  This is supported by ample detailed genomic analyses demonstrating that many CRISPR modalities, in particular prime editing, often do not have any detectable off-targeting (!) and therefore are safer than going out in the sun or eating grilled meat.  And don’t get me started with analysts and investors pretending that small molecule drugs, 'dirty drugs' by design, are much safer in that regard when many of them like methotrexate and hydroxyurea are known to cause cancer which barely gets a mention or is routinely accepted as part of the risk-benefit of a drug.  Similarly, the currently more widely embraced antisense and RNAi technologies exhibit considerably more off-targeting, which in theory could result in cancer development with chronic use, than the average CRISPR therapeutic candidate today. 

Prime editing is the ultimate CRISPR manifestation

Prime editing is the foreseeable endgame for genome editing involving edits up to 50 nucleotides.  This is because in addition to being able to knock out genes like (Cas9) nuclease or base editing, it allows the developer to change nucleotides at will and with incredible specificity, and for gain-of-function.  It has therefore surprised me to see that prime editing is still such a niche part in these conferences and barely used in industry and even academia where IP is less of an issue.  This can likely be explained with it requiring a good deal of mental gymnastics when devising a prime editing strategy and subsequent tinkering to optimize efficacy.  Prime editing will likely also be part of strategies for achieving even larger edits, including whole gene replacements that are often desirable.

In some ways this is reminiscent of zinc fingers which make for poor screening and quick molecular biology tools and were quickly forgotten when CRISPR came along with the promise of simple sgRNA design.  However, a panel at the Copenhagen CRISPR meeting by genome editing veterans made it clear that when optimized, zinc fingers can be every bit as powerful as CRISPR and currently have a leg up where delivery is going to be viral for some time to come.  

This is particularly true for the CNS, the fourth major tissue/organ target for genome editing applications after the liver, hematopoietic stem cell, and immune cells.  Not only is it impossible to fit in prime and base editors in single AAV vectors, expressing a CRISPR effector nuclease of bacterial origin for years may be tricky (but not unsolvable) in terms of immunogenicity.  There is also some unease about having nucleases loiter around in cells for years after their job has been done.  Self-targeting/inactivation strategies may here be called for.  Zinc fingers by being small and mimicking human proteins by contrast are ready for clinical use, a fact, as the deal flow by Sangamo Therapeutics illustrates, is increasingly being recognized by the wider industry.

Genome editing versus non-permanent modalities

Another popular argument against CRISPR Therapeutics questions why one should take a ‘risk’ with permanently altering the genome when you have oligonucleotide therapeutics options that need to be administered as infrequently as every quarter, half annually, or even annually.  

While there is some application overlap between genome editing and oligonucleotide therapeutics, especially when it comes to knocking down genes, a closer look shows that the overlap is limited.  Where there is clear genetic evidence that a gene can be disabled for life without safety risks, then genome editing is the endgame, or at least capture a good portion of the market, and transient modalities may serve to de-risk the targets first.  

When it comes to bringing pathways back into finely tuned balance and/or the disease is not chronic and likely requires only temporary treatment (e.g. some cases of hypertension), transient options are preferable.  Still in other cases such as prion or Huntington’s disease where it is not clear whether it is the overall level or distribution of gene knockdown that is more important for efficacy, the preferred modality has yet to emerge from clinical studies. 

Part of the Wall Street fashion show

Wall Street is a fashion show when it comes to biotech platforms.  A little less than 10 years ago, it predicted that CRISPR would kill off the RNAi Therapeutics industry. Today, Alnylam sports a $30B market cap, about 4x that of the entire CRISPR industry combined (much of it in cash).  Of course, investing in technologies ahead of their time is fatal. The electric vehicle industry is just one example.  As I have laid out above, genome editing, however, is now and here to stay.  Having the potential to save the healthcare system money (e.g. $2M for a one-and-done HAE/ATTR treatment as opposed to $500k annually) or to lead to drastically improved outcomes (as can be predicted from chronic LDLc lowering) got to be embraced by patients, their caregivers, docs, regulators, and insurers alike.  

It's been a rough couple of years investing in development-stage, cutting-edge biotechs and current politics does not seem helpful, but if this is when it is darkest, then generational wealth awaits the survivors with the guts to hold on during a volatile comeback.  One of my two conviction bets that I look up to in this regard is therefore CRISPR therapeutic biotech Verve Therapeutics.  Uniqure, which works in the similarly unloved gene therapy arena and has a promising DNA-directed RNAi candidate for Huntington’s disease, is the other in case you were wondering.  

Verve Therapeutics Nails Cardiovascular Disease CRISPR Study

Patients do not benefit from drugs they do not take.  This is especially true in the cardiovascular disease space aimed at lowering atherogenic LDL-cholesterol where the majority of patients starting on oral options like statins do not take their pills after just one year.  This is also true for once every 2 to 4 weeks next-generation PCSK9 antibodies and even semiannual PCSK9 RNAi therapeutic inclisiran, though to a lesser degree in the latter case.

With this realization in mind, Verve Therapeutics set out to develop a PCSK9 CRISPR base editing treatment that should lower LDL-cholesterol for life by at least -40% after just a single administration of an intravenous LNP formulation.  Unfortunately, a first generation formulation, VERVE-101, had to be abandoned a year ago because of laboratory abnormalities, in particular ALT/AST elevations 5 to 10-fold above the upper limit of normal as well as a case of dangerously low platelet counts in a first clinical trial.  In addition, the intra-dose variability of the PCSK9 knockdown and LDLc lowering between subjects and the dose-responsiveness were not optimal.

Liver enzyme elevations (here ALT) with VERVE-101 in the HEART-1 study

All evidence pointed towards the LNP formulation, not the PCSK9 as the target or the base editing process, to be the culprit for the safety issues.  Verve therefore decided to replace some of the lipids in the liposomal formulation and add GalNAc sugars so as to allow the LNP to be taken up by both the LDL-receptor (via ApoE)- and ASGPR (via GalNAc).  This is helpful for two patient populations that are most in need for new treatment options and which lack LDL receptors (heFH and hoFH).  The base editor and guide RNAs were left unchanged from VERVE-101. 

Based on data from the first 14 subjects treated with VERVE-102 revealed today the theory translated perfectly into clinical practice.  At doses above 50mg of the LNP, the mean LDLc reduction was -59%, in line with the most potent PCSK9 agents (antibodies) and significantly more potent than inclisiran, especially in the heterozygous FH (heFH) population.  Moreover, there was a beautiful dose response for both PCSK9 and LDLc lowering and very little inter-patient variability.

Dose-related LDLc lowering in the HEART-2 trial with VERVE-102

Even more importantly, the safety was pristine.  There was hardly a blip with no outliers in terms of ALT/AST changes upon LNP administration, a stark difference to VERVE-101.  Similarly, no platelet changes were seen.  Only a single case of grade 2 infusion reaction was observed which rapidly resolved and does not pose an obstacle to further clinical development and commercialization.  Anybody familiar with LNP technology understands that GalNAc-LNPs are now the gold standard in the delivery of genome editing in the liver.

Verve Therapeutics is wrapping up the HEART-2 study with a final higher dose to see whether there is further LDLc lowering and then proceed to a ~60-subject phase II study aimed at locking down one of two fixed doses of VERVE-102 for the registrational phase of clinical development.

Today marks a milestone in moving genome editing to large, indeed very large patient populations. 

Disclosure: I owned some Verve Therapeutics shares going into data and doubled down on it after seeing the emerging VERVE-102 product profile.

Hepcidin Agents Set to Improve Polycythemia Vera Care

Protagonist Therapeutics earlier this month reported positive results from its phase III VERIFY study of hepcidin mimetic rusfertide for the treatment of polycythemia vera (PV).  This marks an important milestone in bettering the care of PV patients as it showed a reduction in the need for phlebotomies that, importantly, was further accompanied by a measurable increase in quality of life. Notably, this did not come at the cost of a greater risk of developing cancer and other side effects such as fatigue that current standard of care agents suffer from.

Subsequent to the release of the VERIFY results, Ionis Pharmaceuticals licensed global rights to sapablursen to Japanese Ono Pharmaceuticals for $280M in upfront.  

Mechanism of action

Similar to synthetic peptide rusfertide, the RNaseH antisense sapablursen aims to increase hepcidin pathway activity by facilitating its  release from the liver.  This can be achieved by knocking down its negative regulator TMPRSS6.  As a master regulator of global iron uptake, storage, and dynamics in the body, hepcidin suppresses the overproduction of red blood cells (erythrocytosis) by restricting iron supply to the bone marrow.  It is the overabundance of red blood cells in circulation and subsequent viscosity that leads to an increased risk of thromboembolic events.  Night sweats, abdominal discomfort, and bone pain are some of the other consequences people with PV suffer from.

The expected life expectancy from diagnosis, typically around the age of 60, is about 20 years.  In about 10-15% of cases, PV progresses to myelofibrosis which carries a poorer prognosis.

Current standard of care

The first-line treatment for PV is ‘blood thinning’ aspirin in addition to bloodletting (phlebotomy) in a procedure that is essentially the same as when you donate blood.  The goal here is to get the fraction that red blood cell occupy in the blood to below 45%.  This is considered to reduce the risk of thromboembolism by 4 fold compared to having a hematocrit value of 45-50%.  The main side effects from phlebotomies is fatigue and general iron deficiency.

When phlebotomy is not enough, or when you are above 60, cytoreductive therapy is indicated.  The typical reason for red blood cell overproliferation in PV is an acquired mutation in the JAK2 gene (V617F)  in hematopoietic cells leading to increased cytokine signaling.  Blood cell lineages other than the erythropoetic one may also be affected.  Second-line agents (used in combination with bloodletting) aim to inhibit subsequent cellular proliferation.

Unfortunately, second-line agents are generally blunt instruments that carry a lot of safety and tolerability baggage.  

First off is hyroxyurea which is, hold on, a DNA synthesis and repair inhibitor and, unsurprisingly is recognized to cause cancer, especially non-melanoma skin cancer.  Add to this the nausea and immune dysfunctions to mention only a few of the other side effects.  I get it: small molecule and cheap, but give me a safer, alternative medicine (and since we are at it, HU is a reminder of all the widely described carcinogenic small molecule drugs and we are agonizing about genome editing agents with mutation rates well below natural sunlight). 

Next is interferon.  Anybody following the hepatitis B virus treatment field knows that this is a very poorly tolerated agent leading  to depression and flu-like symptoms causing patients to frequently stop taking the medication.

Ruxolitinib, a JAK2 inhibitor, is certainly an advance in the cytoreductive approach in PV as it targets the root cause: JAK2 activity.  This, however, also means an increase in the risk of infections (due to suppression of immune cell lineages) and, once again, non-melanoma skin cancer.  Approved for myelofibrosis already, it will be important to see whether its use in PV can also inhibit the progression to myelofibrosis.

Role of hepcidin agents

Due to the safety and tolerability issues noted above, the hepcidin pathway agents should be well positioned to grab a major share of the second-line treatment market.  In addition to not showing an increased rusfertide-related cancer risk or other major safety issues, VERIFY demonstrated that patients actually felt better on the drug.

In some patients, weekly subQ injections eliminated the need for phlebotomies altogether as more than 76.9% on the drug did not qualify for it during weeks 20-32 compared to  32.9% on placebo.  72.8% did not undergo a phlebotomy for the entirety of the primary observation period of the study (week 0-32) compared to only 21.9% on placebo.  

Importantly, the ~300 study participants could be on cytoreductive background therapy.  This may also explain that the mean number of phlebotomies during weeks 0 to 32 for those on placebo was just 1.8, i.e. in line with a regular blood donor.  Adding rusfertide reduced this to 0.5.  

 

PK/PD comparison of hepcidin agents

In addition to the difference of mimicking hepcidin versus inhibiting an inhibitor of hepcidin, another important differentiator is the PK/PD profile of the two approaches differ.  Since peptides typically do not last long in circulation, rusfertide needs to be given weekly with more than 10x differences in peak-to-trough levels.  By contrast, both the Ionis antisense (sapablursen) and Silence Therapeutics SLN124 (divesiran) RNAi TMPRSS6 knockdown agents lead to sustained 3-5 fold increases in endogenous hepcidin depending on dose and dose frequency.

In a study in PV patients, SLN124 led to a more than 10x reduction in phlebotomy frequency compared to the run-in period, although this difference may be more moderate in a placebo-controlled study similar to the Protagonist experience.  In any case, my base case is that efficacy in terms of phlebotomy frequency will turn out to be similar between the two approaches with the more sustained, physiological increase in endogenous hepcidin possibly paying dividends over the longer term.  The reduced drug administration frequency (monthly subQ likely for sapablursen, q6w currently for SLN124) would also favor the oligonucleotide options.

Ionis has been more secretive about the performance of IONS-TMPRSS6 in PV.  They did, however, disclose in an investor presentation that during the partnering process, Ono Pharmaceuticals and other competing companies got to see those data. Based on comparable hepcidin elevations in human volunteer studies, I would expect phlebotomy and other efficacy endpoints to be roughly on par with what Silence Therapeutics has seen, although the 9mg/kg cohort with SLN124 could set a new benchmark if confirmed in a larger study.

Additional Market considerations

There is considerable interest in developing next-generation PV therapeutics.  This is also illustrated by recent deal activity in the space.  In January 2024, Takeda Pharmaceuticals paid $300M upfront to Protagonist for 50:50 US co-development and co-commercialization rights and exclusive ex-US rights following the successful completion of phase II studies.  At the time, rusfertide peak sales were projected to be in the $1-2B range.

This week, another Japanese pharmaceutical company, Ono, obtained full rights to sapablursen from Ionis for $280M in upfront following full enrolment of a PV phase II study, a deal that was likely informed by the rusfertide results.  Though enhanced milestone payments compared to the Protagonist-Takeda deal may somewhat compensate for the lower upfront consideration, the deal indicates that the estimates for the market potential for the hepcidin entrants either have come down or that this market is now expected to be divided up between more players than initially envisioned.

Clearly, the US, with a patient population of 100-150,000, will be the major source of expected profits.  Similar to the hereditary angioedema (HAE) space, similar efficacy, but much better safety, tolerability, and convenience of the new HAE therapeutics have grown that into a multi-billion dollar market despite the availability of cheap alternatives like androgens and a small patient pool of at most 10,000.  

Androgens, however, are still widely used outside the US, even in wealthy countries like Singapore, and unlike HAE, PV is largely diagnosed in older people.  This means that reducing the number of annual phlebotomies by 2 will unlikely justify a $200,000 price tag.  To justify that, hepcidin pathway agents need to have robust phlebotomy-lowering activity in the absence of any other current second-line agents (remains to be seen in the full VERIFY dataset) in addition to demonstrating improved measures of well-being as was demonstrated in VERIFY.  

Disclosure: SLN124 is the core asset of Silence Therapeutics of which I currently own shares.

Base Editor Beam Therapeutics Sets New Record in Alpha-1-Antitrypsin Correction Race

Today Beam Therapeutics reported initial data for BEAM-302, a CRISPR-based base editor for the correction of the Z mutant form of alpha-1-antitrypsin (Z-AAT).  With a mean total serum AAT of 12.4 micromolar (uM) at the high 60mg dose it surpasses the 10.8uM reported by Wave Life Sciences last October, with WVE-006 applying the transient, oligonucleotide-based RNA editing technology.

Importantly, ‘total’ serum AAT for BEAM-302 would include bystander-edited AAT as well as wildtype (M) AAT and Z-AAT.  Both the biological activity and safety of bystander-edited AAT are controversial. 

As discussed in my preview of the unfolding competitive AAT disease space, homozygous Z-AAT mutation leads to lung damage due to the inability of AAT to get out of the liver into circulation and up to 50% of such carriers eventually develop some kind of liver abnormalities as a result of Z-AAT accumulation in hepatocytes. Because Z-AAT may retain some protease inhibitor function, the amount of total serum AAT is considered a key biomarker in the development of AAT-based therapy for the lung disease with 10uM being the therapeutic threshold to beat.  Personally, I would appreciate the actual biological AAT activity (numbers, not a general statement that total AAT was functional) in terms of elastase activity.    

This, however, is just the beginning of the battle for the hearts and minds of AAT patients.  Beam said that it planning further dose escalation beyond 60mg for what could be a one-time treatment.  I would caution, however, that grade 1 liver enzyme elevations were seen ‘in some’ patients and only 3 patients had been given 60mg.  Since Verve Therapeutics had run into a show-stopping LNP-related liver safety issue with a lipid formulation similar to the one being used by Beam Therapeutics and at similar, if not lower dose levels, I would wait for larger patient numbers before giving the all-clear in this regard.

In another bold move, Beam Therapeutics further wants to test 302 in AAT patients with mild to moderate liver disease.  This population had been excluded so far for the noted safety considerations.  While a -78% decline in circulating Z-AAT was noted today, the liver patient cohort will likely include biopsies which would allow to relate that number to the actual alpha-1-antitrypsin gene correction percentage…as well as to the amount and nature of bystander editing. 

Meanwhile, Wave Life Sciences is not standing still and should be able to surpass the 12.4uM marker since they have only reported single dose results for the lowest patient cohort.  A 200mg every other week cohort is dosing as is a single dose 400mg cohort per the latest update.

Clinical Data Support PepGen’s Potentially Disruptive Myotonic Dystrophy Type 1 Approach

Yesterday, PepGen showed first clinical data for PGN-EDODM1 in Myotonic Dystrophy Type 1 (DM1).   Although it is years behind the DMPK knockdown competition by Avidity Biosciences and Dyne Therapeutics, the single-dose data hint that its differentiated mechanism of action may prove superior in this big orphan disease indication.

DMPK1 knockdown versus CUG structural disruption

Myotonic dystrophy is an autosomal dominant condition caused by the CUG triplett expansion in the 3’ UTR non-coding region of the DMPK1 gene.  It is thought that this sequesters the MBNL1 protein and the subsequent inability of MBNL1 to carry out its RNA processing functions (alternative splicing).  As DMPK1 is largely expressed in muscle (including heart) and the CNS, the disease symptoms (most noticeably myotonia, but also muscle weakness, heart arrythmia and cognitive impairment etc) relate to muscle and to some degree the nervous system. 

Avidity’s AOC-1001 (phase 3 enrolment to be complete in mid-2025) and Dyne’s DYNE-101 address this by reducing DMPK1 transcript levels thereby liberating bound MBNL1.  Although Avidity uses RNAi triggers conjugated to an antibody and Dyne RNaseH antisense oligos attached to Fab fragments, these 2 Tfr1-targeted molecules both achieve ~-40% DMPK1 RNA knockdown of the nuclear retained transcript.

PepGen’s PGN-EDODM1, however, approaches the problem by targeting oligonucleotides to the CUG repeat itself thereby disrupting the repeat CUG helical structures that act as MBNL1 sponges.

The reason why I quite like this approach is because it does not affect DMPK1 expression.  Mouse models show that DMPK deficiency causes deficits like myotonia and cardiac conduction problems.  In DM1, due to the nuclear retention of the CUG-expanded RNA, DMPK levels are already reduced by 50% and reducing it by another 40% (as AOC-1001 and DYNE-101 do…on average) raises on-target safety questions not posed by the PepGen approach. 

Early splice data support validity of CUG disruption

PepGen has now evaluated about a handful patients each after 28 days following a single dose of 5mg/kg and 10mg/kg for the CASI22 score.  CASI22 is a measurement of MBNL1-related alternative splicing and should be the first measurable change along the mechanistic therapeutic trajectory.  At this early timepoint, there is a nice dose-dependent response of -12.3 and -29.1 for the 5 and 10mg/kg cohort, respectively.

Such clean dose dependency has not been seen in the Avidity and Dyne programs.  Moreover, -29.1 is clearly superior that of -12 (2mg/kg) and -9 (4mg/kg) seen with not 1, but 2 doses of Avidity’s molecule and roughly on par with Dyne’s -25 after 2 doses of 6.8mg/kg.

Whether this translates to the clear functional improvements in myotonia and other symptoms specific to DM1 as for AOC-1001 and DYNE-101 remains to be seen, but logic would say ‘yes’.

A concern with the PepGen approach is that it uses oligonucleotides attached to a cationic cell-penetrating peptide for delivery.  Not only is that less specific than the Tfr1-targeting of Avidity and Dyne, similar approaches, for example by Sarepta in their next-gen DMD exon skipping program, have run into safety issues.  This certainly needs to be watched as PepGen escalates doses further and repeat doses.

Increasing the Reach of ADAR Therapeutics by Protein Structure Prediction

'Only' being able to convert an ‘A’ to an ‘I’ when genome editing can seemingly re-write the code at will had been seen as a major limitation of the technology.  Examples such as the large and underserved market in correcting the piZZ genotype in alpha-1-antitrypsin disease using A-->I RNA editing were the exception.  With the help of artificial intelligence-enhanced structure prediction tools, however, the financial incentive to pursue genetic disease should increase again.  Indeed, ProQR’s first Rett Syndrome candidate already points in this direction.

Addressing the p.R270X mutation

Rett Syndrome is an X-linked dominant genetic haploinsufficiency neurological disorder caused by mutations in the MeCP2 protein leading to decreased functional activity as a master regulator of gene expression and neuronal development.  There are many ways to cause the loss of activity of a protein, so mutations can typically be found throughout an affected haploinsufficiency gene.

ProQR’s 1st candidate for Rett Syndrome addresses the p.R270X mutation where the arginine codon CGA at position 270 in the protein is mutated to the stop codon UGA, thus leading to a truncated protein that is also destabilized at the mRNA level via the NMD pathway.  Luckily, the CGA codon contains an actionable ‘A’ and although editing it to a G-like Inosine would not restore the wild-type protein, it happens that mice with tryptophan-coding UGG at position 270 behave like rescued wild-type mice.

Beyond p.R270X

It is well established that a second mutation can modify, if not rescue a disease caused by a first mutation.  At a protein level, this may be due to functional restoration by coaxing the protein back to its original functional structure.  

Rett Syndrome affects around 50,000 females in the US and EU of which ~3,500 would be due to p.R270X.  Point mutations across the MeCP2 gene overall account for 60% of cases. Such numbers are too low for one to expect to come across compensatory mutations in the MeCP2 from population genetics.  So instead of relying on serendipity one may systematically ask whether the structural pathological change resulting from a given point mutation or group of point mutations (characterized for example by destabilization of the DNA-binding domain of MeCP2) could be reverted back towards wild-type if one ADRA edited one of the ~350-400 Adenosines in the MeCP2 mRNA based on AI-powered structure prediction tools like AlphaFold.

This could then be verified by a cellular functional assay of MeCP2 as a master epigenetic regulator.  Regarding approval and clinical trial population, a label may just say that a patient with a very rare mutation that could not be confirmed in clinical trials due to low subject numbers may still qualify for the drug as long as such an assay supported it.  This path has already been trodden, for example with Vertex’ Cystic Fibrosis drugs.

AI increases IP value around platform drug modalities

Artificial intelligence is an amazing development.  The above strategy is just one example of how it may decrease future drug development cost and efficiency, thus increasing the attractiveness of going after rare diseases again.  I would not be surprised therefore if structure prediction may help to address the most common missense mutation in Rett Syndrome, p.R106W, which affects 3x the patient number of p.R270X.  

There are, of course, many more applications also to RNA editing such as chemistry based on structure prediction around the A to be edited when paired to the editing oligo. 

AI, however, is also a scary development for people like me.  When I came across this concept, it seemed like Gemini had it all figured out already.  I fully expect that in a year’s time, I will have to re-think the point of blogging full-stop when AI can tell for itself which are the more or less valuable concepts.  One thing is sure, AI will open the flood-gates for therapeutic strategies leveraging genetic platform technologies like ADAR, RNAi, antisense, CRISPR and gene therapy.  Investing in companies with fresh, gate-keeping IP in these technologies could therefore more valuable than ever.  It is therefore possible that sooner than later I will be watching all this from the beach as a passive investor in these platforms.