Landmark ATTR-Polyneuropathy Data by Intellia Caps Off Momentous Week in CRISPR Therapeutics

This has been a most remarkable week in CRISPR Therapeutics as momentum continues to build. 

Bespoke therapeutic in 6 months

First, the drug development world and beyond was captivated by the story of how a baby born with life-threatening point mutations in the CPS1 gene was able to receive a bespoke base editing therapy in just 6 months by harnessing the platform potential of nucleic acid-targeted therapeutics and regulators getting out of the way (Musunuru et al 2025). 

Every pharma CEO will be asking her business development underlings about recent underinvestment in the technology when the report shows how development timelines and expenses can be slashed by a factor of 10 when everybody applies ‘common sense’.

I purposely make use of new US administration lingo, because while the CPS1 deficiency story happened under the watch of Peter Marks who was fired as CBER chief because of his involvement in Covid19 mRNA vaccines, there is every reason to believe that drug development will continue to be streamlined by cutting out time-consuming bureaucratic hurdles and applying AI-based document reviews.  Accordingly, Trump's HHS and FDA has repeatedly called for accelerated drug development based on common sense, including biological plausibility.  As further evidence of that, it is phasing out certain lengthy animal toxicology studies.

The most immediate beneficiaries of the story are nucleic acid-targeted therapeutics addressing severe, underserved diseases by harnessing proven delivery and which have a clean off-target profile.  Besides CRISPR-based therapeutics, this also includes oligo-mediated RNA editing which has exquisite on-target specificity and where Rett Syndrome could serve as a template when addressing disease populations segmented by numerous mutations.   

 

First patient treated with prime editing medicine

Though behind a paywall, STAT reported last week that the first patient had been treated with a CRISPR prime editing agent.  The timing is fitting, as prime editing, by virtue of it being able to address any small mutation, including non-transition mutations and small deletions, is the most universal iteration of CRISPR.  It is also the safest of them all with Prime Medicine claiming no detectable off-targeting for any of its development candidates.

The CPS1 urea cycle story could have been even better if they had used the safer and more effective delivery of VERVE-102 instead of VERVE-101 used by former Verve employee and co-founder Kiran Musunuru.  Also, the base editor in question had not been tested before in the clinic and was selected by comparing a number of adenine base editors in cell lines which also differed in terms of PAM sites and bystander editing.  A prime editing approach by contrast is not subject to PAM constraints as the edit can happen well within a 50 nucleotide window of a given PAM without losing much efficacy.  There is also no bystander editing to worry about.  This way, the same (proven) prime editor mRNA could be used in the same LNP formulation.

The key to quickly applying prime editing in such circumstances would be (AI/machine) learning from the growing dataset of prime editing experiments to find guide RNAs of high efficacy.

Prime Medicine has made great strides towards getting editing efficiencies up to standard Cas9 and base editing levels.  With the first patient dosed, we can expect data in support of that well before the end of the year (2 months for engraftment in the CGD setting).

 

CRISPR Therapy sets new standard in ATTR-Polyneuropathy

And as if all this was not enough, Intellia today reported 2-year data from their phase I/II study of its Cas9 CRISPR agent NTLA-2001.  Unlike prior TTR knockdown agents by Alnylam (RNAi) and Ionis (RNaseH antisense), key mNIS+7 and Norfolk quality of life measures show that after 2 years of sustained -90% TTR reductions, NTLA-2001 not only stabilizes patients, but the majority of patients improve.  In the dose expansion cohort, there was a clinically highly impactful -8.5 point improvement in mNIS+7. 

Clinically meaningful >4 point improvements were also seen in 5 out of the 6 patients that had been on an RNAi treatment (Patisiran) before.  It is also an improvement over what had been observed at the 12-month timepoint before with NTLA-2001 and sends a strong message:

A one-course treatment permanently changing genetics for the better leads to superior outcomes as the body itself becomes the healing agent. 

I look forward to seeing histology data looking at TTR deposition and whether they start to disappear as the balance shifts towards clearance.

The superior outcome may not come as a surprise when considering that with a 90% gene knockout efficacy, NTLA-2001 halves the amount of TTR being produced following therapy compared to what knockdown agents have been able to achieve.  Still, the fact that improvements seem to accelerate over time is remarkable.

Concordantly, there were no new adverse events and illustrates that acute infusion reactions and possibly transient liver damage around LNP administration is the main safety and arguably only concern of liver-directed CRISPR therapeutics.  Safety challenges arising from having to maintain a certain level of drug concentration, which may e.g. lead to low chronic inflammation and associated transcriptionopathies, do not apply to RNA-/oligo-based CRISPR therapeutics.

With this data, NTLA-2001 should own the ATTR-polyneuropathy market, not just because of its superior efficacy and safety, but also because it is a genetically defined disease and could be given earlier, perhaps even before symptoms manifest.  This would be a hard sell from a health economics point of view for drugs that need to be taken chronically for life.  In the same vein, Intellia reported just yesterday that NTLA-2001 similarly improves the lives of people with genetic ATTR-cardiomyopathy, leading to never seen before increases in the 6 minute-walk-distance measure, not with vutrisiran and not with acoramidis.

Phase 3 studies of NTLA-2001 in ATTR-PN and ATTR-CM are ongoing and should gather steam with the new data.

It is possible that together with the recent PCSK9 data by Verve Therapeutics, last week’s developments and increased signs that regulatory flexibility will continue to be applied if not greatly accelerated by the new administration could mean that the worst for CRISPR investors could be behind.

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.  

The Nucleic Acid Therapeutics Race to Revolutionize Alpha-1-Antitrypsin

Alpha-1-antitrypsin disease (AATD) is caused by mutations in the SERPINA1 gene coding for alpha-1-antitrypsin (AAT).  There are an estimated 100000 alpha-1 patients in the US alone, making it a rare, but not ultra-rare disease.

Correcting these mutations, replacing AAT through gene therapy, or inhibiting the particularly pathogenic Z-allele is subject to the efforts of a number of nucleic acid-based drug developers, most notably Arrowhead Pharmaceuticals (RNAi), Wave Life Sciences and Korro Bio (RNA Editing) as well as CRISPR genome editing companies Beam Therapeutics (Base Editing) and Intellia Therapeutics (CRISPR Cas9 and targeted gene insertion). 

The protein name is somewhat misleading as it’s main function is to antagonize neutrophil elastase activity in the lung. Insufficient AAT activity can lead to lung injury during pulmonary stress, especially respiratory infections or smoking.  Historically, lung disease has been addressed by smoking cessation and preventing lung infection (e.g. through vaccination). 

In those patients that do progress to symptomatic lung disease, the standard of care still remains weekly infusions with plasma-derived (!) alpha-1-antitrypsin.  Although the evidence of benefit is substandard, partly the result of having a ‘good-enough’ therapy approved decades ago on simple biochemical measures, this is now a $1B+ market and growing with the increased identification of this genetic form of chronic obstructive pulmonary disease (COPD).  Growing awareness of the liver aspect of the genetic condition also contributes to better patient identification.

Achieving 50-60% of normal AAT activity is expected to be therapeutic based on human genetics.   

As lung health and longevity has been improving in alpha-1, it is estimated that 15% of adult patients develop the serious condition of liver cirrhosis.  There is also an infant form AAT liver disease manifesting in ~10% with alpha-1 mutations that can result in cirrhosis and the need for liver transplantation.  Although this is less well understood than the adult form, it is likely to involve excessive accumulation of alpha-1-antitrypsin in the liver.  These patients typically carry the Z allele on both chromosomes (piZZ).  This allele is particularly prevalent among the European and US AATD populations (~90% of 235k worldwide).  As true AAT null mutations are rare, piZZ is by far the most prevalent genotype of patients presenting with either lung or liver disease. 

The Z alpha-1 antitrypsin variant protein misfolds, aggregates and gets stuck in the endoplasmic reticulum of the liver.  This results in liver inflammation and progressive injury (cirrhosis, hepatocellular carcinoma/HCC).  A small fraction (10-15%) of Z-AAT does get exported, but even if it makes it to the lung it is less functional and may even exacerbate lung inflammation due to its propensity to precipitate.

Removing Z-AAT is expected to halt and even reverse liver disease based on human genetics (1 Z allele not sufficient to cause disease) and preclinical animal models.

Here I will discuss some of the more promising, new innovative approaches utilizing a number of nucleic acid therapeutics modalities to address the lung and/or liver complications of AATD.  It also explains the following rank order of the approaches in terms of promise for AAT lung and liver disease.

1.    RNAi for A1AT-related liver disease (Arrowhead Pharmaceuticals and Takeda)

While innovation in the lung space of AATD has stalled, the disease attracted fresh attention in the pharmaceutical industry about a decade ago for its liver-related complications as (piZZ) alpha-1 patients get older and increasingly suffer from liver failure and HCC.  This time also saw the rise of new therapeutic modalities such as RNAi. 

The RNAi Therapeutic ARO-AAT by Arrowhead Pharmaceuticals has demonstrated almost complete elimination of the highly expressed gene in phase I and II clinical trials.  In preclinical models, this has been shown to reduce existing liver Z-AAT aggregates and inflammation over time.

In a small (n=25), 2:1 ARO-AAT/placebo randomized phase II study in Z-AAT patients with liver fibrosis, there was a robust -68% reduction in liver AAT globule burden.  At 52 weeks, this translated to 50% of subjects on ARO-AAT having a 1 or more point improvement in Metavir fibrosis (scale: 0/no fibrosis to 4/cirrhosis).  Due to the small study size and the 3/8 responses (38%) in the placebo group, this did not reach statistical significance.   Another small open-label study demonstrated a similar 50% fibrosis response.

Importantly, RNAi knockdown of Z-AAT did not worsen pulmonary health over 1 year in the controlled (no smoking etc) trial setting.  This may be partly due to Z-AAT being functionally impaired anyway and may do more harm than good in the lung. 

A longer 2 year 160 patient pivotal phase 3 study with F2-4 disease is underway to statistically confirm the benefit of ARO-AAT (aka TAK-999) on liver fibrosis (in F2+3 patients).  Results from that study can be expected in early 2026. 

2 years should be plenty of time for liver globules to turn over.  And as the liver is good in regenerating once you take the fibrogenic trigger away (see HCV, NASH etc)- as long as the liver is not in a late-stage cirrhotic stage already- this should translate into a fibrosis benefit.

For AAT liver disease, Arrowhead enjoys at least a 5 year headstart over the non-RNAi competition which has yet to enter the clinic.  Dicerna, now a Novo Nordisk company, has also been developing an RNAi trigger (belcesiran) for AAT which is in a phase II and has demonstrated -77% knockdown following a single dose.  

In terms of efficacy, Arrowhead’s RNAi approach with it’s almost complete elimination of AAT in the liver appears to be substantially superior over the competition with non-RNAi approaches struggling to get to -70-75% Z-AAT reductions.  This assumes that more knockdown is correlated with efficacy or at least the time for efficacy to manifest.  Based on human genetics, the equivalent of life-long treatment, where subjects with just one Z allele have not much added risk of developing liver disease, this may not be necessary.

 

2.    CRISPR Cas9 for Liver Disease 

The non-RNAi approach in development for AAT liver disease that is likely the next most efficacious one is CRISPR Cas9 DNA cleavage as developed by Intellia Therapeutics.  Intellia has already demonstrated 90%-type gene knockout efficiencies in hepatocytes for TTR amyloidosis and hereditary angioedema in the clinic, so expectations are for similar target engagement in the AAT program. Cas9-targeted DNA cleavage is certainly a powerful tool to downregulate gene expression.

The question, however, is whether you would want to risk disabling a gene permanently when you have non-permanent alternatives like RNAi that are at least equally efficacious.   Similar to transthyretin in TTR amyloidosis, alpha-1-antitrypsin is a highly expressed gene in the liver that has important functions in human biology and health.  TTR for example is a carrier of thyroxin and retinol binding protein (à vitamin A) while AAT is involved in the homeostasis of protease activity for example during infection in the lung and probably has similar homeostatic functions in other tissues. 

Side effects from the long-term ablation of AAT may only manifest after years and may then require life-long supplementation (vitamin A, thyroxin), or after certain stress situations (non-genetic COPD etc).  To my knowledge, unlike for say PCSK9, human genetics does not support that lifelong absence of AAT is ideal.  Similarly, regulatory agencies will be worried about cancer resulting from genome re-arrangements rearing their ugly heads 10 years or so down the line following on- or off-target DNA cleavage in and outside liver cells (including germline).

In my opinion, unless genome editing can demonstrate clear efficacy advantages over otherwise quite safe and non-onerous, non-permanent alternatives, it is only with the accumulation of long-term safety data that we will be able to tell whether CRISPR Cas9 can be used more broadly.

 

3.    RNA Editing for Lung and Liver Disease (Wave Life Sciences, Korro Bio)

When it comes to addressing AATD lung disease, my favorite approach is via RNA Editing with an exciting candidate by Wave Life Sciences (WVE-001) about to enter the clinic.  Korro Bio aims to enter a competing RNA Editing candidate into the clinic in late 2024. 

However, Korro Bio candidate would likely have to be relatively frequently (weekly) administered via intravenous infusion and has no obvious efficacy advantage over WVE-001 and LNP-related toxicities to be expected (infusion reactions, triggering of innate immunity etc).  As a second mover with an inferior therapeutic profile, I am struggling to understand Korro Bio’s business rationale here (also discussed here).  

As discussed on this blog, RNA Editing in AATD aims to convert the pathogenic piZ allele into the healthy M allele.  Based on human genetics where MZ carriers are protected from both liver and lung disease, a 50% AàI editing rate may suffice for both indications.  Wave Life Sciences has been able to meet that bar in preclinical studies.  Given the newness of RNA Editing, results from the first clinical study for this modality utilizing Wave’s subcutaneously administered oligonucleotide chemistry will still have to show just how efficacious and sustained (in terms of dosing frequency) their approach will prove to be in humans. 

A significant uncertainty is how long it will take for even robust >60% editing to translate into actual clinical benefit. Unlike for the liver where the natural turnover of pathogenic globules will likely be rate-limiting for liver health improvement to manifest, generating healthy, wild-type alpha-1-antitrypsin should be immediately beneficial to the lung.   Identifying a patient population with still relatively healthy lungs but rapid functional decline should therefore be most promising for a clinical trial.

For this, Wave Life Science has recruited pulmonary disease powerhouse GSK through a out-licensing as setting a new standard of care will not be as easy as simply demonstrating AAT blood biomarker as the incumbents had gotten away with.  The fact that plasma-derived products from the stone age of biotechnology still dominate what today has grown into a blockbuster market shows how difficult it has been to find new therapeutic strategies worth investing in.  As the plasma-derived products have been unable to demonstrate a clear therapeutic benefit in controlled studies, this would likely involve running a relatively large and long-term clinical study being very mindful of stratifying the diverse patient population. 

The reason why RNA Editing could represent a meaningful improvement to the standard of care in AAT lung disease is that it promises to offer more sustained, tonic amounts of AAT instead of the spiked pharmacokinetics from weekly infused AAT.  Moreover, because RNA Editing converts mutant to wild-type AAT that is transcribed from the native gene under physiological controls (e.g. promoter activity), adverse effects from supraphysiological levels of AAT should not be observed.  

Wave Life Sciences claims that RNA Editing can not only address lung AATD, but also its liver manifestations.  To find out, GSK would have to run a separate study and hope that clinical success is not linear with Z-AAT reduction. Because if this were the case, RNAi would likely win out over RNA Editing not only in terms of knockdown efficacy, but also dosing frequency.  There is some preclinical evidence, however, that wildtype AAT may aid cellular export of Z-AAT, so a 50% mRNA conversion may reduce intracellular Z-AAT more than 50%.  Possibly worth a competitive gamble.

 

4.    Base Editing for Lung and Liver Disease (Beam Therapeutics)

Similar to Wave Life Sciences, Beam Therapeutics aims to correct the piZZ mutation, but this time applying CRISPR genome base editing for permanent correction.  Unlike traditional CRISPR Cas9, Beam’s CRISPR proteins are unable to make double-strand. Instead, a base-editing enzyme is tethered to the Cas protein which is guided to the target location by the guide RNA.  In this case, the base editor is an Adenine Base Editor converting proximal adenines into guanine.

Unlike RNA Editing where you can precisely determine the editing site through secondary fit and oligonucleotide modifications with essentially no off-target editing, tethered base editors will act on what is close by.  Most problematic for the Beam program appears to be a bystander adenine that is 2 bases away from the targeted adenine such that for each desired single edit you seem to get equal amounts of double-edited AAT mRNAs resulting in alpha-1 antitrypsin  that is significantly less functional.

This also raises that question on how many more unidentified off-target base edits there are.  The genome in the nucleus is not linear, but dynamic with tertiary interactions between chromosomes, within a chromosome and transcriptional hubs bringing multiple genes into close vicinity.  So imagine a crowded nucleus with thousands of CRISPR-tethered base editors floating around looking for adenine substrates.  It will sure be interesting how regulatory agencies around the world will be looking at this as well as the risk of germline editing following LNP delivery.

Base editing efficiencies are slightly less than RNA Editing in preclinical models with the added caveat around the double edits.

Beam intends to file for clinical trial applications in Q1 2024.   

  

5.    Integrational Gene Therapy for Lung Disease (Intellia Therapeutics)

Finally, in addition to gene demolition using Cas9 for liver disease, Intellia is advancing a separate CRISPR-mediated gene insertional approach for AAT lung disease.  Here, an LNP delivers Cas9 mRNA-gRNA to open up DNA downstream of the albumin promoter, highly active in hepatocytes.  An AAV carrying AAT cDNA gets administered alongside so that a certain fraction gets incorporated as the DNA damage repair machinery attempts to mend the lesion.

Preclinical non-human primate data support that marked expression can thus be achieved as the albumin promoter now drives transcription of AAT-cDNA.  It is noteworthy that albumin drop-in has gone a bit out of fashion in the genome editing field after Sangamo Biosciences had similarly claimed high preclinical expression for hemophilia and lysosomal storage disease almost a decade ago.  Strangely, as so often has been the case with Sangamo, this could not be reproduced at all in the clinic (barely detectable levels if any at all).  Intellia is using a curious inverted repeat design as their drop-in cassette and believes this to be a game-changer in the approach.  They may have done this to double their chances that the insertion happens in the correct orientation, but as a former molecular biologist trained in RNA polymerase II transcription and RNAi this looks like inviting trouble to me.

In any case, a surprising pivot by Intellia for AAT lung disease and we will have to see how this approach can thread the needle of achieving substantial, but not exaggerated amounts of AAT….over the long-term…and with little interpatient variability.

Intellia intends to submit a clinical trial application for NTLA-3001 by year-end.