CMN Weekly (20 October 2023) - Your Weekly CRISPR Medicine News

Top picks

• The first Phase 3 trial for an in vivo CRISPR-based therapy will soon be underway. Intellia Therapeutics announced this week that the FDA has cleared its IND application to initiate a pivotal Phase 3 trial of NTLA-2001 for the treatment of transthyretin (ATTR) amyloidosis with cardiomyopathy. NTLA-2001 is jointly developed by Intellia Therapeutics and Regeneron and was the first CRISPR therapy to be administered to humans via the bloodstream. It is designed to treat ATTR by selectively reducing the levels of mutated TTR protein in the blood, through CRISPR-based inactivation of the TTR gene in liver cells. The global Phase 3 trial is expected to be initiated by the end of 2023. Read more about NTLA-2001 in previous clinical trial updates here.

Research

• In an article published yesterday in Nature, scientists in New Zealand and Denmark present a distinct type of CRISPR–Cas inhibition strategy based on small non-coding RNA anti-CRISPRs (Racrs). The team demonstrates that Racrs mimic the repeats found in CRISPR arrays and are encoded in viral genomes as solitary repeat units. They also show that a prophage-encoded Racr strongly inhibits the type I-F CRISPR–Cas system by interacting specifically with Cas6f and Cas7f, resulting in the formation of an aberrant Cas subcomplex. Racr candidates were identified for almost all CRISPR–Cas types encoded by a diverse range of viruses and plasmids, and functional testing of nine candidates spanning the two CRISPR–Cas classes confirmed their strong immune inhibitory function.
• A team in Germany, Switzerland, United States and Netherlands has reported a dual adeno-associated virus (AAV) vector technology based on reconstitution via mRNA trans-splicing (REVeRT). They demonstrate that REVeRT is flexible in split site selection and can reconstitute different split genes in numerous in vitro models, human organoids, and in vivo. They also show that REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. REVeRT enabled the reconstitution of full-length ABCA4 after intravitreal injection in a mouse model of Stargardt disease. The full study findings were published yesterday in Nature Communications.
• In an article published earlier this week in PLoS One, a team of scientists in Australia report that Cas12a target and off-target cleavage behaviour are a factor of nucleotide bias combined with nucleotide mismatches relative to the protospacer adjacent motif (PAM) site. Using these features to train a Random Forest machine learning model, the team could improve the accuracy by at least 15% over existing algorithms to predict guide RNA efficiency for the Cas12a enzyme. The researchers argue that their findings highlight the need for more representative datasets and further benchmarking to reliably and accurately predict guide RNA efficiency and off-target effects for Cas12a endonucleases.
• The TDP-43 proteinopathies, which include amyotrophic lateral sclerosis and frontotemporal dementia, are a devastating group of neurodegenerative disorders characterised by the mislocalisation and aggregation of TDP-43. In an article published this week in Nature Communications, a team in United States demonstrate that RNA-targeting CRISPR effector proteins, a programmable class of gene-silencing agents that includes the Cas13 family of enzymes and Cas7–11, can be used to mitigate TDP-43 pathology when programmed to target ataxin-2, a modifier of TDP-43-associated toxicity. Encouragingly, they report that the in vivo delivery of an ataxin-2-targeting Cas13 system to a mouse model of TDP-43 proteinopathy improved functional deficits, extended survival, and reduced the severity of neuropathological hallmarks, highlighting the potential of such a therapeutic approach to treating the TDP-43 group of diseases.
• Scientists in China report the establishment of a human papillary thyroid carcinoma (PTC) cell line in which the HMGA2 gene was knocked out using CRISPR-Cas9 gene editing. This gene encodes the high-mobility group A2 (HMGA2) protein, which is known to play a crucial role in PTC metastasis. The team found that knockout of the HMGA2 gene significantly reduced the proliferation, growth, and invasion of the tumour cell line, and that it delayed the conversion of the G2/M phase and promoted cell necrosis. Their findings were published in Advances in Medical Sciences.
• In an article published in Journal of the American Chemical Society, scientists in China and United States report improved lipid naoparticles for in vivo mRNA delivery. They rationally introduced a disulfide bond-bridged ester linker to modularly synthesise a library of 96 linker-degradable ionisable lipids (LDILs) for improved mRNA delivery in vivo. In their manuscript, the authors point out that the chemistry adopted in the study can be further extended to develop new biodegradable ionisable lipids for broad applications such as gene editing and cancer immunotherapy.
• Researchers in United States present a precise and non-invasive, tunable strategy for controlling the expression of multiple endogenous genes both in vitro and in vivo, utilising ultrasound as the stimulus. By engineering a hyper-efficient dCas12a and effector under a heat shock promoter, the team demonstrates a system that can be inducibly activated through thermal energy produced by ultrasound absorption. They show that the new system offers versatile thermal induction of gene activation or base editing across cell types, including primary T cells, and enables multiplexed gene activation using a single guide RNA array. In mouse models, they found that localised temperature elevation guided by high-intensity focused ultrasound effectively triggered reporter gene expression in implanted cells. Their findings were published this week in Nature Communications.
• Earlier this week, scientists in China reported that fusing human e18 protein, a RING type E3 ubiquitin ligase variant, with adenine base editors can significantly improve editing precision and narrow the editing windows compared with ABEmax and ABE8e, by reducing the overall abundance of base editor protein. As a proof of concept, they found that the resulting ABEs - ABEmax-e18 and ABE8e-e18 - dramatically decrease Cas9-dependent and Cas9-independent off-target effects compared with traditional adenine base editors. Their findings were published in International Journal of Biological Macromolecules.
• In an article published this week in Nature Plants, a team in China describes the development of a split deaminase for safe editing (SAFE) system applicable to base editors (BEs) containing distinct cytidine or adenosine deaminases, with no need for external regulators. In SAFE, a BE was split at a deaminase domain embedded inside a Cas9 nickase, simultaneously fragmenting and deactivating both the deaminase and the Cas9 nickase. The gRNA-conditioned BE reassembly conferred robust on-target editing in plant, human and yeast cells, while minimising both gRNA-independent and gRNA-dependent off-target DNA/RNA edits. The team also demonstrated that SAFE substantially increased product purity by eliminating indels, and they propose that SAFE provides a generalisable solution for BEs to suppress off-target editing and improve on-target performance.

Industrial

• Earlier this week, Editas Medicine announced in a press release that it has been granted the FDA's Regenerative Medicine Advanced Therapy (RMAT) designation for EDIT-301, for the treatment of severe sickle cell disease (SCD). In June 2023, Editas announced positive initial safety and efficacy data from the first four patients with SCD treated with EDIT-301 in the ongoing RUBY Phase 1/2 trial trial. Read more here.
• Intellia Therapeutics recently announced that the European Medicines Agency had awarded a Priority Medicines (or PRIME) designation to its Phase 1/2 gene-editing candidate, NTLA-2002, for the treatment of hereditary angioedema (HAE). NTLA-2002 is an in vivo CRISPR candidate that is designed to be a single-dose treatment for HAE, and the most recent clinical data, released earlier this year from the Phase 1 portion of the ongoing Phase 1/2 trial of NTLA-2002, revealed that across all patients evaluated at their latest follow-up, a single treatment with NTLA-2002 led to a 95% mean reduction in monthly severe inflammatory attacks seen in HAE patients. See our recent clinical trial update for more details.
• Beam Therapeutics announced its portfolio prioritisation and strategic restructuring plan yesterday, which is focused on potential near-term value drivers and long-term growth of precision genetic medicines pipeline. Briefly, the updates include: BEAM-101 and ESCAPE for sickle cell disease and BEAM-302 for alpha-1 antitrypsin deficiency are the company's top priority programmes, the company will explore partnership opportunities for continued development of select programmess, and that the anticipated cost savings, which include laying off 20 % of the staff, should extend the company’s cash runway into 2026.
• Prime Medicine expects to highlight positive pre-clinical developments across its prime-editing pipeline and platform at upcoming industry conferences in October and November 2023. The presentations will include proof-of-concept data from in vivo rodent and large animal studies.
• Epic Bio will present at the upcoming annual European Society of Gene and Cell Therapy congress, which will be held next week in Brussels. The company is developing novel therapies to modulate gene expression using compact, non-cutting dCas proteins. Its lead programme, EPI-321, is in IND-enabling studies for treatment of facioscapulohumeral muscular dystrophy. Additional programmes seek to address alpha-1 antitrypsin deficiency, heterozygous familial hypercholesterolemia, and other indications.

Clinical

• Caribou Biosciences announced yesterday that the FDA has cleared its IND Application for CB-012, an allogeneic anti-CLL-1 CAR-T cell therapy for the treatment of relapsed or refractory acute myeloid leukaemia. CB-012 will become the first allogeneic CAR-T cell therapy with both checkpoint disruption and immune cloaking to enter the clinic, and the company expects to initiate enrolment for the AMpLify Phase 1 clinical trial by mid-2024. Learn more about Caribou's approach to therapeutic gene editing in our recent interview with CSO Steve Kanner PhD here.
• Excision BioTherapeutics announced yesterday in a press release that it will present interim clinical safety and biodistribution data for EBT-101 in latent HIV at the upcoming European Society of Gene and Cell Therapy (ESGCT) 2023 Annual Congress, which will be held in Brussels next week. EBT-101 is being evaluated in a first-in-human Phase 1/2 clinical study 'EBT-101-001' to assess its safety and efficacy in people with HIV on antiretroviral therapy. Read more about EBT-101 in a previous clinical update here.

Detection

• Researchers in China have uncovered the essential features that determine the ability of Cas12f1, a highly compact RNA-guided nuclease with potential for diagnostic applications, to recognise specific single-nucleotide polymorphisms. In an article published yesterday in the Journal of Medical Virology, the team describe those features, which include the length of spacer region and the base-pairing region that determines the trans-cleavage of ssDNA.

Reviews

• Advancements of the CRISPR/Cas9 System in the Treatment of Liver Cancer. This review outlines the research progress of CRISPR/Cas9 gene-editing technology in the treatment of liver cancer and provides a theoretical basis for its research and application in the treatment of liver cancer.
• CRISPR-based Biosensors for Human Health: A Novel Strategy to Detect Emerging Infectious Diseases. Numerous CRISPR-based biosensors have been developed for application in environmental monitoring, food safety, and point-of-care diagnosis, however, there remains a critical need to summarise and explore their potential in human health. This review aims to address that gap by focusing on the latest advances in CRISPR-based biosensors for infectious disease detection. The authors provide an overview of the current status, pre-amplification methods, the unique features of each CRISPR system, and the design of CRISPR-based biosensing strategies to detect disease-associated nucleic acids.
• Advances in gene therapy for inborn errors of immunity. This review provides an overview of the landmark accomplishments and state of the art of gene therapy for inborn errors of immunity. Gene therapy, involving the use of a viral vector to add a copy of the therapeutic gene (viral gene addition) and gene editing, using programmable nucleases to precisely correct mutations, disrupt a gene or introduce an entire copy of a gene at a specific locus, are discussed.
• Current and emerging targeted therapies for spinal muscular atrophy. The authors of this review describe existing therapy for spinal muscular atrophy (SMA) as well as recent clinical trials for antisense oligonucleotides, viral gene therapy, and splice modulators and the potential routes for correcting the underlying disease-causing mutation to provide therapeutic levels of SMN protein, whose inufficiency or complete absence leads to SMA.

News from CRISPR Medicine News

• On Wednesday, we published brief updates for two clinical-stage gene-editing candidates, which recently received new designations from the US FDA and European Medicines Agency for the treatment of severe sickle cell disease and hereditary angioedema, respectively. Read the update here.