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CRISPR-Cas9 has reshaped what’s possible in genetic engineering. By giving scientists a precise way to cut DNA, it opened the door to targeted gene therapies, disease modeling, and even the prospect of correcting inherited disorders at the source.
But CRISPR isn’t perfect. Its mechanism, making double-strand breaks in DNA, relies on the cell’s own repair system, which can be unpredictable. That makes it difficult to insert large pieces of DNA cleanly, and raises concerns about off-target effects and safety.
Now, a lesser-known tool may offer a way around those limitations. CRISPR-associated transposases, or CAST systems, combine CRISPR’s targeting ability with the DNA-inserting function of transposases. The result: a system that can slot entire genes into the genome without cutting both strands of DNA.
Recent studies, including one published this spring by Metagenomi in Nature Communications, suggest CAST is more than just an academic curiosity. It’s starting to show real potential in human cells and could one day complement or even improve on the genome-editing tools we rely on today.
Table of contents
What is CAST, and why is it promising?
CASTs are a novel class of genome-editing tools that combine the targeting precision of CRISPR systems with the DNA-inserting capabilities of transposases. Unlike traditional CRISPR-Cas9, which introduces double-strand breaks (DSBs) to edit genes, CASTs enable the insertion of large DNA sequences without causing such breaks, reducing the risk of unintended mutations.
The CAST system operates by using a guide RNA to direct the insertion machinery to specific genomic locations. Once there, the transposase components integrate the desired DNA sequence into the genome. This method allows for the precise addition of large genetic elements, making it particularly valuable for applications requiring the insertion of entire genes or regulatory sequences.
One of the most studied CAST systems is the type V-K, which utilizes a single Cas12k protein for targeting. Early CAST systems were mostly limited to bacteria and required multiple protein components to function, which made them difficult to adapt for therapeutic use. The discovery of Type V-K, which relies on a single protein (Cas12k) for targeting, was a turning point. Its relative simplicity and smaller size make it more compatible with delivery systems like lipid nanoparticles or viral vectors.
Recent studies have demonstrated the potential of Type V-K CASTs in human cells, showing successful integration of therapeutic genes at specific genomic sites with minimal off-target effects.
The ability to insert substantial DNA fragments without relying on the cell’s repair mechanisms opens new avenues in gene therapy, synthetic biology, and functional genomics. By minimizing genomic disruptions and enhancing insertion precision, CASTs represent a promising advancement in the field of genome engineering.
What is it up against, and how does it compare?
Over the past decade, CRISPR-Cas9 has revolutionized genome editing by enabling precise cuts in DNA. However, the field has rapidly evolved, introducing tools like base editing and prime editing, each addressing specific limitations of earlier technologies. Now, CASTs are emerging, offering unique capabilities that could further expand the genome editing toolkit.
Tools like base and prime editing were developed to sidestep the risks of double-strand breaks. Base editing enables single-letter DNA changes, while prime editing allows for broader modifications, including insertions and deletions, all without cutting both strands of DNA. These technologies have already reached the clinic: Verve Therapeutics’ base editing program, VERVE-102, is in phase 1 for familial hypercholesterolemia, while Prime Medicine’s PM359 is showing early promise in treating chronic granulomatous disease.
While base and prime editing technologies are making strides in clinical settings, CAST systems are still in the research phase. However, their unique ability to insert large DNA sequences without inducing DSBs positions them as promising tools for applications requiring substantial genetic additions, such as the integration of entire genes or regulatory elements. This capability could be particularly valuable in treating diseases that necessitate the replacement or addition of large genetic sequences.
CASTs are progressing, but aren’t there yet. “Metagenomi is leading the clinical charge. Its first-in-human studies should start in 2026. This means that approval of CAST-based therapeutics will not happen for at least 5 to 7 years,” said Fady Riad, chief executive officer (CEO) of Centurion Life Sciences, an intelligence firm.
While CRISPR-Cas9, base editing, and prime editing have each advanced the field of genome editing in distinct ways, CAST systems could offer a complementary approach with the potential to address challenges that current technologies cannot fully overcome. As research progresses, CASTs may become integral components of the genome editing toolkit, expanding the possibilities for genetic therapies.
CAST in the spotlight?
Saying CAST is in the spotlight might be a bit of a stretch, but it is indeed gaining momentum.
In March 2025, Metagenomi published a study in Nature Communications describing a compact Type V-K CAST system that achieved targeted integration of a therapeutic gene in human cells. The system successfully inserted the full-length Factor IX gene, relevant for hemophilia B, into the AAVS1 safe harbor locus across multiple cell types. The all-in-one mRNA format used in the experiments also points to a more delivery-friendly setup, potentially opening the door to in vivo applications.
A few weeks later, Metagenomi presented additional CAST data at the ASGCT 2025 Annual Meeting, including updates on extrahepatic delivery and ongoing optimization of insertion efficiency.
The company’s lead candidate, MGX-001, is designed as a potential one-time treatment for hemophilia A. It employs a novel nuclease, MG29-1, to insert a B-domain-deleted Factor VIII gene into the albumin safe harbor locus in hepatocytes. In preclinical studies, MG29-1 demonstrated high specificity, with no detectable off-target editing or chromosomal translocations in primary human hepatocytes.
Academic labs have also been working to improve CAST systems, which in their natural form tend to work poorly in human cells. “I am keeping a close eye on the Liu/Sternberg evoCAST collaboration because their CAST system achieved 10-30% targeted integration efficiency in human cells,” said Riad.
Indeed, a research team from Columbia University and the Broad Institute, led by David Liu and Samuel Sternberg, recently developed an upgraded version of CAST systems called evoCAST. Using a lab-based evolution technique, they were able to boost its efficiency dramatically, from under 1% to as high as 30% in human cells. The system was also able to insert full-length genes at several clinically relevant sites without introducing double-strand breaks. These advances bring CAST a step closer to being usable in therapeutic contexts, even if delivery and reproducibility still need to be addressed.
“The momentum is very real. The potential to cure genetic diseases such as Duchenne Muscular dystrophy or Huntington’s disease, which so far have been incurable, as well as loss-of-function conditions like hemophilia A and B, is driving investments in CAST platforms,” said Riad.
While CAST work is still largely academic or early-stage, interest is growing. Some companies, like Mammoth Biosciences, are focused on miniaturized CRISPR systems like Cas14 and CasΦ — not CAST per se, but compatible with the kind of delivery constraints CAST systems face. Others, such as Scribe Therapeutics and Prime Medicine, are expanding the frontiers of precision editing in directions that could intersect with or inform CAST development over time.
If base and prime editing technologies continue to validate themselves in the clinic, and if CAST research maintains its current pace, more companies may begin investing in tools that push genome editing beyond the limits of classic CRISPR systems.
However, some challenges remain, notably delivery. “While CAST avoids double-strand break toxicity, off-target integration is still a challenge even if the industry is currently addressing it via protein engineering. A very active area of research in genome editing tools is delivery. Traditionally, the industry has relied on adeno-associated viruses (AAVs), but those are immunogenic, so now the focus is on optimizing lipid nanoparticles. Given that the CAST-based therapeutics will be inserting large cargoes, developing the right delivery mechanism is even more complicated,” noted Riad.
So far, Metagenomi remains the clear CAST frontrunner. “Metagenomi’s discussions with the U.S. Food and Drug Administration and its timeline for first-in-line trials are very encouraging. This shows that the regulators have a degree of confidence in the potential of CAST-based therapeutics,” said Riad.
As research teams continue to improve the technology, particularly in integration efficiency and delivery, the space is likely to see more entrants, especially in areas where existing tools fall short.
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