Delivering Prime Editors With Virus-like Particles

Much as a precious parcel cannot reach its destination without a reliable mail carrier, gene editors cannot make it to their target DNA without safe and effective delivery methods. Viral vectors and chemical approaches enable researchers to edit genomes in cell culture and in vivo with clustered  regularly interspaced short palindromic repeats (CRISPR) and related technologies such as base editing and prime editing.¹  However, these delivery techniques face challenges related to prolonged editor expression, limited cargo size capacity, and suboptimal delivery efficiency.

Engineered virus-like particles (eVLP) offer a potential new solution to these problems. In their latest work published in Nature Biotechnology, a research team led by molecular biologists and biochemists David Liu at Harvard University and Krzysztof Palczewski at the University of California, Irvine created eVLP that efficiently delivered prime editors to cells in culture and corrected genetic vision loss in mouse models of retinal degeneration.² Because eVLP do not carry genetically encoded cargo, this work may provide a transient means of delivering in vivo CRISPR-mediated gene editing therapies.  

“These are basically noninfectious viruses in which the viral DNA or RNA has been replaced by your cargo protein or your cargo RNA,” said Liu. “We became interested in using these virus-like particles for the delivery of therapeutic proteins because, in theory, they seem to offer some of the best advantages of both viral and nonviral delivery.”

This study builds on previous work from the combined research team, in which they identified and corrected bottlenecks that limit eVLP-mediated base editor delivery in vivo. However, the system that they optimized for base editing proved less effective for prime editing due to differences in the editor components. “There are several different properties of a prime editor which makes it harder to deliver,” said Meirui An, a graduate student in Liu’s laboratory who led this study. “It is large, it has several components that previous editing technologies do not have.” 

We all know prime editing is a good editing method, but right now it is hard to deliver the prime editing machinery for transient expression.
–Baisong Lu, Wake Forest University

Unlike base editors or other CRISPR associated nucleases, prime editors rely on a Cas9-reverse transcriptase fusion protein, a nicking guide RNA, and a long prime editor guide RNA with a complex structure. Although these differences are advantageous in terms of on-target genome editing, they impede delivery through previously established methods. 

The researchers engineered changes in the packaging and targeting components of their base editor eVLP system and modified linker molecules in the prime editor to improve editor assembly, particle packaging, and delivery efficiency. “Overall, we improved the efficiency of prime editing following delivery by these prime editor-engineered virus-like particles, these PE-eVLP, by an average of something like 65-fold,” Liu said. 

By using these improved particles in mice, the researchers achieved therapeutically relevant levels of prime editing locally through retinal injection and successfully partially restored visual function in a vision loss mouse model. “Those results are significant because they are, to our knowledge, the first time that a prime editor has been delivered as a protein-RNA complex in its final, most transient form, into an animal to rescue a genetic disorder,” Liu added

“This is quite interesting work,” said Baisong Lu, a biochemist at Wake Forest University who develops gene therapy delivery methods for CRISPR systems and who was not involved in this study. “We all know prime editing is a good editing method, but right now it is hard to deliver the prime editing machinery for transient expression.” 

The next step is to further improve the in vivo efficiency and tailor eVLP to target different tissues. Because eVLP include the envelope and structural proteins that help viral delivery methods home in on their destination,¹ PE-eVLP may hold the key to future minimally invasive gene editing therapeutics that reach their target destinations. “I’m quite glad to see that they actually tested in vivo,” said Lu. “If it is found that systemic delivery is also efficient, then there will be a lot of applications.”

David Liu cofounded and consults for Beam Therapeutics, Prime Medicine, Pairwise Plants, Exo Therapeutics, and YKY Therapeutics.

References

1. Yip BH. Recent advances in CRISPR/CAS9 delivery strategies. Biomolecules. 2020;10(6):839.
2. An M, et al. Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo. Nature Biotechnology. Published online January 8, 2024.