New delivery particles for prime editors boost efficacy against retinal disease in mice

Prime editors delivered via a new type of particle have partially restored vision in blind mice.

In a study published Jan. 8 in Nature Biotechnology, a research team from Harvard University and the Broad Institute—led by David Liu, Ph.D., founder of Prime Medicine—reported that they had used a delivery system called prime editor engineered virus-like particles, or PE-eVLPs, to transport prime editors to the eyes of two different mouse models with genetic retinal diseases. The tool could not only improve the efficacy of prime editing, but also make it safer, the researchers said in their study.

“This study represents the first time to our knowledge that delivery of protein-RNA complexes has been used to achieve therapeutic prime editing in an animal,” Liu, one of the creators of prime editing, said in a press release.

Prime editing is a gene editing approach that is billed as a more precise and potentially safer upgrade to CRISPR, the most widely-known gene editing tool. Where CRISPR is like a Swiss Army knife with the ability to cut, remove and reinsert sequences of DNA into the genome, prime editing is more like the search-and-replace function on a word processor, swapping out base pairs without breaking both strands of DNA or requiring DNA templates, as CRISPR usually does. 

But even as Prime Medicine’s tech advances—the company announced in October 2023 that the tool was used to repair a mutation involved in a rare liver disease—prime editing still faces delivery challenges. Lipid nanoparticles like the ones Prime Medicine used in its liver disease therapy work well for liver conditions because they tend to accumulate in the organ, but they’re less effective for getting therapies to other tissue types.

More promising are viral delivery methods, which some research groups have used with some success, including in treating mice with retinal degeneration. One in particular stood out to Liu’s team: Virus-like particles, or VLPs, molecules with an exterior that’s coated in virus proteins but don’t contain any genetic material. VLPs are already used in vaccines, most notably the Gardasil series that prevents infection with the human papillomavirus. The Harvard and Broad Institute researchers had already engineered some for use with base editing, another type of gene editing tool, which they dubbed eVLPs. 

Unfortunately, the eVLPs developed for base editing didn’t work for prime editing. When the researchers tried to test engineered VLPs containing prime editors on human cells, they saw “almost no prime editing at all,” Liu lab graduate student and first author Meirui An said in the press release. But after a couple modifications, prime editing efficacy improved by as much as 19-fold, the scientists wrote in the study. 

Next, the researchers redesigned the VLPs to overcome what they described in the Nature paper as “mechanistic bottlenecks." This included adjustments to how the prime editors were packaged into and exported from the particles as well as the way they were delivered into the nuclei of target cells. Together, the changes “yielded large increases in prime editing efficiencies” compared to the original version used in base editing, the researchers wrote in their paper, with improvements of roughly 100-fold, Liu said in the release. They also noted in the paper that the improved particles made base editing more effective too, despite being designed for prime editing. 

After additional experiments to test the PE-eVLPs’ precision and ability to deliver prime editors to the brain, the researchers moved to test the particles in mice with genetic retinal diseases. Their first model had a mutation that causes a form of retinal degeneration similar to retinitis pigmentosa in humans. Analyses conducted at the end of the study showed that the gene mutation had been successfully corrected, with no signs of off-target editing or toxicity. 

The particles were then tested in a mouse model with a more severe retinal disease that’s also more challenging to treat via gene editing. In that case, the prime editors were able to correct the mutation at an efficacy rate higher than had previously been reported when viral delivery methods were used. It also made “substantial” improvements to their visual function, as demonstrated by the animals’ response to stimuli where one eye was treated and the other was not. 

“Together, these results demonstrate that in vivo application of optimized PE-eVLPs can correct a pathogenic mutation and partially rescue disease phenotype in animals,” the researchers wrote in the paper. 

Liu’s team plans to continue adapting the particles to target other tissue types, according to the release.