Gene editing has emerged as a powerful approach for targeting the genetic causes of disease, yet delivering the editing machinery into the correct cells efficiently, safely, and at the scale needed for therapies remains one of the biggest bottlenecks.  

Among the leading delivery vehicles are engineered virus-like particles (eVLPs), which can enter human cells similar to viruses but carry no viral genes. Instead, these delivery vehicles carry gene editing tools for therapeutic applications.  

In a new study published in Nature Communications titled, “Genome-wide screening reveals producer-cell modifications that improve virus-like particle production and delivery potency,” researchers from Whitehead Institute have developed a platform that systemically identifies which genes drive or block particle assembly to engineer cells that yield more potent delivery vehicles. 

“We can engineer the particles as much as we want, but if we don’t understand how the producer cells are actually making the particles, we’re limited in how much we can improve production,” said Aditya Raguram, PhD,  Valhalla Fellow at Whitehead Institute and corresponding author of the study.

As virus-like particles are assembled inside cultured human cells, the authors ran a genome-wide search to identify which genes are crucial in the production process by generating a large pool of producer cells in which nearly every gene in the human genome was switched off in the population. This approach generates eVLPs loaded with guide RNAs that identify the genetic perturbation in the cell that produced a particular particle. The team could then identify which gene shutdowns enabled and disabled particle production. 

“One thing that surprised me was how clearly the search was able to highlight specific pathways that play a major role in the production of these particles,” said Diana Ly, research technician at Whitehead Institute and first author of the study. 

The single gene whose removal most boosted production normally reduces the cell’s output of guide RNAs. Disabling this gene enabled cells to generate more guide RNA and particles to carry more functional cargo. 

The improvement also extended across different gene editing tools and particle designs. The team tested the modified producer cells with diverse gene editors and four other delivery-vehicle systems from external labs, and produced improved particles. 

“Because guide RNA loading is basically universal across different cargo types and particle types, this improvement could be quite broadly useful beyond the particles we’ve developed,” Raguram says. 

Looking ahead, the authors are extending the screening platform to expand beyond switching off one gene at a time to examine how other cellular changes influence particle production. The team is sharing its engineered cell lines with the research community to improve the delivery of gene editing tools into immune cells, neurons, and other cell types important for treating disease. 

For Raguram, the work speaks to a broader task facing the gene editing field. 

“This delivery challenge is one of the last remaining bottlenecks that really limits the widespread application of gene editing technologies,” he says. “Solving the challenges associated with production could move virus-like particles closer to being ready for use in patients.” 

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