Gene editing has emerged as a powerful approach for targeting the genetic causes of disease, but getting the editing machinery into the right cells efficiently, safely, and at the scale needed for therapies remains one of the biggest set of challenges in the field. Among the leading delivery vehicles are engineered virus-like particles, which resemble viruses – and share their knack for entering human cells – but carry no viral genes. Scientists load them with gene editing tools and use them to make precise changes in targeted cells.
Most efforts to improve these particles have focused on redesigning the particles themselves. A new study led by Valhalla Fellow at Whitehead Institute Aditya Raguram and lab technician Diana Ly focuses instead on the human cells that produce them. Published on April 24 in Nature Communications , the research introduces a platform for systematically identifying which genes in these cells drive or block particle assembly, and using those findings 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," Raguram says.
Engineering the optimal producer cell
Because virus-like particles are assembled inside cultured human cells, Ly and colleagues ran a genome-wide search to identify which of those cells' genes matter most to the production process.
They created a large pool of producer cells in which nearly every gene in the human genome was switched off somewhere in the population, one gene per cell. The way virus-like particles package their cargo – the gene editing tools — meant that each particle ended up carrying a small piece of genetic material identifying the gene that had been switched off in the cell that made it. By reading those genetic tags in the final particles, the team could see which gene shutdowns helped particle production, which ones hurt it, and which ones had no effect.
"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," Ly says.
A standout gene
The single gene whose removal most boosted production normally acts as a brake on the cell's output of guide RNAs—short pieces of RNA that direct gene editors to their targets. When the researchers disabled that gene, producer cells generated more guide RNAs, and each particle carried more functional cargo.
The improvement also extended across different gene editing tools and particle designs: the team tested the modified producer cells with several kinds of gene editors and with four other delivery-vehicle systems from other labs, and in every case, the engineered cells produced better 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.
The search also identified a group of genes that had a more complicated effect. Removing these genes increased production of the protein components of the particles, but decreased delivery potency. In specialized production settings where protein cargo is the limiting ingredient, however, the same modified cells substantially boosted potency.
Expanding the platform
The Raguram Lab is already extending the screening platform in new directions, moving beyond simply switching off one gene at a time to examine how other kinds of cellular changes influence particle production. The team is sharing its engineered cell lines with the research community and collaborating with other groups 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."
The ultimate goal, Ly says, is to use these particles to treat genetic diseases.
ABOUT WHITEHEAD INSTITUTE
Whitehead Institute is a nonprofit, independent biomedical research institute founded in 1982. The institute advances pioneering research in cancer, developmental biology, genetics, genomics, and related fields, with a mission to pursue bold, curiosity-driven science that deepens our understanding of life and improves human health. Led by 24 principal investigators and a global community of trainees and scholars, Whitehead Institute maintains a teaching affiliation with Massachusetts Institute of Technology (MIT) but is fully independent in its research programs, governance, and finances.
Nature Communications