Researchers at the Broad Institute and the McGovern Institute for Brain Research at MIT have developed a new protein delivery approach that can be programmed to deliver a variety of proteins to different cell types. The system could potentially be a safe and efficient way to deliver gene therapies and cancer therapies.
Led by Feng Zhang, the team took advantage of a tiny syringe-like injection structure, produced by a bacterium, that naturally binds to insect cells and injects a protein payload into them. The researchers used AlphaFold to engineer these syringe structures to deliver a range of useful proteins to both human cells and cells in live mice.
“Delivery of therapeutic molecules is a major bottleneck for medicine, and we will need a deep bench of options to get these powerful new therapies into the right cells in the body,” explained Zhang. “By learning from how nature transports proteins, we were able to develop a new platform that can help address this gap.”
Symbiotic bacteria use the roughly 100-nanometer-long syringe-like machines to inject proteins into host cells to help adjust the biology of their surroundings and enhance their survival. These machines, called extracellular contractile injection systems (eCISs), consist of a rigid tube inside a sheath that contracts, driving a spike on the end of the tube through the cell membrane. This forces protein cargo inside the tube to enter the cell.
On the outside of one end of the eCIS are tail fibers that recognize specific receptors on the cell surface and latch on. Previous research has shown that eCISs can naturally target insect and mouse cells, but Joseph Kreitz, first author of the Nature paper, thought it might be possible to modify them to deliver proteins to human cells by reengineering the tail fibers to bind to different receptors.
Using AlphaFold, which predicts a protein’s structure from its amino acid sequence, the researchers redesigned tail fibers of an eCIS produced by Photorhabdus bacteria to bind to human cells. By reengineering another part of the complex, the scientists tricked the syringe into delivering a protein of their choosing, in some cases with remarkably high efficiency.
The team made eCISs that targeted cancer cells expressing the EGF receptor and showed that they killed almost 100 percent of the cells, but did not affect cells without the receptor. Though efficiency depends in part on the receptor the system is designed to target, Kreitz reported that the findings demonstrate the promise of the system with thoughtful engineering.
The researchers also used an eCIS to deliver proteins to the brain in live mice—where it didn’t provoke a detectable immune response, suggesting that eCISs could one day be used to safely deliver gene therapies to humans.
Kreitz says the eCIS system is versatile, and the team has already used it to deliver a range of cargos including base editor proteins, proteins that are toxic to cancer cells, and Cas9.