Researchers at the Massachusetts Institute of Technology, from the McGovern Institute for Brain Research and the Broad Institute, have harnessed a natural bacterial system to develop a new approach to protein delivery in human cells and animals. The work has been reported in Nature.
The technology can deliver a variety of proteins, including those for gene editing, to different cell types. The system could potentially deliver gene therapies and cancer therapies in a safe and efficient way.
The research team, led by Feng Zhang of MIT, exploited the tiny syringe-like injection structure produced by a bacterium that naturally binds itself to insect cells and injects proteins into them. The researchers used AlphaFold, an AI tool, 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,” Zhang said. “By learning from how nature transports proteins, we were able to develop a new platform that can help address this gap.”
Symbiotic bacteria (like gut bacteria in humans) use the roughly 100 nm-long syringe-like structure to inject proteins into host cells to alter the biology of their surroundings and enhance their chance of survival. These machines, called extracellular contractile injection systems (eCISs), consist of a rigid tube inside a sheath, which contracts to drive forward a spike at the end of the tube that forces the protein payload inside to enter the cell.
On the outside of one end of the eCIS are tail fibres that recognise specific receptors on the cell surface and latch on. It is known that eCISs can naturally target insect and mouse cells, but the study’s first author Joseph Kreitz thought it might be possible to modify them to deliver proteins to human cells by re-engineering the tail fibres to bind to different receptors.
Using AlphaFold, which predicts a protein’s structure from its amino acid sequence, the researchers redesigned tail fibres of an eCIS produced by Photorhabdus bacteria to bind to human cells. By re-engineering another part of the complex, the scientists tricked the syringe into delivering a protein of choice, in some cases with remarkably high efficiency.
The team made eCISs that targeted cancer cells expressing the epidermal growth factor receptor and showed that they killed almost 100 per cent of the cells, but cells without the receptor remained unaffected. Though efficiency depends in part on the receptor the system is designed to target, the findings demonstrate the promise of the system with thoughtful engineering, Kreitz said.
The researchers also used an eCIS to deliver proteins to the brain in live mice—where it did not provoke a detectable immune response, suggesting that eCISs could one day be used to safely deliver gene therapies to humans.
Kreitz said the eCIS system was versatile, and the team had already used it to deliver a range of cargoes, including base editor proteins (which can make single-letter changes to DNA), proteins that are toxic to cancer cells, and Cas9, a large DNA-cutting enzyme used in many gene editing systems.
“We and others have shown that this type of system is incredibly diverse across the biosphere, but they are not very well characterised,” Kreitz said. “And we believe this type of system plays really important roles in biology that are yet to be explored.”