Researchers at the McGovern Institute for Brain Research at MIT and the Broad Institute at MIT and Harvard have harnessed a naturally occurring bacterial system to develop a new protein delivery approach that works in human and animal cells. The technology, described today in Nature, it can be programmed to deliver a variety of proteins, including gene-editing ones, to different types of cells. The system could potentially be a safe and efficient way to deliver gene therapies and cancer therapies.
Led by MIT Associate Professor feng zhangwho is a McGovern Institute Investigator and Senior Fellow at the Broad Institute, the team took advantage of a tiny syringe-like injection structure produced by a bacterium, which it naturally binds to insect cells and injects a protein payload into them. The researchers used the artificial intelligence tool AlphaFold designing these syringe structures to deliver a variety of useful proteins to both human cells and cells in living mice.
“This is a really beautiful example of how protein engineering can alter the biological activity of a natural system,” says Joseph Kreitz, the study’s first author, a graduate student in biological engineering at MIT and a member of Zhang’s lab. “I think it substantiates protein engineering as a useful tool in bioengineering and the development of new therapeutic systems.”
“The delivery of therapeutic molecules is a major bottleneck for medicine, and we will need a large bank of options to get these powerful new therapies to the right cells in the body,” Zhang adds. “By learning from how nature transports proteins, we were able to develop a new platform that can help address this gap.”
Zhang is the study’s senior author and is also the James and Patricia Poitras Professor of Neuroscience at MIT and an Investigator at the Howard Hughes Medical Institute.
shrink injection
Symbiotic bacteria use syringe-like machines about 100 nanometers long to inject proteins into host cells to help adjust the biology of their environment and enhance their survival. Called extracellular contractile injection systems (eCIS), these machines consist of a rigid tube inside a sheath that contracts, propelling a spike at the end of the tube through the cell membrane. This forces the 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 eCIS can naturally target mouse and insect cells, but Kreitz thought it might be possible to engineer them to deliver proteins to human cells by reengineering the tail fibers to bind to different receptors.
Using AlphaFold, which predicts the structure of a protein from its amino acid sequence, the researchers redesigned the tail fibers of an eCIS produced by Fotorhabdus bacteria to attach to human cells. By reengineering another part of the complex, the scientists tricked the syringe into delivering a protein of their choice, in some cases with remarkably high efficiency.
The team made eCIS 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. Although efficiency depends in part on the intended recipient of the system, Kreitz says the findings demonstrate the promise of the system with careful engineering.
The researchers also used an eCIS to deliver proteins to the brain in live mice, where it did not elicit a detectable immune response, suggesting that eCIS could one day be used to safely deliver gene therapies to humans.
packaging proteins
Kreitz says the eCIS system is versatile, and the team has already used it to deliver a range of payloads 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.
In the future, Kreitz says, the researchers could design other components of the eCIS system to tune other properties or to deliver other payloads like DNA or RNA. He also wants to better understand the function of these systems in nature.
“We and others have shown that these types of systems are incredibly diverse in the biosphere, but they are not very well characterized,” Kreitz said. “And we think this type of system plays a very important role in biology that hasn’t been explored yet.”
This work was supported, in part, by the National Institutes of Health, Howard Hughes Medical Institute, MIT Poitras Center for Research in Psychiatric Disorders, MIT Hock E. Tan and K. Lisa Yang Center for Autism Research. MIT, K. Lisa Yang and Hock E. Tan Molecular Therapeutics Center at MIT, K. Lisa Yang Brain-Body Center at MIT, Broad Institute Programmable Therapeutics Gift Donors, The Pershing Square Foundation, William Ackman, Neri Oxman, J. and P Poitras, Kenneth C. Griffin, BT Charitable Foundation, Asness Family Foundation, the Phillips family, D. Cheng, and R. Metcalfe.
