Engineering bacteria to intelligently sense and respond to disease states, from infections to cancer, has become a promising focus of synthetic biology. However, while current synthetic biology tools can create an enormous number of programmed cells, researchers' dependence on animal-based testing has greatly limited the number of therapies that can be tested and how quickly.
In a paper published yesterday in PNAS, researchers at Columbia Engineering reported the development of a system that enables them to study tens to hundreds of programmed bacteria within mini-tissues in a dish, condensing the time of study from months to days. As a proof of concept, they focused on testing programmed antitumor bacteria using tumor spheroids. The speed and high throughput of their technology, which they call BSCC for "bacteria spheroids co-culture," allows for stable growth of bacteria within tumor spheroids enabling long-term study. The method can also be used for other bacteria species and cell types.
"We're very excited at how efficient BSCC is and think it will really accelerate engineered bacterial therapy for clinical use," explains Tal Danino, assistant professor of biomedical engineering. "By combining automation and robotics technology, BSCC can test a large library of therapies to discover effective treatments. And because BSCC is so broadly applicable, we can modify the system to test human samples as well as other diseases. For example, it will help us personalize medical treatments by creating a patient's cancer in a dish, and rapidly identify the best therapy for the specific individual."
The researchers knew that while many bacteria can grow inside a tumor because of the reduced immune system there, bacteria are killed outside the tumor where the body's immune system is active. Inspired by this mechanism, they searched for an antibacterial agent that can mimic the bacteria "killing" effect outside the spheroids. They developed a protocol to use the antibiotic gentamicin to grow bacteria inside spheroids that are similar to tumors in the body. Using BSCC, they then rapidly tested a broad range of programmed anticancer bacterial therapies made of various types of bacteria, genetic circuits, and therapeutic payloads.
"We used 3D multicellular spheroids because they recapitulate conditions found in the human body, such as oxygen and nutrient gradient—these can't be made in a traditional 2D monolayer cell culture," says the paper's lead author Tetsuhiro Harimoto, who is a Ph.D. student in Danino's lab. "In addition, the 3D spheroid provides bacteria with enough space to live in its core, in much the same way that bacteria colonize tumors in the body, also something we can't do in the 2D monolayer culture. Plus, it's simple to make large numbers of 3D spheroids and adapt them for high-throughput screening."
The team used the BSCC's high-throughput system to rapidly characterize pools of programmed bacteria and then to quickly narrow down the best candidate for therapeutic use. They discovered a potent therapy for colon cancer, using a novel bacterial toxin, theta toxin, combined with an optimal drug delivery genetic circuit in attenuated bacteria Salmonella Typhimurium. They also found new combinations of bacterial therapies that can improve anticancer efficacy even more.
Image: The image shows engineered bacteria (green) in tumor spheroids cultured in a multi-well plate. Image courtesy of Tetsuhiro Harimoto/Columbia Engineering