Genetic Circuits Target Cells For Boolean Logic And Arithmetic

A new platform offers a fast and more efficient way to target and program mammalian cells as genetic circuits, even complex ones.

Wilson Wong, professor of biomedical engineering at Boston University, explains:

“The problem synthetic biologists are trying to solve is how we ask cells to make decisions and try to design a strategy to make the decision we want it to. With these circuits, we took a completely different design approach and have created a framework for researchers to target specific cell types and make them perform different types of computations, which will be useful for developing new methods for tissue engineering, stem cell research, and diagnostic applications, just to name a few.”

Historically, engineered genetic circuits were inspired by circuit design in electronics, following a similar approach using transcription factors, proteins that induce DNA conversion to RNA, which is tricky to work with because it’s hard to predict an entirely new strand of genetic code.

Mammalian cells are especially tricky to work with because they are a much more variable environment and express highly complex behaviors, rendering the electronics approach to circuit design time consuming at best and unreliable at worst.

Boolean Logic And Arithmetic Through DNA Excision

Wong’s approach uses DNA recombinases, enzymes that cut and paste pieces of DNA sequences, allowing for more targeted manipulation of cells and their behavior.

The result is a platform named “BLADE,” or “Boolean logic and arithmetic through DNA excision,” referring to the computer language that programs the cells and the computations they can be programmed to carry out. BLADE will allow researchers to use different signals, or inputs, in one streamlined device to control the outputs, or behaviors, of the cells they target.

First author of the paper Benjamin Weinberg, a graduate student in Wong’s laboratory, said:

“The idea was to build a system simple and flexible enough that it can be customized in the field to get any desired outcome using one simple design, instead of having to rebuild and retry a new design every time. Essentially, with BLADE, you can implement any combination of computations you want in mammalian cells.

For this particular paper, we might not have built the particular behavior you need, but we wanted to illustrate that using BLADE, you should be able to build the circuit you need to fulfill the behavior you are looking for.”

Medical Diagnostic Applications

Their study describes over one hundred examples of circuits that researchers built using the BLADE platform, with a 96.5% success rate. Weinberg notes that the researchers intentionally built complex circuits with complicated functions to illustrate the possibilities using their design, including some that program human cells to add or subtract numbers.

He uploaded the design plans to an open-source online repository so that other researchers could begin downloading the tools to use in their projects immediately.

“Before BLADE, any one of these circuits would have taken several years to build and make functional and then you would have to use trial-and-error to make it work the way you want it to,” says Wong. “I have been doing synthetic biology research for 15 years and I’ve never seen such complex circuits work on the first try like with this platform. We’re excited to get it out there so people can start using it, and we’re excited to see what they come up with.”

Weinberg will continue to refine the technology and incorporate into a software program to make it even easier to use, while Wong plans on using the platform to explore medical diagnostic applications.

Benjamin H Weinberg, N T Hang Pham, Leidy D Caraballo, Thomas Lozanoski, Adrien Engel, Swapnil Bhatia & Wilson W Wong
Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells
Nature Biotechnology (2017) doi:10.1038/nbt.3805

Image: Wilson Wong

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