Scientists turn mammalian cells into complex biocomputers

Computer hardware is getting a softer side. A research team has come up with a way of genetically engineering the DNA of mammalian cells to carry out complex computations, in effect turning the cells into biocomputers. The group hasn’t put those modified cells to work in useful ways yet, but down the road researchers hope the new programming techniques will help improve everything from cancer therapy to on-demand tissues that can replace worn-out body parts.

Engineering cells to function like minicomputers isn’t new. As part of the growing field of synthetic biology, research teams around the globe have been manipulating DNA for years to make cells perform simple actions like lighting up when oxygen levels drop. To date, most such experiments have been done in Escherichia coli and other bacteria, because their genes are relatively easy to manipulate. Researchers have also managed to link multiple genetic circuits together within a single cell to carry out more complex calculations in bacteria.

Scientists have tried to extend this to mammalian cells to create genetic circuitry that can help detect and treat human diseases. But efforts to construct large-scale genetic circuits in mammalian cells have largely failed: For complex circuits to work, the individual components—the turning on and off of different genes—must happen consistently. The most common way to turn a gene on or off is by using proteins called transcription factors that bind to and regulate the expression of a specific gene. The problem is these transcription factors “all behave slightly differently,” says Wilson Wong, a synthetic biologist at Boston University.

To upgrade their DNA “switches,” Wong and his colleagues steered clear of transcription factors and instead switched human kidney cell genes on and off using scissorlike enzymes that selectively cut out snippets of DNA. These enzymes, known as DNA recombinases, recognize two target stretches of DNA, each between 30 to 50 or more base pairs long. When a recombinase finds its target DNA stretches, it cuts out any DNA in between, and stitches the severed ends of the double helix back together.

To design genetic circuits, Wong and his colleagues use the conventional cellular machinery that reads out a cell’s DNA, transcribes its genes into RNA, and then translates the RNA into proteins. This normal gene-to-protein operation is initiated by another DNA snippet, a promoter, that sits just upstream of a gene. When a promoter is activated, a molecule called RNA polymerase gets to work, marching down the DNA strand and producing an RNA until it reaches another DNA snippet—a termination sequence—that tells it to stop.

To make one of their simplest circuits, Wong’s team inserted four extra snippets of DNA after a promoter. The main one produced green fluorescent protein (GFP), which lights up cells when it is produced. But in front of it was a termination sequence, flanked by two snippets that signaled the DNA recombinase. Wong and his team then inserted another gene in the same cell that made a modified recombinase, activated only when bound to a specific drug; without it, the recombinase wouldn’t cut the DNA.

When the promoter upstream of the GFP gene was activated, the RNA polymerase ran headfirst into the termination sequence, stopped reading the DNA, and didn’t produce the fluorescent protein. But when the drug was added, the recombinase switched on and spliced out the termination sequence that was preventing the RNA polymerase from initiating production of GFP. Voila, the cell lit up.

As if that Rube Goldbergian feat weren’t enough, Wong and his colleagues also showed that by adding additional recombinases together with different target strands, they could build a wide variety of circuits, each designed to carry out a different logical operation. The approach worked so well that the team built 113 different circuits, with a 96.5% success rate, they report today in Nature Biotechnology . As a further demonstration, they engineered human cells to produce a biological version of something called a Boolean logic lookup table. The circuit in this case has six different inputs, which can combine in different ways to execute one of 16 different logical operations.

“It’s exciting in that it represents another scale at which we can design mammalian genetic circuits,” says Timothy Lu, a synthetic biologist at the Massachusetts Institute of Technology in Cambridge. Although the current circuits are a proof of concept, both Lu and Wong say synthetic biologists want to use them to create new medical therapies. For example, scientists could engineer T cells, sentinels of the immune system, with genetic circuits that initiate a response to wipe out tumors when they detect the presence of two or three “biomarkers” produced by cancer cells, Lu says. Another example being explored by Wong and others is to engineer stem cells so they develop into specific cell types when prompted by different signals. This could let synthetic biologists generate tissues on demand, such as insulin-producing β cells, or cartilage-producing chondrocytes.