Novel platform opens new opportunities in synthetic biology

Using synthetic biology, researchers can include new functions to cells, like the ability to generate new materials or identify and answer in certain ways to diseases.

The new process mimics the way a cell naturally functions and emulates the ways cells typically communicate with one another. Image Credit: iStock/Jian Fan.

Although the applications are interesting, the methodology has some drawbacks, one of which Xiaojing Gao, a chemical engineer from Stanford University, is working to avoid.

For several years, researchers have studied how to program these novel abilities in cells through gene circuits—synthetic networks of genes, which can be combined into cells so that they sense certain triggers and provide the desired response.

However, the genes in gene circuits need to be first converted into proteins to respond. A quicker option would be a “protein circuit” that rules out the mediator by creating the circuits from the proteins themselves, states Gao. However, this comes with a drawback. Protein circuits function completely inside cells, whereas most biological processes need cells to interact with each other.

Gao, along with a team of researchers, has now taken protein circuits a step further in cell-to-cell interaction. In a study published on February 17^th, 2022, in Nature Communications, the team describes a novel platform developed that allows circuits to display them on the cell surface or release the proteins from the cell. The researchers hope that the cells will be capable to respond to these proteins in the future.

Alexander Vlahos, a postdoctoral scholar in chemical engineering and the study lead author, says that the effect will be that “you can engineer a very small subset of cells that can then have an effect on other cells.”

A new process

Vlahos states that this new process imitates the way a cell naturally works. Each cell has normal circuits in which proteins get data and pass it to the next protein. In turn, it can alter the next protein in the track. One approach to make these types of modifications naturally is with proteases—enzymes that cut proteins at certain sites, in turn, activating or deactivating them in the process.

Synthetic protein circuits function in a similar way to include new functions to cells, but they could do so silently, with no interaction with the cell’s usual functions.

The novel platform also outdoes the ways cells normally communicate with each other. Many cells make use of proteins to interact, secreting or exhibiting them so that neighboring cells can feel these proteins and answer.

The platform, known as RELEASE, or Retained Endoplasmic Cleavable Secretion, adds this capability to secrete and exhibit proteins to protein circuits, escalating what these circuits could do. “We’re not reinventing the wheel,” states Vlahos.

The interior of cells is like a congested city in some sense, with tens of millions of proteins rushing about to their destination. Generally, the proteins know precisely where they need to go, with the aid of short tags directing them where to head.

In RELEASE, Vlahos and Gao utilize these tags, adding one of them to the protein that required secreting. This particular tag retains the protein sequestered inside cells, but it can be eliminated by a specific protease. When this protease is added to cells with the protein circuit, it slashes the tag in two, “RELEASE-ing” or freeing the protein, enabling it to be secreted.

“Circuit as medicine”

One prospective application for the study is to combat cancers—caused by mutant proteins that are tough to fight with conventional drugs. For such cancers, Vlahos and Gao, the senior author on the paper, predict a “circuit as medicine” method, in which a cells’ subset carrying the circuit will sense the mutant protein and answer in two methods: killing the mutant cells and, at the same time, secreting proteins that trigger a response of immunity against cancer.

Protein circuits and RELEASE are the two steps toward obtaining the “circuit as medicine” method. Other steps would design extra platforms to enable protein circuits to wholly contribute to cell-to-cell communication in the coming days. These comprise including sensors that will enable programmed cells to respond to alterations in their environment and examine how neighboring cells respond to the secreted proteins from the circuits.

For Vlahos, whose expertise is in regenerative medicine, the further step is to keep optimizing RELEASE and utilize all the benefits of protein circuits to make better programmable cells that can be used in regenerative medicine and cell therapies.

Xiaojing and I developed RELEASE with an end goal in mind: trying to have programmable cells that can talk to other things. That’s fundamentally the big picture.”

Alexander Vlahos, Study Lead Author and Postdoctoral Scholar, Stanford University