Next-gen ‘smart cells’ take a major step forward

A new building kit for creating unique sense-and-respond circuits in human cells has been created by bioengineers at Rice University. The study, which was published in the journal Science, is a significant advancement in synthetic biology that has the potential to transform treatments for difficult diseases like cancer and autoimmune disease.

Imagine tiny processors inside cells made of proteins that can ‘decide’ how to respond to specific signals like inflammation, tumor growth markers, or blood sugar levels. This work brings us a whole lot closer to being able to build ‘smart cells’ that can detect signs of disease and immediately release customizable treatments in response.”

Xiaoyu Yang, Graduate Student and Study Lead Author, Rice University

Phosphorylation, a natural process by which cells react to their surroundings by adding a phosphate group to a protein, is the basis for the novel method of designing artificial cellular circuits.

The conversion of extracellular signals into intracellular responses, such as moving, secreting a substance, responding to a pathogen, or expressing a gene, is one of the many cellular processes in which phosphorylation plays a role.

Phosphorylation-based signaling frequently has a multi-stage cascading effect, similar to falling dominoes, in multicellular organisms. Re-engineering native, pre-existing signaling pathways has been the main focus of prior attempts to use this mechanism therapeutically in human cells. However, applications have remained relatively limited due to the pathways' complexity, which makes them challenging to work with.

However, phosphorylation-based advancements in “smart cell” engineering may see a notable increase in the upcoming years as a result of the discoveries made by Rice researchers. This breakthrough was made possible by a change in viewpoint:

From cellular input that is, something the cell experiences or senses in its surroundings to output that is, what the cell does in response phosphorylation is a sequential process that develops as a sequence of interconnected cycles.

Each cycle in a cascade can be viewed as an elementary unit, and these units can be connected in novel ways to create completely new pathways that connect cellular inputs and outputs. This is what the research team discovered and set out to demonstrate.

This opens up the signaling circuit design space dramatically. It turns out, phosphorylation cycles are not just interconnected but interconnectable this is something that we were not sure could be done with this level of sophistication before. Our design strategy enabled us to engineer synthetic phosphorylation circuits that are not only highly tunable but that can also function in parallel with cells’ own processes without impacting their viability or growth rate.”

Caleb Bashor, Assistant Professor and Study Corresponding Author, Rice University

Although this might seem simple, it was quite difficult to figure out the guidelines for constructing, connecting, and fine-tuning the units, including the design of the intracellular and extracellular outputs. Furthermore, it was not a given that artificial circuits could be constructed and used in living cells.

We did not necessarily expect that our synthetic signaling circuits, which are composed entirely of engineered protein parts, would perform with a similar speed and efficiency as natural signaling pathways found in human cells. Needless to say, we were pleasantly surprised to find that to be the case. It took a lot of effort and collaboration to pull it off.”

Xiaoyu Yang, Graduate Student and Study Lead Author, Rice University

The ability of native phosphorylation cascades to amp up weak input signals into macroscopic outputs is a key systems-level capability that can be replicated using a do-it-yourself, modular approach to cellular circuit design.

The value of the new framework as a fundamental tool for synthetic biology was further supported by experimental observations of this effect, which confirmed the team's quantitative modeling predictions.

Since phosphorylation happens quickly in just a few seconds or minutes the new synthetic phospho-signaling circuits may be able to be programmed to react to physiological events that take place on a comparable timescale.

This is another clear benefit of the new approach to sense-and-respond cellular circuit design. On the other hand, a lot of earlier artificial circuit designs relied on various molecular mechanisms, like transcription, which can take several hours to initiate.

The circuits' sensitivity and responsiveness to outside stimuli, such as inflammatory factors, were also examined by the researchers. The team demonstrated the framework's translational potential by using it to design a cellular circuit that can identify these variables, potentially reducing immunotherapy-associated toxicity and controlling autoimmune flare-ups.

“Our research proves that it is possible to build programmable circuits in human cells that respond to signals quickly and accurately, and it is the first report of a construction kit for engineering synthetic phosphorylation circuits,” said Bashor. 

Bashor is the Deputy Director of the Rice Synthetic Biology Institute, which was established earlier this year to leverage Rice's extensive knowledge of the field and encourage teamwork in research.

The study's results, according to Institute Director Caroline Ajo-Franklin, are an illustration of the groundbreaking work being done in synthetic biology by Rice researchers.

“If in the last 20 years synthetic biologists have learned how to manipulate the way bacteria gradually respond to environmental cues, the Bashor lab’s work vaults us forward to a new frontier controlling mammalian cells’ immediate response to change,” said Ajo-Franklin, a Professor of Biosciences, Bioengineering, Chemical and Biomolecular Engineering and a Cancer Prevention and Research Institute of Texas Scholar.