Bioengineers have created a new kit for building custom circuits in human cells that can sense and respond to various stimuli. This groundbreaking research has the potential to transform treatments for complicated diseases such as autoimmune disorders and cancer.
Researchers from Rice University have introduced an innovative construction kit aimed at crafting custom sense-and-respond circuits within human cells. Their findings, published in the journal Science, signify a significant advancement in synthetic biology that could change how we approach therapies for intricate conditions like autoimmune diseases and cancer.
“Envision tiny protein-based processors residing within cells that can ‘decide’ how to react to specific signals like inflammation, indicators of tumor growth, or blood sugar levels,” explained Xiaoyu Yang, a graduate student in Rice’s Systems, Synthetic, and Physical Biology Ph.D. program and the lead author of the study. “This research gets us much closer to creating ‘smart cells’ capable of detecting illness and quickly delivering tailored treatments in response.”
The novel method for designing artificial cellular circuits utilizes phosphorylation, a natural cellular response mechanism where a phosphate group is added to a protein. This process is crucial for various cellular functions, including translating external signals into internal responses—like movement, substance secretion, pathogen response, or gene expression.
In multicellular organisms, the signaling that utilizes phosphorylation often follows a complex, multi-step chain reaction, akin to a line of dominoes falling. Earlier attempts to utilize this mechanism for therapeutic applications in human cells have typically centered on re-engineering existing signaling pathways. However, the intricate nature of these pathways has limited their usability.
Fortunately, thanks to this new research from Rice, there is hope for increased advances in “smart cell” engineering through phosphorylation innovations in the near future. The key to this breakthrough was a change in how the researchers viewed the process:
They recognized that phosphorylation occurs in a stepwise manner with interconnected cycles that navigate from cellular input (what the cell encounters or senses in its surroundings) to output (the cell’s responses). The research team discovered and demonstrated that each cycle in a cascade could be regarded as a basic unit, allowing these units to be linked together in novel ways to create entirely new pathways that connect cellular inputs to outputs.
“This significantly expands the landscape for designing signaling circuits,” noted Caleb Bashor, an assistant professor of bioengineering and biosciences, and the study’s corresponding author. “We found that phosphorylation cycles are not only interconnected but can also be interconnected in ways we didn’t think possible at such a sophisticated level before.”
“Our design method allowed us to create synthetic phosphorylation circuits that are highly adjustable and can operate in tandem with the cell’s own mechanisms without disrupting viability or growth rates.”
Although this might seem simple, determining how to construct, connect, and fine-tune these units—including designing both internal and external outputs—was quite challenging. Additionally, it was not guaranteed that synthetic circuits could be created and function successfully within living cells.
“We weren’t completely certain that our synthetic signaling circuits, which consist solely of engineered protein components, would operate with the same speed and efficiency as natural signaling pathways found in human cells,” Yang shared. “We were pleasantly surprised to learn that they did. It required extensive collaboration and effort to succeed.”
The modular, do-it-yourself approach to cellular circuit design successfully replicated a crucial systems-level feature of natural phosphorylation cascades: the ability to amplify weak input signals into significant outputs. Observations from experiments confirmed the team’s predictive models, underscoring the new framework’s potential as a vital tool for synthetic biology.
Another significant benefit of this new methodology for cellular circuit design is that phosphorylation occurs quickly, often in mere seconds or minutes. Consequently, synthetic phospho-signaling circuits could be programmed to respond to physiological events that happen within a comparable timeframe. In contrast, many earlier synthetic circuit designs relied on molecular processes like transcription, which can take hours to activate.
The researchers also evaluated the circuits for their sensitivity and responsiveness to external signals, such as inflammatory factors. To demonstrate the potential for practical application, the team engineered a cellular circuit capable of detecting these inflammatory factors, which could be utilized to manage autoimmune flare-ups and mitigate the toxicity associated with immunotherapy.
“Our findings confirm that it is feasible to construct programmable circuits in human cells that respond to signals swiftly and accurately, and this is the first report of a toolkit for engineering synthetic phosphorylation circuits,” said Bashor, who is also deputy director for the Rice Synthetic Biology Institute. The institute was established earlier this year to leverage Rice’s significant expertise in synthetic biology and spur collaborative research initiatives.
Caroline Ajo-Franklin, the institute director, emphasized that the study exemplifies the transformative research Rice is undertaking in synthetic biology.
“If synthetic biologists have spent the past two decades figuring out how to manipulate bacteria’s gradual responses to environmental changes, the work from the Bashor lab propels us forward to a new era—managing the immediate responses of mammalian cells to changes,” stated Ajo-Franklin, a professor of biosciences, bioengineering, chemical and biomolecular engineering, as well as a Cancer Prevention and Research Institute of Texas Scholar.
