Using an RNA sensor, MIT engineers have designed a new way to trigger cells to turn on a synthetic gene. The researchers demonstrated that their sensor could accurately identify cells expressing a mutated version of the p53 gene, which drives cancer development, and turn on a gene encoding a fluorescent protein only within those cells. Their novel approach may lead to targeted therapies for cancer and other diseases.

Their findings are published in Nature Communications in an article entitled, “Autocatalytic base editing for RNA-responsive translational control.”

“Genetic circuits that control transgene expression in response to pre-defined transcriptional cues would enable the development of smart therapeutics,” wrote the researchers. “To this end, here we engineer programmable single-transcript RNA sensors in which adenosine deaminases acting on RNA (ADARs) autocatalytically convert target hybridization into a translational output. Dubbed DART VADAR (Detection and Amplification of RNA Triggers via ADAR), our system amplifies the signal from editing by endogenous ADAR through a positive feedback loop.”

“There’s growing interest in reducing off-target effects for therapeutics,” explained James Collins, PhD, the Termeer professor of medical engineering and science in MIT’s Institute for Medical Engineering and Science (IMES) and department of biological engineering. “With this system, we could target very specific disease cells and tissues, which opens up the possibility of identifying cancer cells and then delivering highly potent therapeutics.”

In 2021, Collins’ lab developed a control switch for RNA therapies known as eToehold. This system is based on RNA molecules called internal ribosome entry sites (IRES), which can be designed to respond to a particular messenger RNA (mRNA) sequence within a cell.

In the current study, the researchers sought to create a system that would be easier to program. Instead of IRESes, they used a synthetic strand of RNA as the targeting molecule.

“With this new system, we have a very straightforward, programmable way of creating control elements that will respond only in the presence of those target sequences,” Collins said.

The researchers harnessed an enzyme that naturally exists in most animal cells, known as adenosine deaminase acting on RNA (ADAR).

“We only require a very small amount of ADAR to initially trigger the network. And then through a positive feedback design, that small trigger gets the cells to express high levels of a compact form of that enzyme that’s built into the construct,” Collins said. “This broadens the potential application uses for the system in that now it’s not restricted to cells that have large background levels of ADAR.”

“We show that you can get very high resolution and very high precision for these sensors,” MIT postdoc Raphaël Gayet, PhD, said. “With a carefully designed sensor, you can get a different level of activation depending on whether or not the cells produce some RNA that includes a mutation.”

The researchers are planning to test their system in animal models of cancer, to see if they can deliver synthetic constructs that would selectively kill tumor cells by producing lethal compounds only within those cells.

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