Turning genes on with caffeine and CRISPR

Caffeine reversibly controlled gene expression in a human cell line when linked to an engineered protein system.

Researchers at Texas A&M University developed the technique by linking CRISPR-based gene-regulation systems – which can switch genes on or off without altering the DNA sequence – to small molecules such as caffeine or rapamycin. Rather than permanently changing DNA, the approach uses an external trigger to reversibly control gene expression, allowing the activity of targeted cells to be precisely turned on or off. The strategy, known as chemogenetics, uses engineered proteins and well-characterised small molecules to control cellular activity with high precision. Instead of affecting whole tissues, it allows specific cells to be activated or silenced on demand.

'You can also engineer these antibody-like molecules to work with rapamycin-inducible systems, so by adding a different drug like rapamycin, you can achieve the opposite effect,' explained Professor Yubin Zhou, principal investigator of the study, and director of the Centre for Translational Cancer Research. 'For example, if at first proteins A and B are separate, adding caffeine brings them together; conversely, if proteins A and B start out together, adding a drug like rapamycin can cause them to dissociate.'

In the study published in Chemical Science, researchers first demonstrated reversible control of gene expression in a human cell line using caffeine-linked engineered proteins. To further test and redesign the chemically induced proximity systems the researchers attached nanobodies to their components in cultured mouse cells. Specifically, they reprogrammed the caffeine-operated COSMO system so that caffeine caused two proteins to bind, creating a controllable ON switch. Similarly, the rapamycin-controlled system was reversed into an OFF switch, causing proteins to separate rather than join. These experiments demonstrate how the redesigned switches could later be connected to CRISPR-based gene-regulation systems, for reversible control of gene expression.

The authors note that these redesigned switches could potentially be applied to engineered immune cells, such as CAR‑T cells, to provide reversible, drug-controlled regulation of therapeutic genes. They suggest that caffeine- or rapamycin-triggered systems might one day allow doctors to precisely control when and how strongly immune cells are activated, offering a way to fine-tune treatments in a controlled and reversible manner.

'What excites us is the idea of repurposing well-known drugs and even commonly found food ingredients like caffeine to do entirely new tricks,' Professor Zhou said. 'Instead of acting as therapies themselves, molecules like caffeine or rapamycin can serve as precise control signals for sophisticated cell and gene therapies. Because these compounds are already well understood, this approach opens a practical path toward translation. Our hope is that one day, clinicians could use simple, familiar inputs to finely tune powerful therapies in a safe and reversible way.'

By repurposing these systems, researchers address gaps in current biological tools without needing to design entirely new chemistries – often costly and time-consuming – while offering reversible, drug-controlled ways to fine-tune gene expression.