Scientists have engineered the compact protein TnpB to boost its genome editing effectiveness by 4.4 times, potentially revolutionizing treatments for genetic disorders like familial hypercholesterolemia.
Scientists at the University of Zurich (UZH) and ETH Zurich have developed a groundbreaking compact genome editing tool that could transform genetic therapies. Utilizing protein engineering and artificial intelligence, the researchers have boosted the efficiency of the small protein TnpB by 4.4 times, making it a powerful alternative to larger CRISPR-Cas systems.
“By engineering the small but powerful protein TnpB, we were able to design a variant that shows a 4.4-fold increase in efficiency of modifying DNA – making it more effective as a gene editing tool,” Gerald Schwank, group leader at the Institute of Pharmacology and Toxicology at UZH, said in a news release.
The TnpB protein originates from the bacterium Deinococcus radiodurans, an extremophile known for its resilience against radiation. Despite its potential, the native TnpB protein exhibited limited efficiency and targeting ability in mammalian cells.
The researchers overcame these hurdles by optimizing TnpB to ensure it targets alternative genomic sequences and localizes more effectively in the nucleus where genomic DNA is found. By testing the protein on 10,211 different DNA target sites, the team, in collaboration with Michael Krauthammer’s group at UZH, developed an AI model capable of predicting TnpB’s editing efficiency at specific sites.
“Our model can predict how well TnpB will work in different scenarios, making it easier and faster to design successful gene editing experiments. Using these predictions, we achieved up to 75.3% efficiency in mouse livers and 65.9% in mouse brains,” added first author Kim Marquart, a doctoral student in Schwank’s lab.
The smaller size of the TnpB system offers significant advantages over traditional CRISPR-Cas9 systems, particularly in terms of delivery. The TnpB components can be housed within a single adeno-associated viral vector, unlike the larger CRISPR-Cas9 components that require multiple vectors and higher doses.
The team’s promising results included treating familial hypercholesterolemia, a genetic disorder leading to high cholesterol and increased cardiovascular disease risk. Their gene-editing strategy reduced cholesterol levels in treated mice by nearly 80%.
“We were able to edit a gene that regulates cholesterol levels, thereby reducing the cholesterol in treated mice by nearly 80%,” Schwank added. “The goal is to develop similar gene editing strategies in humans in order to treat patients suffering from hypercholesterolemia.”
The research marks a significant step forward in genetic medicine, promising efficient and accurate gene editing therapies for numerous genetic conditions. The findings are published in the journal Nature Methods.