Engineers at the University of Pennsylvania and Rice University have perfected a technology to edit single genetic “base pairs” to a new level of precision, opening the door to safer, more reliable treatments for a wide range of genetic diseases and to potential treatments for some cystic fibrosis patients that may yield better results than existing treatments.
Unlike infectious diseases, many of which respond to the same treatments—such as antibiotics that kill many types of bacteria—genetic diseases often require highly specific treatments, which can vary from patient to patient, even for the same disease.
“More than a thousand different genetic mutations can cause cystic fibrosis,” says Xue “Sherry” Gao, Penn Engineering’s Presidential Associate Professor of Chemical and Biomolecular Engineering (CBE) and Mechanical Engineering (BE), and co-senior author of a new paper in Molecular Therapy describing progress. “The fact that different mutations require separate corrective tools underscores the importance of precision medicine.”
In other words, to treat conditions like cystic fibrosis, researchers need to develop a range of tools rather than a single treatment. But even when scientists know exactly which DNA letter they want to change, today’s gene-editing technologies can inadvertently change nearby letters as well, introducing “ghost” mutations that raise safety concerns.
“It’s a bit like editing a document,” says Gao. “We can already recognize and replace a certain letter in a certain word. How we change just this one letter without accidentally corrupting the letters next to it?’
The challenge of exchanging C for Ts
A common cause of genetic diseases, including cystic fibrosis, is the random replacement of a nucleotide base—a single “letter” in the genetic code—with another.
“In some cases, the letter should be T,” says Tyler C. Daniel, a Penn Engineering CBE doctoral candidate and co-first author of the new paper, referring to thymine, one of the four bases in human DNA, along with adenine (A), guanine (G) and cytosine (C). “Instead, it’s a C, which can damage or completely disable the function of the gene, leading to disease.”
While it is already possible to use editors to change C to T, including a base pair editor invented by the same researchers in 2020, and even selectively modify just one of two adjacent Cs, problems arise when multiple cytosine pairs occur close together, in “CC… CC” patterns, separated by a few other base pairs.
The challenge is hardly theoretical: among the tens of thousands of known disease-causing C-to-T and T-to-C mutations this type of base-pair editing can address, three-quarters involve multiple cytosine pairs clustered together.
The point is accuracy. How do you constrain the editor to modify only the targeted C letter you want and leave its neighbors alone?”
Tyler C. Daniel, Penn Engineering PhD candidate in CBE
Designing a more accurate editor
In order to change the letters in DNA, base pair editors combine two basic functions: one component that locates a specific sequence in the genome and another that modifies the DNA. These two parts are physically connected by a segment of molecules known as a “linker”.
Just as the length of a dog’s leash determines how far it can get away from its owner, the properties of the linker dictate how freely the DNA-editing enzyme can move to its target site.
By shortening and stiffening the linker, the team effectively limited the enzyme’s reach. “We essentially tightened the belt to ensure that only our target was processed,” says Daniel.
The researchers also modified how strongly the base pair editor interacts with DNA, weakening its tendency to act on neighboring letters.
In laboratory tests on human cells, the redesigned processor led to dramatic reductions in unintended bystander editing: The most accurate variant reduced bystander mutations by more than 80% while maintaining high levels of the original processor’s activity at the target site.
Towards a permanent cure for cystic fibrosis
Cystic fibrosis is caused by mutations in a gene that controls how the cells lining the lungs move salt and water in and out. When this process breaks down, thick mucus builds up in the lungs, making breathing difficult and leaving patients vulnerable to recurrent infections.
While drugs developed in recent years, such as Tricafta, have changed the lives of many people with cystic fibrosis, the drugs must be taken daily and can add up to staggering annual costs. Because many of the mutations that cause cystic fibrosis involve changes in a single DNA letter, base pair editors could, in principle, help treat the disease even when Tricafta is ineffective—but only if they can avoid causing harmful off-target mutations.
“We were able to introduce specific cystic fibrosis mutations into human epithelial cells associated with the disease, creating cell models that will improve our understanding,” says Gang Bao, Foyt Family Professor of Biotechnology at Rice University and co-senior author of the study. “We were also able to reverse these mutations and show improved cellular functions using the same processor, demonstrating the level of gene editing control that this technology now offers and the potential of base pair processors to treat disease.”
The work remains at an early, preclinical stage. However, at several CF-related genetic loci affecting a subset of CF patients, the refined editor reduced unintended alterations from 50–60% to less than 1%, while largely preserving the desired change in DNA.
By directly correcting the underlying genetic error, the method shows the possibility of a long-term, potentially permanent cure. “The more precise we can make these tools,” adds Bao, “the greater their potential to change the way we treat genetic diseases with a high level of efficacy and safety.”
A wider toolbox for genetic diseases
Beyond cystic fibrosis, the refined base editor could help researchers tackle a wide range of genetic diseases caused by single-letter changes in DNA. Because the tool allows scientists to introduce — and correct — specific mutations with much greater precision, it offers a powerful way to study how individual genetic variations affect disease and drug response.
This ability is especially valuable for rare mutations, which may affect only a small number of patients and are difficult to study through large clinical trials. By creating accurate cellular models of these mutations in the lab, researchers can test existing drugs, explore new treatment strategies, and begin to identify which treatments are most likely to work for specific patients.
“The ability to accurately model disease-causing mutations gives us a much clearer window into how those mutations behave, including how they might respond to different treatments,” says Gao. “This kind of insight is necessary to move toward more personalized approaches to treating genetic diseases.”
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