Engineers sharpen gene-editing tools to target cystic fibrosis

Engineers at Penn’s School of Engineering and Applied Science have collaborated to refine a technology for editing individual genetic “base pairs” to a new level of precision, opening the door to safer, more reliable therapies for a wide range of genetic diseases, and to potential treatments for some cystic fibrosis patients that may yield better outcomes than existing therapies.

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“More than a thousand different genetic mutations can cause cystic fibrosis,” says Xue “Sherry” Gao, Presidential Penn Compact Associate Professor in Chemical and Biomolecular Engineering (CBE) and in bioengineering (BE) at Penn Engineering, and co-senior author of a new paper in Molecular Therapy describing the advance.

To treat conditions like cystic fibrosis, researchers need to develop a suite of tools, rather than a single therapy. But even when scientists know exactly which DNA letter they want to change, today’s gene-editing technologies can unintentionally alter nearby letters as well, introducing “bystander” mutations that raise safety concerns.

“It’s a bit like editing a document,” says Gao. “We can already identify and replace a particular letter in a specific word. How do we change only that one letter without accidentally altering the letters next to it?”

One common cause of genetic diseases, including cystic fibrosis, is the accidental substitution of one nucleotide base—a single “letter” in the genetic code—for another.

“In some cases, the letter should be a T,” says Tyler C. Daniel, a Penn Engineering doctoral candidate in CBE 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 impair or completely abolish the function of the gene, leading to disease.”

While it’s already possible to use editors to change the C to a T, including a base-pair editor the same researchers devised in 2020, and even to selectively modify just one of two adjacent Cs, problems arise when multiple pairs of cytosines appear close together, in “CC … CC” patterns, separated by just a few other base pairs.

“The issue is precision,” says Daniel. “How do you restrict the editor so it only modifies the targeted letter C you want and leaves its neighbors alone?”

In order to change letters in DNA, base-pair editors combine two essential functions: one component that locates a specific sequence in the genome and another that modifies DNA. Those two parts are physically connected by a segment of molecules known as the “linker.”

By shortening and stiffening the linker, the team effectively limited the enzyme’s reach. “We essentially tightened the leash to ensure only our target was edited,” says Daniel.

Read more at Penn Engineering.