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Perez-Pinera and team create new tools to disrupt disease-causing genes, affecting multiple diseases


Susan McKenna

Mutated genes cause many diseases that currently have no cure. But, if researchers can interrupt a mutation by forcing genes to skip over code that causes the disease and can do so without the need for repeated treatments, then a cure is a real possibility.

In research at the University of Illinois at Urbana-Champaign, Bioengineering Assistant Professor Pablo Perez-Pinera, Physics Professor Jun S. Song, and their team have developed effective new tools and are using them with predictive computer modeling to edit genes that cause several diseases such as Duchenne muscular dystrophy (DMD) and dystrophic epidermolysis bullosa. The work was published in the Winter 2019 issue of Nature’s journal, Cell Discovery.

In Duchenne muscular dystrophy, mutations in the DMD gene prevent the necessary amount of the protein dystrophin from being produced, which results in damaged cardiac and skeletal muscles that progressively atrophy and eventually stop working.

The four bases in a DNA molecule — adenine, cytosine, guanine and thymine (ACGT) — form the bonds (AG and CT) that hold together the two winding DNA strands. When the RNA converts that genetic information from the DNA, exons, the coding sections of the RNA, translate the information into necessary proteins. Perez-Pinera and his team describe how adenine base editors (ABEs) can be used to skip the exon coding — to bypass the disease-inducing portions of the RNA — more effectively than before and to do so permanently. They also are doing the editing without breaking the DNA strands. The team has created several improved variants of the ABE that edit with higher efficiency than earlier versions and with improved editing rates.

“The ability to control gene splicing without creating double strand breaks has a lot of therapeutic potential,” Perez-Pinera said. “By demonstrating that it can be accomplished utilizing adenine base editors, we are drastically increasing the number of exons that can be targeted, which will enable novel therapeutic applications.”

Previous research showed that other DNA base editors, such as cytosine-to-thymine (CBEs), could be used to disrupt gene-splicing communications and cause the desired skip to stop disease-causing mutations, but many exons can’t be targeted with the CBEs, some of those techniques are expensive, and many resulted in the need for regular treatments to alleviate disease symptoms.

The Illinois team has expanded the CRISPR-SKIP (clustered regularly interspaced short palindromic repeats) gene-editing toolbox to include the new, higher-efficiency ABEs and are working on addressing the limitations of the technology.

The team also is using the gene-editing tools they developed to “investigate new gene targets that exon skipping hasn’t been applied to yet but could prove useful,” Perez-Pinera said. “It is critical to have a large toolbox to be able to find the tool that fits a particular application. … Beyond treating diseases, the technology also allows us to explore the role of specific exons in protein functions.”

As part of this work, the team “created a split ABE system that can be packaged into adeno associated virus (AAV), a type of virus that is particularly promising for therapeutic applications, to facilitate in vivo delivery,” Perez-Pinera said.

“Creating an ABE system that can be packaged into AAV is a critical step forward in progressing this technology towards clinical applications,” he said, “as it enables us to deliver the base editor to live animal models for testing of this system as a gene therapy for treating multiple diseases.”