Friedreich’s ataxia mutations disrupted with gene editing
Technique swaps one nucleotide for another, interrupting sequence repetitions
A new gene editing technique disrupted the mutations that cause Friedreich’s ataxia (FA) in a mouse model, a study reports.
A type of base editing, the technique swaps one genetic building block, or nucleotide, for another. These edits can interrupt long repetitions of three-letter DNA sequences (trinucleotide repeats, or TNRs) which cause more than 40 diseases, including FA. The research team hopes this might provide a new therapeutic approach for FA.
“A lot more studies would be needed before we can know if disrupting these repeats with a base editor could be a viable therapeutic strategy to treat patients,” David Liu, PhD, a professor at the Broad Institute, said in a news story. “But being able to illuminate the biological consequences of interrupted repeats is a really useful and important milestone.”
In a separate mouse model, the researchers also disrupted the TNR mutations associated with Huntington’s disease. The study, “Base editing of trinucleotide repeats that cause Huntington’s disease and Friedreich’s ataxia reduces somatic repeat expansions in patient cells and in mice,” was published in Nature Genetics.
FA is a rare condition that primarily affects nerves and muscle. Mutations in the FXN gene cause low levels of the protein frataxin, which helps cells produce energy. This leads to symptoms that include difficulties with coordination and balance.
Interrupting long DNA sequences
Normally, FXN contains a three-nucleotide sequence, GAA, that repeats about five to 33 times. In people with FA, however, this TNR can occur 66 to more than 1,000 times. Generally, patients with interruptions in these repeats, meaning slightly different combinations of nucleotides, have milder symptoms and slower disease progression than those with uninterrupted repeats.
DNA repair mechanisms can cause further repeat expansions in response to the abnormal structure and instability of these DNA regions. Liu and his team hypothesized that a base editor could replace nucleotides in the TNRs associated with FA and Huntington’s disease, preventing these DNA repeats from expanding.
“Base editing is a precision genome-editing technology that directly introduces targeted changes to the DNA in living cells,” wrote the researchers, who focused on editing DNA in nerve cells.
For FA, the researchers altered several of the A (adenine) nucleotides in the GAA repetition, turning them to Gs (guanines). As nucleotides pair together in the DNA double helix, doing this also edited the partner nucleotides from Ts (thymines) to Cs (cytosines). The researchers engineered a virus to deliver the editor to neurons.
When injected into newborn mice, the base editor successfully altered GAA repeats. Also, the editing significantly reduced the gene’s instability and the length of the repeats. After 24 weeks, or about 5 months, DNA editing made FXN gene copies more prone to contractions than to expansions.
Base editors may affect other parts of DNA and have a negative impact on cell function, the researchers said. “Minimizing the off-target activity is desirable for both the investigation and potential future treatment of TNR diseases using base editors,” they wrote, noting most of the off-target effects they saw occurred in portions of the genome that don’t encode proteins.
Along with providing a potential therapeutic approach for diseases related to TNRs, base editing may help researchers study the disease mechanisms. “What’s really exciting is that we now have a tool to introduce interruptions in cell and animal models and study how they affect the biology of these diseases,” said Zaneta Matuszek, PhD, a co-first author on the study.
Also, “the base-editing approach [used here] can also be applied to study any of over a dozen repeat disorders,” said Mandana Arbab, PhD, the other study co-first author.
While the mouse models in the study mimic the genetic origins of FA and Huntington’s, the researchers said more work is needed in cells and animal models that more closely mirror what happens in people. “There’s still a lot of work to be done, but we’re hopeful that this approach could really accelerate therapeutic development for a lot of these diseases,” Arbab said.
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