Mitochondria have been linked to multiple diseases and aging. Unlike other cellular organelles, mitochondria contain their own DNA, and that DNA can be damaged or mutated so that it no longer functions correctly. A cell might contain up to 1000 copies of the mitochondrial DNA (mtDNA), and the copies might be a mixture of mutated and wildtype mtDNAs, a state known as mtDNA heteroplasmy.

A disease is manifested only if there are too few wildtype copies to maintain normal function. Until recently, few if any treatment options were available.

The discovery of genome editing has initiated a new era of possibilities. However, translating  it to living organisms is challenging. Now a group of researchers, led by Carlos Moraes at the University of Miami, applied genome editing to a mouse model of mitochondrial disease.1 These mice are heteroplasmic for a mutation in the gene for the alanine transfer RNA. Thus, the researchers used a cytosine base editor to insert a compensatory edit into the mtDNA. That edit restored the tRNA function by allowing it to reassume its native stem-loop structure. However, at higher doses,  off-target editing of mtDNA occurred, emphasizing the need for more precise editing.

These exciting results indicate that genome editing may be a useful therapeutic strategy for treating the previously intractable mitochondrial disorders and that additional research efforts would accelerate the translation of these approaches to the clinics.

Discussion with Dr. Carlos T. Moraes

Your work is the first to use this technique in vivo. What are the challenges to expanding this strategy?

MtDNA base editing has been used mostly to create mtDNA mutations. There are very few mouse models of mtDNA mutations, and even the one we used could not be directly corrected with the approaches available when we started the project.

It is encouraging that your strategy worked in multiple mouse organs, but in a practical sense, is it really scalable to mitochondrial diseases in large organs, such as skeletal muscle?

As in any gene therapy approach, the bottle neck is the ability to deliver genes to the desired organ. Muscle is actually a good target, as AAV viruses have been shown to deliver genes to muscle after intravenous injections. The brain is a bit more difficult.

In your experiment, the disease mutation was well known. Is that true of other diseases or will potential application of your method have to await elucidation of those mutations? This is not meant as a criticism. It’s just a question about expanding its application in the future.

We are very good at detecting disease mutations these days. However, each mutation would require a specialized base editor, which could make the treatment expensive.

Do you have any thoughts on how to reduce the number of off-target edits?

Work around the world is focusing on this question. Some mutations in the base editors have already improved the ratio of on-target/off-target, but further experimentation will be required.

What mitochondrial diseases are the “low-hanging fruit” that might be cured or treated with gene editing?

There are basically two modalities of mtDNA gene editing: 1) mitochondrial nuclease. These cut specifically mutant mtDNA. Precision Biosciences is gearing up for clinical trials on the m.3243G mutation, targeting skeletal muscle. 2) Base editing, as reported in our publication. This maybe more appropriate for homoplasmic mutations, such as Leber hereditary optic neuropathy. These can be treated by AAV injection of the base editor gene into the eye.

How did you first get interested in studying mitochondria?

I have been studying mtDNA disease since my PhD, starting in 1987, at the time where the first mtDNA mutations in patients were described. 38 years and counting!

 

Reference

1Barrera-Paez JD, Bacman SR, Balla T, Van Booven D, Gannamedi DP, Stewart JB, Mok B, Liu DR, Lombard DB, Griswold AJ, Nedialkova DD, Moraes CT (2025) Correcting a pathogenic mitochondrial DNA mutation by base editing in mice. Science Translational Medicine 17: DOI: 10.1126/scitranslmed.adr0792.