Editing the mitochondrial genome

Scientists in Cambridge have developed a system to fix a class of devastating genetic diseases called mitochondrial enzyme defects. They occur when structures called mitochondria, which supply our cells with energy, don’t function properly. This happens because some of the mitochondria, which contain their own small piece of DNA, carry genetic changes or mutations that prevent them from working properly. Now there might be a way to fix the problem: Payam Gammage from the Medical Research Council’s Mitochondrial Biology Unit at Cambridge University has developed a gene editing system that knocks out selectively the defective mitochondria so they’re replaced by healthy working ones. Payam spoke to Katie Haylor...

Payam - Severe mitochondrial diseases are likely to result in the patient not often leaving the hospital, serious mobility problems, they’ll likely have cognitive difficulties requiring round the clock care most of the time. And life can really be very very difficult, and in slightly less severe cases being wheelchair bound and struggling to live an independent life.

We aimed to develop a system that would enable us to target the mutated mitochondrial DNA and take that percentage down from, say 90 percent mutated down to 50 percent mutated. Then hopefully, someone who did have the clinical disease no longer has it any more.

Katie - So you’re talking about editing someone’s genes?

Payam - We’re talking about selectively removing one entire subpopulation, yeah.

Katie - So how on earth do you do that?

Payam - We took some genome engineering tools, which had been developed in a different form for different purposes: zinc fingers - zinc finger nucleases to be precise. And what these things do is allow you to do is target specific portions of DNA and cut it. If you cut the mitochondrial genome it gets degraded, and so if you can selectively cut the versions of the mitochondrial genome that have a mutation. Then you selectively remove them from the total pool and so hopefully you change the percentage of mutated versus healthy.

We created these zinc fingers that would be specific to the mutation in this particular mouse that has a relatively mild form of mitochondrial disease, and it has a mutation which is very similar to a human mutation. We tested it in mouse cells to see if we could alter this ratio of mutated to unmutated and we put it into the mouse. So injecting into the bloodstream the genetic instructions for these zinc fingers using a harmless virus that’s been repurposed for this kind of thing, and this virus really really likes to be taken up by heart cells, predominantly. We measured the levels of healthy mitochondrial DNA versus mutant starting, from about 70 percent and going down to about 30/35.

Katie - So that’s well below the level at which people would show symptoms?

Payam - Yes, yes. Well below the threshold. Cells generally like to maintain a total number of mitochondrial DNA molecules, so say it’s a thousand. If we’ve removed say 20 percent of them or 30 percent of them,  what will happen is the remainder will be replicated. And so basically, every time you remove one molecule you’re increasing the chance that it will be replaced by a healthy one.

Katie - How far are you away from doing this in humans?

Payam - The beauty of this approach is that its generalisable. So every time we want to target a new mutation all we have to do is re-engineer the parts that bind DNA and then it’ll work. That will take us a certain period of time; a few months perhaps to design some new ones to human mutations and then to get ourselves into a position to be performing clinical trials in humans - that could take a little bit longer. We’re hoping to have something on the cards within the next year or so.

Katie - Are the mutations in people who suffer from mitochondrial disease different from each other and, if so, do you have to personalise this tool for every single person that you treat?

Payam - There is a pretty broad selection, yeah, of mitochondrial mutations that occur in humans and cause disease. But there are some real standout candidates that appear much more commonly than others; for example there’s one which counts for about 30 percent of all mitochondrial DNA mutations in humans. So there is definitely going to be a required level of re-engineering for different people in a personalised medicine kind of approach, but a good proportion of the population should be served by a handful of these therapies.

Katie - You’re just doing this with mitochondrial DNA, are there any risks to the nuclear DNA?

Payam - We can’t find any evidence of any activity of what we’ve developed in the nuclear genome. We took parts of the nuclear genome that looked very very similar to the area in the mitochondrial genome that we were targeting, and then we assessed the area around it to see if anything had changed, and in our experiments where we did this we found absolutely no changes.

In a world where you don’t have an effective treatment it’s a potential silver bullet. Obviously, there’s a lot of caveats that go with that and a lot of optimisation and careful testing and safety assurances. It potentially, is a very very big step change for people who suffer from these diseases.