Editing the human genome could one day help to heal serious hereditary diseases – initial approaches have already been made. But one component of the genome was largely left out: the DNA of the mitochondria. Now, for the first time, a research team has developed a tool that can also convert the DNA base adenine into the base guanine in mitochondrial DNA. After all, such a correction could repair 39 of the 90 known disease-causing mutations in the mitochondrial genome – this opens up new approaches for research and therapies.
Even changing a single “letter” in the base code of our genome can, in extreme cases, lead to serious, sometimes even fatal diseases. So far, most of these diseases are not curable. Only with the development of new gene editing technologies such as the CRISPR/Cas9 gene scissors are possibilities of gene therapy for such diseases within reach. However, these tools for exchanging individual DNA bases or entire gene sections only work with the DNA in our cells’ nucleus. They are not suitable for the genome of the mitochondria, the “power plants” of the cells, because they usually cannot penetrate the mitochondria. As a result, there has been a lack of approaches to treat diseases caused by mutations in mitochondrial DNA. After all, about one person in 5000 is affected by such a mostly hereditary mitochondrial disease and these diseases can also cause severe suffering and even be fatal.
Three molecular tools combined
So far, however, there are only a few ways to repair genetic defects in the mitochondrial DNA. It was only in 2020 that US researchers first developed a molecular tool that can convert the DNA base cytosine in mitochondrial DNA into the DNA base thymine. However, because this editing technique is only effective for some of the misplaced cytosine bases, the medical effect is limited: Even if this editing tool is ready for clinical use, it will only be able to repair nine of around 90 known mitochondrial mutations. “We therefore looked for ways to overcome this limitation,” explains lead author Sung-Ik Cho from the Institute for Basic Research in Daejeon, South Korea.
By combining three different molecular components, Cho’s team succeeded in developing an editing tool that can now also convert the DNA base adenine into guanine in the mitochondrial genome. On the one hand, it consists of a variant of the cytosine deaminase already developed by the US team, which is combined with a so-called Transcription Activator-like Effector (TALE), which can specifically recognize and control a section of the mitochondrial DNA. The third component is TadA8e, an adenine deaminase that promotes the conversion of adenine into guanine. Through tests with human cell lines, the team was able to optimize the combination to such an extent that this gene tool replaces up to 49 percent of the faulty adenine bases in the mitochondria of the test cells with the correct guanine base. In the tests, the editing tool also proved not to be cell-damaging and there was no destabilization of the mitochondrial DNA.
Correction of 39 of the 90 pathogenic mutations possible
“Our new TALED platform dramatically expands the possibilities of mitochondrial genome editing,” says Cho. Because with this base exchange, a further 39 of the 90 pathogenic mutations can now be corrected. “This could make a major contribution to creating new disease models and also to developing a therapy,” says the researcher. Up until now, research into the treatment of mitochondrial diseases has also been hampered by the fact that it has not previously been possible to replicate the mutations that occur in patients in animal models – because genome editing is normally required for this as well. “In the long term, TALEDs could pave the way to correcting disease-causing mutations in mitochondrial DNA in embryos, fetuses, newborns, or adult patients, ushering in a new era of mitochondrial gene therapy,” write Cho and his team.
However, before the new genetic tool can be used in animals or even humans, a lot of research and optimization is still necessary, as the researchers also admit. Because the effectiveness and also the specificity of the base exchange still have to be significantly increased. Admittedly, when the method was used on human cells, no undesirable base conversions – so-called off-target effects – occurred in the nuclear DNA of the cells. In the mitochondrial DNA of the treated cells, however, there was a two- to four-fold increase in the proportion of undesired conversions, the team reports.
Source: Sung-Ik Cho (Institute for Basic Science, Daejeon) et al., Cell, doi: 10.1016/j.cell.2022.03.039