Genetic Revolution: Human Mitochondrial DNA Successfully Edited For The First Time

Scientists have managed, for the first time, to correct mutations in the DNA of mitochondria, structures that produce energy in cells, using a precise and safe gene editing technique. This innovation could pave the way for treating serious inherited diseases that until now had no cure, such as neurological and metabolic disorders. The method uses RNA and nanoparticles to deliver the "correction" efficiently, with few side effects. It is a promising advance towards future genetic therapies for mitochondrial diseases.

Mitochondria are structures present inside almost all cells in our body, with the exception of red blood cells, and function as true power plants, transforming nutrients into fuel to keep cells and organs functioning.

Unlike the rest of the cell, they have their own DNA, mitochondrial DNA (mtDNA), which is inherited exclusively from the mother. Mutations in this genetic material can lead to serious diseases, such as metabolic and neurological syndromes, in addition to being associated with aging and certain types of cancer. These disorders compromise the ability to produce and distribute energy.

With less energy available, important cells can be damaged or die, which affects the functioning of entire organs. Regions that need the most energy, such as the brain, muscles, nerves and heart, are the most affected, leading to symptoms such as muscle weakness, motor difficulties, heart problems, seizures, constipation and vision loss.

These diseases are hereditary, transmitted by the mother, and although rare, with an estimated rate of 12.5 cases per 100,000 adults worldwide, they are usually serious.

Among the best-known variants are Leigh Syndrome, which affects the central nervous system and usually appears in the first years of life; Leber Hereditary Optic Neuropathy, which causes sudden loss of vision in youth; and Mitochondrial Myopathy, which mainly affects muscles and nerves, affecting various parts of the body.

Little Indi Gregory, who died of an incurable mitochondrial disease after being turned off her life support, has been authorized by English judges.

Despite advances in gene editing, such as CRISPR/Cas9, treating these diseases has remained a challenge, as these tools cannot access the DNA inside mitochondria. However, a new technology is changing this scenario: mitochondrial base editing.

Researchers at the University Medical Center Utrecht in the Netherlands have demonstrated the promising use of a novel technique called DdCBE, a cytosine base editor derived from a bacterial toxin. This tool allows the precise alteration of a specific “letter” of mitochondrial DNA (in this case, the base cytosine, converted to thymine) without the need to cut the DNA, making the process safer.

The scientists used DdCBE to introduce a mutation into the DNA of human liver organoids (small models of livers grown in the laboratory), deliberately reducing energy production. This intervention generated varying degrees of mutation in the cells, which allowed the researchers to study in more depth how different levels of mutation affect mitochondrial function.

Differences between DNA in the cell nucleus and mitochondrial DNA (mtDNA). Source: FISH chromosomes © Applied Imaging, UK; all text material © 2005 by Steven M. Carr

In addition to creating disease models, the researchers have also shown that it is possible to correct real mutations in human cells derived from patients. Using the same tool, they successfully corrected a specific mutation (m.4291T>C) in skin cells from a patient with a syndrome associated with mitochondrial dysfunction.

The correction restored the ability of mitochondria to maintain their basic energy function, a sign that the cell was once again operating normally in this regard.

To bring the application of this technology closer to clinical reality, scientists tested different ways of delivering gene editors to cells.

They found that sending the editors in the form of messenger RNA (mRNA) wrapped in lipid nanoparticles (a type of fat capsule also used in RNA vaccines, such as those for COVID-19) was more efficient and less toxic than previous DNA-based methods.

This delivery method not only preserved cell viability, but also resulted in more precise and specific edits, with minimal unwanted side effects.

This approach represents a major breakthrough because, until now, studies of mitochondrial editing in humans have been limited to introducing mutations for research purposes, often using viruses as a vector. In this new study, the functional correction of real mutations in primary adult human cells was successfully demonstrated, something unprecedented and crucial to transforming the technique into a real treatment for patients.

In short, the researchers have not only shown that it is possible to create accurate models of mitochondrial diseases in the laboratory, but they have also taken the first concrete steps towards personalized mitochondrial gene therapy.

They have managed to repair mutations in real human cells, with a safe and promising approach. Although more testing is still needed before these techniques are available in clinics, the study represents a light at the end of the tunnel for people affected by mitochondrial diseases who, until now, had no effective therapeutic options.

READ MORE:

Correction of pathogenic mitochondrial DNA in patient-derived disease models using mitochondrial base editors

Indi P. Joore, Sawsan Shehata, Irena Muffels, Jose Castro-Alpízar, Elena Jiménez-Curiel, Emilia Nagyova, Natacha Levy, Ziqin Tang, Kimberly Smit, Wilbert P. Vermeij, Richard Rodenburg, Raymond Schiffelers, Edward E.S. Nieuwenhuis,

Peter M. van Hasselt, Sabine A. Fuchs, and Martijn A. J. Koppens  

PLoS Biol 23(6): e3003207.

https://doi.org/10.1371/journal.pbio.3003207

Abstract: 

Mutations in the mitochondrial genome can cause maternally inherited diseases, cancer, and aging-related conditions. Recent technological progress now enables the creation and correction of mutations in the mitochondrial genome, but it remains relatively unknown how patients with primary mitochondrial disease can benefit from this technology. Here, we demonstrate the potential of the double-stranded DNA deaminase toxin A-derived cytosine base editor (DdCBE) to develop disease models and therapeutic strategies for mitochondrial disease in primary human cells. Introduction of the m.15150G > A mutation in liver organoids resulted in organoid lines with varying degrees of heteroplasmy and correspondingly reduced ATP production, providing a unique model to study functional consequences of different levels of heteroplasmy of this mutation. Correction of the m.4291T > C mutation in patient-derived fibroblasts restored mitochondrial membrane potential. DdCBE generated sustainable edits with high specificity and product purity. To prepare for clinical application, we found that mRNA-mediated mitochondrial base editing resulted in increased efficiency and cellular viability compared to DNA-mediated editing. Moreover, we showed efficient delivery of the mRNA mitochondrial base editors using lipid nanoparticles, which is currently the most advanced non-viral in vivo delivery system for gene products. Our study thus demonstrates the potential of mitochondrial base editing to not only generate unique in vitro models to study these diseases, but also to functionally correct mitochondrial mutations in patient-derived cells for future therapeutic purposes.