Japanese scientists have engineered enzymes that can precisely increase or decrease mutated mitochondrial DNA in human stem cells, paving the way for both better disease models and potential therapies for debilitating conditions like MELAS syndrome.
Key Points at a Glance
- New enzyme tools enable precise editing of mitochondrial DNA mutation levels
- Allows creation of stem cell models with custom heteroplasmy ratios
- Supports research into MELAS syndrome and other mitochondrial diseases
- May lead to future therapies to reduce harmful mtDNA mutations in patients
- Technology uses optimized mpTALENs for safe, targeted manipulation
Mitochondria—often called the “powerhouses” of the cell—house their own unique DNA, which, when mutated, can cause a range of serious, often incurable diseases. Until now, the difficulty of precisely manipulating mitochondrial DNA (mtDNA) has severely limited our ability to model these disorders in the lab or develop targeted treatments. But researchers at Fujita Health University in Japan have changed that narrative with a breakthrough tool that enables scientists to finely tune the ratio of mutated to healthy mtDNA inside living cells.
Mitochondrial diseases affect roughly 1 in 5,000 people globally, producing symptoms that range from muscle fatigue to stroke-like episodes. A notorious mutation known as m.3243A>G is linked to MELAS syndrome (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes), as well as forms of diabetes. These conditions are notoriously hard to study because affected cells typically contain a mix of normal and mutated mtDNA—a phenomenon known as heteroplasmy. The severity of the disease often correlates with the proportion of mutated mtDNA, but until now, there has been no reliable method to control that ratio in laboratory settings.
The team, led by Dr. Naoki Yahata from the Department of Developmental Biology at Fujita Health University, has developed a novel mitochondrial-targeted genome-editing platform using specially engineered enzymes called mpTALENs—platinum transcription activator-like effector nucleases. These tools can selectively recognize and cleave specific sequences of mtDNA, allowing researchers to either increase or decrease the mutation load with precision.
To test their system, the scientists used induced pluripotent stem cells (iPSCs) derived from patients carrying the m.3243A>G mutation. They then applied two different versions of their optimized mpTALENs: one targeting the mutant mtDNA for destruction, and another that reduced the proportion of normal mtDNA—effectively allowing for “dialing up” or “dialing down” the mutation load. The result was a library of otherwise identical stem cells with heteroplasmy levels ranging from as low as 11% to as high as 97%.
What makes this development especially powerful is that the edited cells retained their ability to differentiate into various tissue types, enabling accurate modeling of how mitochondrial mutations behave in different organ systems. This is critical for studying diseases like MELAS, which can affect the brain, muscles, pancreas, and more.
Moreover, the engineering behind the system is as elegant as it is effective. The mpTALENs incorporate novel repeat-variable di-residues and obligate heterodimeric FokI nuclease domains to maximize DNA cutting specificity while minimizing the risk of off-target damage. Combined with metabolic conditioning techniques, such as uridine supplementation, the researchers were able to stabilize even those cell lines with high mutation loads—often difficult to maintain under normal lab conditions.
This bi-directional control over heteroplasmy represents a scientific milestone. “Our study is the first to demonstrate an increase in the proportion of pathogenic mutant mtDNA by programmable nuclease,” noted Dr. Yahata. “Our optimized mpTALENs created a useful tool for altering heteroplasmy levels in patient-derived iPSCs, improving their potential for studying mutation pathology.”
Beyond basic science, the therapeutic implications are profound. Many mitochondrial disorders remain untreatable because there is no way to selectively remove or reduce the burden of mutant mtDNA. This new technology offers a conceptual pathway toward that goal—either by editing stem cells for transplantation or developing in vivo systems to directly target mitochondrial mutations in patients.
Importantly, the approach is modular. While this study focused on m.3243A>G, the mpTALEN platform can be adapted to target other disease-causing mutations within mtDNA. This opens the door to tailored interventions across a spectrum of mitochondrial conditions, potentially transforming how we understand and treat these elusive diseases.
“Our proposed method could be adapted for other mutant mtDNAs,” concludes Dr. Yahata, “and may contribute to understanding their associated pathologies and developing new treatments, potentially benefiting patients with various forms of mitochondrial disease.”
Source: Fujita Health University
