Modeling Human Mitochondrial Diseases

In a paper published in Cell, a research group led by Agnel Sfeir at Memorial Sloan Kettering Cancer Center showed that gene editing can be used to engineer specific mtDNA mutations.

Mitochondria are unusual cell organelles in that they contain their own mitochondrial (mt)DNA, and like other DNA, mtDNA can develop mutations that result in diseases. Some mutations involve the deletion of parts of the coding sequences. Fortunately, cells typically have more than 1,000 mitochondria, and in many cases, a minimum number of healthy mitochondria are sufficient to avoid disease. Nevertheless, mitochondrial diseases can be highly debilitating.

Advances in genome engineering and editing (e.g., TALENS, CRISPR, zinc finger nucleases) have raised the possibility of reconstituting point mutations repairing defective mtDNA to curing the diseases. However, mtDNA deletions in human cells have been challenging. Recently, a research team at Memorial Sloan Kettering Cancer Center, led by Agnel Sfeir, succeeded in engineering mtDNA deletions with an innovative approach by expressing bacterial DNA end joining enzymes in human cells.

The Sfeir team developed a group of human cell lines with deletions to the mtDNA of varying extents (Fu et al., 2025). Cells with deletions in more than 75% of the mitochondria had affected mitochondrial function. With these cells, the team found two patterns of effects on nuclear genes. One was activated at the deletion threshold. The other was in response to increasing levels of mutations.

More importantly, this combination of tools facilitates modeling of disease-associated mtDNA deletions in different cell types. In addition, the panel of cell lines with the different levels of deletions will greatly benefit the research community and help in developing therapeutics.

A Discussion with Agnel Sfeir

What are the next steps in your research?

Our research focuses on elucidating the molecular pathways that govern the propagation versus elimination of mtDNA deletions. Understanding these mechanisms is crucial for identifying factors influencing mtDNA integrity and stability.

Additionally, we aim to investigate how cells, particularly neurons and muscle cells, respond to mtDNA deletions. These cell types are highly dependent on mitochondrial function and are disproportionately affected by mtDNA mutations, leading to severe pathologies. By studying their adaptive or maladaptive responses, we hope to uncover potential therapeutic targets that could mitigate the impact of mtDNA deletions in mitochondrial diseases.

You note that you can use this system to examine stem cells. It sounds like that is a great way to look at looks of cell types, especially muscle and brain. Maybe even iPS cells could be used.

Yes, that’s exactly what we are in the process of doing. IPS cells provide a powerful strategy for studying a wide range of cell types, including muscle and neuronal cells, which are particularly affected by mitochondrial dysfunction. By differentiating iPS cells into specific lineages, we can systematically investigate how mtDNA deletions impact various cell types and really model disease-relevant phenotypes. This approach also allows for high-throughput screening of potential therapeutic interventions in a controlled and physiologically relevant system.

The ability to switch the carbon source between galactose and glucose is a real advantage to your system.

Absolutely. The ability to switch between glucose and galactose as carbon sources is a key advantage of our system. Heteroplasmy refers to the proportion of mutated mtDNA within a cell, and when it surpasses 75%, cells typically exhibit severe respiratory defects and abnormal morphology. However, the RPE1 cells we used primarily rely on glycolysis, allowing them to proliferate normally in glucose-containing media—even with heteroplasmy levels exceeding 75%. The defect became evident only when glucose was replaced with galactose, forcing the cells to rely on oxidative phosphorylation. This metabolic shift was crucial in unmasking the mtDNA deletion-associated defects in galactose-containing media, whereas culturing cells in glucose allowed us to obtain cells with ~100% mtDNA deletion. In fact, to date, no cellular models of mtDNA deletions have been able to achieve near-homoplasmy.

You discuss the application of your method for the study of disease, but I assume it might also be used to explore mitochondrial regulation as well.

While our method is highly applicable to studying disease, it also provides a powerful tool for exploring mitochondrial regulation. By analyzing the dynamic behavior of intact and deleted mtDNA, we can gain valuable insights into key mitochondrial quality control mechanisms, such as mitophagy and selective replication. Specifically, our cellular system allows us to examine how cells manage mutant mtDNA through preferential degradation of dysfunctional mitochondria via mitophagy, or the selective replication of intact mitochondrial genomes. This, in turn, enables us to understand the mechanisms that maintain mitochondrial homeostasis under normal conditions and how they are altered in the presence of mtDNA deletions.

Moreover, our approach provides a window into the biochemical and metabolic adaptations that occur in response to mitochondrial stress. By assessing how cells adjust their energy metabolism, stress signaling pathways, and mitochondrial dynamics, we can uncover the requirements necessary for cellular survival and adaptation. This is particularly crucial for understanding the threshold at which mitochondrial dysfunction becomes pathological and identifying potential targets for therapeutic intervention.

Your work and that of others attempts to correct mutations in mtDNA. Are there any genetic diseases of mitochondria that involve genes in the host genome that are specific to mitochondria?

Nuclear-encoded mitochondrial genes play a crucial role in mitochondrial function, and their mutations can lead to severe disorders. Several mitochondrial diseases arise from mutations in nuclear-encoded genes that regulate mitochondrial DNA replication and transcription. For example, POLG mutations impair mtDNA replication, leading to disorders such as Alpers syndrome, and defects in TFAM reduce mtDNA copy number and transcription.

How did you get interested in mitochondria?

I am a chromosome biologist with a deep fascination for how cells repair DNA breaks to maintain genome integrity. During my training and early career, I focused on nuclear DNA repair pathways and how their deregulation contributes to cancer progression. However, after starting my lab, I felt the need for a new intellectual challenge—an opportunity to step outside my comfort zone and explore an entirely different aspect of biology (something I believe all scientists should do at least once in their careers).

mtDNA had always intrigued me, and I saw a unique opportunity to apply my expertise in nuclear DNA repair to studying this independent genome within a distinct organelle. To immerse myself in the field, I dedicated two months solely to reading the mtDNA literature, identifying key questions, outlining a research plan, and recruiting a student and a post-doc to pursue these challenges. Despite its unique regulatory mechanisms, mtDNA still adheres to fundamental principles of genome maintenance, making it an exciting system to study. Today, half of my lab is dedicated to studying mtDNA biology, and with every discovery we make our curiosity deepens. The same curiosity that led me to work on mtDNA in the first place continues to drive our research forward.

Reference

Fu Y, Land M, Cui R, Kavlashvili T, Kim M, Lieber T, Ryu KW, DeBitetto E, Masilionis I, Saha R, Takizawa M,  Baker D, Tigano M, Lareau CA, Reznik E, Sharma R, Chaligne R, Thompson CB, Pe’er D, Sfeir A (2025) Engineering mtDNA deletions by reconstituting end-joining in human mitochondria. Cell

https://www.sciencedirect.com/science/article/pii/S0092867425001941?dgcid=author

Fu et al. (2025) used nucleases and an end-joining procedure to produce mutations in mitochondrial (mt) DNA. The mitochondria were then introduced into cells, and cell lines were produced with different numbers of mutated mitochondria. The resulting cell lines provide excellent models for testing the effects of the mutated mtDNA in diseases.

In a paper published in Cell, the laboratory of Isha Jain at Gladstone Institutes showed that a small molecule inhibitor can control excess oxygen levels resulting from dysfunctional mitochondria. These results point to a potential new therapeutic strategy for mitochondrial diseases.

Oxygen is well-known to be critical for human life, but too much oxygen can be toxic. Thus, the balance between supply and demand is important. For most of us, that is no problem. However, that careful balance is disrupted in those with some mitochondrial diseases so that excess oxygen is a common feature. Leigh syndrome is the most common pediatric mitochondrial disease.

Since tissue hyperoxia is problematic in these patients, one might wonder if reducing the concentration of oxygen in tissues would be beneficial. A recent study from the laboratory of at Gladstone Institutes and the University of California, San Francisco showed just that. The team, led by Isha Jain, took advantage of mice with a knockout of the Ndufs4 gene (Blume et al., 2025). That mutation results in the loss of an important complex in the electron transport chain that mimics the disease, and these mice are often used as a model for experimentation.

They exposed the mice to a small molecule called HypoxyStat that induces hypoxia by causing oxygen to bind more tightly to hemoglobin, leading to decreased release of oxygen into tissues. Chronic exposure of the mice to the molecule normalized tissue hyperoxia and resulted in significantly longer lifespans in the mice.

Thus, these findings suggest that drugs, such as HypoxyStat, that lower effective oxygen levels might be a promising therapeutic strategy for these diseases in general. Of course, manipulating oxygen levels is challenging, but these results provide valuable insights into mitochondrial diseases.

A video, Science in Seconds, produced by Gladstone tells the story of Jain and her team’s breakthrough, as does an article, Daily Drug Captures Health Benefits of High-Altitude, Low-Oxygen Living, published by Gladstone on the findings.

An interview with Dr. Isha Jain

Do the benefits result from improved mitochondrial function or the reduction of excess oxygen in tissues or both?

Currently, I would say we have the strongest evidence that the benefit occurs due to the alleviation of tissue hyperoxia (excess oxygen) in tissues. Future work is needed to fully understand the mechanism.

You noted that you wanted to determine if you could generalize your results beyond the Ndufs4 mice. What do you see as the next steps in this research?

The next steps include testing whether this compound (or further optimized compounds) work in additional mitochondrial disorders and additionally affected tissues beyond the brain.

Mitochondria have been around for a very long time, and oxygen levels have fluctuated in our atmosphere. Does that mean that mitochondria have adapted to the available oxygen?

It is indeed puzzling that oxygen is both a substrate and a toxin for mitochondrial ATP production. It appears that we have evolved to exist in a very delicate balance of too little or too much oxygen.

The findings are intriguing, but controlling oxygen levels might be a challenge in patients. For example, are those with mitochondrial diseases, such as Leigh syndrome, affected by changes in altitude (e.g., Denver)?

There is anecdotal evidence that this might be the case. However, mitochondrial diseases are rare enough and the altitudes we are talking about are fairly high, so it is difficult to amass enough epidemiological data to make this claim definitively.

You mention pulmonary hypertension as a complication of using drugs, such as these. Are there other potential complications and ways around the problems?

The side effects are the same as living at altitude: things like pulmonary hypertension and increased blood viscosity. A gradual acclimation to the drug (dose escalation) will likely be needed. Many more safety studies are needed before this compound or related compounds can be used in patients.

What initially interested you in the study of mitochondria?

I am broadly interested in developing creative new therapies for metabolic disorders. Of course, mitochondria are where much of metabolism takes place.

Reference

Blume SY, Garg A, Martí-Mateos Y, Midha AD, Chew BTL, Lin B, Yu C, Dick R, Lee PS, Situ E, Sarwaikar R, Green E, Ramanan Y, Grotenbreg G, Hoek M, Sinz C, Jain IH (2025) HypoxyStat, a small-molecule form of hypoxia therapy that increases oxygen-hemoglobin affinity. Cell https://doi.org/10.1016/j.cell.2025.01.029.

Ryu KW, Fung TS, Baker DC, Saoi M, Park J, Febres-Aldana CA, Aly RG, Cui R, Sharma A, Fu Y, Jones OL. Cai X, Pasolli HA, Cross JR, Rudin CM, Thompson CB (2024) Cellular ATP demand creates metabolically distinct subpopulations of mitochondria. Nature 6: 1–9.

You see one; you’ve seen them all. That has been pretty much the view of mitochondria for some time. But maybe that isn’t the case after all. The laboratory of Craig Thompson reports that, under stress conditions, mitochondria assume different roles.  Dr. Thompson is the former president of Memorial Sloan Kettering Cancer Center and currently holds the Douglas A. Warner III Chair in the Cancer Biology and Genetics Program.

Dr. Thompson’s research team began their search with a careful rethinking of mitochondrial functions. While mitochondria have many key functions, they are best known for producing the energy that we all need from the food that we eat.  However, the Thompson lab was interested in the role of mitochondria in wound healing. Repairing tissue requires energy and also proteins, lipids, nucleic acids and other biomolecules. Thus, part of our food goes for the raw materials to synthesize new biomolecules to repair and/or maintain our tissues. They discovered that the amino acid proline is critical for wound healing and that the mitochondria are important for its synthesis.

With that discovery, they became curious about how the mitochondria balance their efforts to make energy and proline. As often happens in science, a few simple experiments conducted by changing the cell culture conditions left them with even more questions. The cells seemed to be able to both make energy and raw materials at the same time. How could that be?

To tackle that question, they exposed cells to 2 different sets of stresses. In one set cells were made to need more ATP, and in the other to need more proline. Surprisingly, when cells were deprived of proline, some of the mitochondria changed their morphology. They developed a series of filaments within the inner membrane that increase their ability to make proline and ornithine. When cells needed more ATP their mitochondria also separated into two distinct subpopulations. In fact, the two types of mitochondria could be differentiated by simple microscopy. The bonus finding was that an enzyme called pyroline-5-carboxylate synthase or P5CS was the key to how glutamate was used to yield the two types.

The separation of activities is closely related to the ability of mitochondria to fuse together and separate by fission. When the cell’s need for oxidative synthesis increases, P5CS is segregated into a subset of mitochondria that lack cristae and ATP synthase, the enzyme that makes ATP.

Thus, the mitochondria can easily rearrange themselves to focus on one process or the other. Interfering with the fission-fusion cycle inhibits their ability to specialize. This paper shows that mitochondrial fission and fusion are intimately involved in maintaining the balance between the need for energy and synthesis of biomolecules.

Reference

Ryu KW, Fung TS, Baker DC, Saoi M, Park J, Febres-Aldana CA, Aly RG, Cui R, Sharma A, Fu Y, Jones OL. Cai X, Pasolli HA, Cross JR, Rudin CM, Thompson CB (2024) Cellular ATP demand creates metabolically distinct subpopulations of mitochondria. Nature 6: 1–9.

According to the CDC, about 38 million Americans suffer from diabetes, and it is the fourth leading cause of death in the United States. More concerning is that the incidence of diabetes—especially type 2 (T2D) or adult-onset diabetes—is increasing.

Diabetes is caused by the inability of pancreatic b-cells to make or other cells to use insulin. An autoimmune process has long been suspected to be involved. Skeletal muscle and b-cells in patients with T2D have multiple morphological and functional defects.^1,2

Recently, a team of researchers at the University of Michigan explored this mitochondrial dysfunction and showed how it might be linked to diabetes.³ The team, led by Scott Soleimanpour, MD and Emily M. Walker, PhD, examined mitochondrial quality control that maintains appropriate mitochondrial function under stress conditions. More specifically, they looked at three pathways that lead to impairments in mitochondrial quality control: decreased mitoDNA levels, preventing elimination of damaged mitochondria, and inhibition of mitochondrial fusion. The initial experiments were done in mice, but the findings were repeated in human pancreatic islet cells.

Interestingly, the result was the same for all three pathways. In all cases, the stress response resulted in interference with the maturation of b-cells. Blocking the stress response allowed them to mature as normal. Thus, these insights suggest that blocking the stress response might be a beneficial therapeutic strategy.

A conversation with Dr. Walker.

T2D is linked to diet. Do your results offer any insight into that link?

In two of our models of impaired mitochondrial quality control, the animals were placed on a high-fat diet to model individuals eating a western-style diet. We saw a much stronger stress response and loss of b-cell maturity when the animals were on this diet. There are a lot of negative impacts for b-cells when they are required to produce more insulin to compensate for weight gain, and also, there are many studies showing that fatty acids themselves damage b-cells. In our study, the high-fat diet sped up the mitochondrial stress responses likely because of this increased damage due to the food they were eating.

Can you speculate on the nature of the signaling molecules that illicit the response?

Our study found that it was the integrated stress response that includes changes to signaling molecules, such as eIF2α, and a transcription factor called ATF4. Activation of this signaling pathway and these factors induced changes in the nucleus that changed what genes were expressed in both b-cells and liver cells. We saw increases in the stress response target genes and decreases in genes that help the cell to have mature function and identity.

Your results provide a window on the process of normal b-cell development. Do you have any thoughts on those mechanisms?

We know that b-cells need proper mitochondrial function to maintain cell maturity. We also know that, during differentiation of stem cells into b-cells, this doesn’t happen in a complete way. Other work in our lab is focused on how to improve mitochondrial function in stem cell-derived b-cells to help them mature better, and we’re just starting to figure out pathways that can help this happen.

The use of ISRIB to block the stress response is an intriguing result. Is that a viable possibility for a therapy? 

Clinical trials for next generation drugs related to ISRIB are being performed to treat different diseases, including ALS. Additionally, another group has investigated the benefits of ISRIB on reducing the immune cells involved in type 1 diabetes. We are interested in following up on potential positive effects of ISRIB, or newer versions of the drug, on islets from T2D donors.

What do you see as the next steps in this research?

Our next steps include what I mentioned above in relation to inhibiting the integrated stress response (with ISRIB or other drugs) and seeing if they positively affect T2D donor islets. We would also like to determine if our findings in liver are applicable to human disease, such as metabolic dysfunction-associated steatotic liver disease.

What interested you in mitochondria in the first place?

We grow up learning about how mitochondria are the “powerhouse of the cell,” but what is really fascinating is that mitochondria do a whole lot of other things in the cell besides just making energy. In this work, we’ve shown that they can actually signal to the nucleus and change the way the DNA is packaged to make certain genes turn off and on! Because metabolism is so important to a cell, it’s really interesting to figure out how exactly the mitochondria direct changes in ways far beyond energy production.

References

¹Flannick J, Mercader JM, Fuchsberger C, et al. (2019) Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls. Nature 570: 71–76.

²Lowell BB, Shulman GI (2005) Mitochondrial dysfunction and type 2 diabetes. Science 307: 384–387.

³Walker EM, Pearson GL, Lawlor N, et al. (2025) Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues. Science. DOI: 10.1126/science.adf2034

Lee RG, Rudler DL, Raven SA, et al. (2024) Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network. Nature Cell Biology 26: 57–71.

www.nature.com/articles/s41556-023-01297-4

To survive, cells rely on collections of organelles, such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, and more. Each has specific critical functions. However, they don’t work in isolation. They interact by communicating signals and exchanging materials in an orderly manner. Amazingly, little is known about how they interact.

The laboratory of Aleksandra Filipovska used an innovative strategy to explore the interrelationships of several key organelles with mitochondria. They first established cell lines that lacked genes specific for the production of peroxisomes, Golgi, and ER with mitochondria. Then they combined observations by scanning electron microscopy with multi-omics profiling to examine the RNAs, proteins, lipids, and glycogens that were affected by the perturbations. In this way, they could carefully examine how dysfunction in one organelle affected the mitochondria.

Because mitochondria influence so many cell activities, it wasn’t surprising that the researchers found effects in many systems. However, they found that lipid transfers were the most affected component. This very complete paper documents the many metabolic and morphological interactions within cells and provides insights into how they might be involved in diseases.

Questions for Dr. Filipovska

Congratulations on a tour-de-force paper! Your strategy here seems to be an interesting variation on the systems biology: eliminate one component and see what happens. Has anyone else tried this strategy?

Thank you! This specific strategy of genome-wide screening coupled with FIB-SEM imaging and quantification has not been tried previously, to the best of our knowledge. One of the reasons we decided to pursue this strategy was to get an unbiased account of inter-organelle interactions and changes as opposed to traditional targeted analyses.

Your calculations on the number of genes that might be involved in inter-organelle dysfunctions and diseases large enough to be concerning. How do you read that?  

We were quite surprised to see so many gene changes, and in addition to the genes reported in Lee et al., we have also analyzed many more that are involved in inter-organelle communication and metabolite exchanges. These numbers are starting to make a lot of sense to us now, given how many of these genes are involved in metabolic and biogenesis pathways that are shared across different organelles. For example, the glycerophospholipid pathway spans the endoplasmic reticulum, Golgi apparatus, mitochondria and peroxisomes. Systems biology methods are key to understanding changes across different organelles, providing a larger picture of metabolic processes and common dysfunctions that manifest in different diseases.

You gave a small hint about future experiments to look at tissues under different metabolic demands near the end of the Discussion. Could you expand on that a little?

We are particularly interested in understanding the tissue-specific defects in multi-systemic diseases, such as mitochondrial diseases where a common molecular defect can manifest in different pathologies depending on the affected tissue in a particular disease. This will enable us to design targeted therapeutics for specific organs. Our study also revealed that different molecular defects can cause mitochondrial dysfunction and that targeted treatments of mitochondrial dysfunction may help alleviate symptoms of other diseases that involve mitochondria.

How did you become interested in mitochondria in the first place?

As an undergraduate student, I became fascinated by the bacterial origin of mitochondria and how they retained a level of autonomy within eukaryotic cells, maintaining a very small genome that is essential for life. At the time, very little was known about the regulation of mitochondrial gene expression, despite the many diseases for which there were no cures or treatments that were caused by defects in the mitochondrial genome. I was inspired to understand how the small mitochondrial genome was regulated that could help identify much needed therapies for mitochondrial diseases that are devastating for the patients, often very young infants and children and their families. I started my career trying to modify the mitochondrial genome and find gene therapies, which of course at the time did not work, and the main reason for this was that there was so little known about the mitochondrial genome, transcriptome and proteome. My goal was to focus on understanding the regulation of the mitochondrial genome in my group to help us devise specific therapies for mitochondrial diseases.

Reference

Lee RG, Rudler DL, Raven SA, Peng L, Chopin A, Moh ES, McCubbin T, Siira SJ, Fagan SV, DeBono NJ, Stentenbach M, Brown J, Rackham FF, Li J, Simpson KJ, Marcellin E, Packer NH, Reid GE, Padman BS, Rackham O, Filipovska A (2024) Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network. Nature Cell Biology 26: 57–71.

www.nature.com/articles/s41556-023-01297-4

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.

The article “Jumping ‘Numts’ from Mitochondria Can Be Fast and Deadly” by Martin Picard, published online in Scientific American on January 3, 2025, sheds new light on a significant biological phenomenon with profound implications for both health and evolutionary biology.

Mitochondria have their own DNA, but over evolutionary time, they have transferred most of their genes to the host genome. Now research teams led by Martin Picard at Columbia University and Ryan Mills at the University of Michigan have found that this process is continuing to the present day, sometimes with profound implications for our health. ^{1, 2, 3}

Mitochondrial DNA (mtDNA) fragments, known as nuclear mitochondrial DNA segments (numts), integrate into the nuclear genome at a surprisingly high rate, approximately once every 4,000 births.⁴ This process, called numtogenesis, does not just occur in the distant evolutionary past but continues actively throughout an individual’s life, particularly in brain cells where it might accelerate aging and reduce lifespan.

The significance of this finding lies in its potential to alter our understanding of genetic stability and disease, and of mitochondria themselves. By inserting into critical parts of our genome, Numts disrupt gene function,⁴ potentially leading to conditions, such as cancer or neurodegenerative diseases. The research also suggests that stress can amplify this DNA transfer, highlighting a new pathway through which environmental factors impact genetic health.

This discovery emphasizes the dynamic interplay between mitochondrial and nuclear genomes. It also reveals another way that mitochondria influence our lives: by changing the genome of our cells. Perhaps most importantly, it demonstrates the need for further investigation into how these interactions shape human health and longevity.

An interview with Martin Picard

1. What made you begin your research into Numts?
   We reviewed the literature on the many ways in which mitochondria influence gene expression and cellular behaviors. This highlighted a plurality of mechanisms.⁵ One of them is the transfer of mtDNA pieces to the nucleus, which could destabilize the genome, a hallmark of aging. This process is known to occur on the scale of millennia. So the initial thought was that this might be a mechanism of aging, just like the activation of “retrotransposons” that already live in our genomes cause aging.⁶ What if mitochondria—and particularly defective mitochondria in primary mitochondrial diseases or acquired mitochondrial defects—spit out pieces of DNA that disrupt the nucleus as a mechanism to speed up evolution but, in the process, end up driving the aging process?
2. How did you or others isolate this phenomenon?
   We took a two-pronged approach. First, we used our Cellular Lifespan Study⁷ system where we can track the same cells over months in vitro, and we asked whether there were new Numts over this short time scale. The answer was a clear yes. It was particularly noted in cells that came from children with primary mitochondrial disorders, as predicted. Second, we had to check if this mattered to people: does it happen in the human body across a person’s lifetime? In blood, new Numts don’t accumulate. So we looked in the brains of about 1000 people who died of various causes. There, we found several new Numts that were “private” and unique to each person, meaning that there is almost no chance that they were inherited. So they must have arisen during a person’s lifetime.
3. If Numts are part of a larger process of the interaction between mtDNA and nuclear DNA, can you explain more about how the two genomes are designed how they interact with each other?
   The mitochondria shipped pieces of their genome to the nuclear genome during evolution, explaining how it went from a full bacterial genome initially (with hundreds of genes) to only 37 now in our mitochondria. So as a result, the two genomes encode mitochondrial proteins and must be functionally coupled to make well-functioning, specialized mitochondria⁸ in each cell type.
4. Where do you see the research going from here, and how many labs, institutes or companies are working on these issues?
   This study puts the process of Numt insertions,  called Numtptogenesis, on the list of mechanisms of aging and possibly other diseases. In the brain, we found that people with more Numts in the prefrontal cortex, especially, died earlier than people with fewer new Numts. So maybe they regulate how long or how healthy we can live. There are many labs working on Numtogenesis as an evolutionary mechanism, and maybe our findings provide a rationale to studying this process in non-immune cells to understand its relevance to health.
5. Clearly, this is a frontier. What do you expect we will know more about in a year?
   I hope we see researchers with whole-genome sequencing data on non-blood tissues explore and quantify the presence of Numts so we can see to what extent these results extend to other organs and health or disease phenotypes. For example, this may be relevant to mitochondrial diseases.

Comment by Alex Sercel

“The key advance of this work is measuring numtogenesis on a short timescale in tissue culture and in the somatic tissues of individuals over their lifespan instead of looking at the rate of Numt inheritance between generations. Genetic changes, such as Numts, are only observed in subsequent generations if they occur in the sperm or egg and are non-lethal to an individual’s progeny. Said differently, damaging numts are likely to be screened out by natural selection and are less likely to be seen in population-genetics studies.

“This work shows that Numts can occur more frequently than previously thought and may arise in all tissues of the body, specifically long-lived cells like neurons in the brain. The Numts that manifest in a person’s organs over the lifespan bear the potential to damage their cells and tissues because these genetic changes have not been subject to the selective pressures that filter out harmful mutations between generations,” Alex Sercel, PhD, MitoWorld’s Director of Scientific Affairs and a former Postdoctoral Scholar in the Picard Lab at Columbia University Irving Medical Center.

References

1. Xue L, Moreira JD, Smith KK, Fetterman JL (2023) The Mighty NUMT: Mitochondrial DNA flexing its code in the nuclear genome. Biomolecules 13(5):753. doi: 3390/biom13050753
2. Zhou W, Karan KR, Gu W, et al. (2024) Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts. PLoS Biol 22(8): e3002723.
   https://doi.org/10.1371/journal.pbio.3002723
3. Picard M (2025) Jumping ‘Numts’ from mitochondria can be fast and deadly. Scientific American.
   https://www.scientificamerican.com/article/jumping-numts-from-mitochondria-can-be-fast-and-deadly/
4. Wei W, Schon KR, Elgar G, et al.(2022) Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes. Nature 611: 105–114.
   https://doi.org/10.1038/s41586-022-05288-7
5. Picard M, Shirihai OS (2022) Mitochondrial signal transduction. Cell Metabolism 34: 1620–1653.
   https://doi.org/10.1016/j.cmet.2022.10.008
6. Gorbunova V, Seluanov A, Mita P et al.(2021) The role of retrotransposable elements in ageing and age-associated diseases. Nature 596: 43–53.
   https://doi.org/10.1038/s41586-021-03542-y
7. Sturm G, Monzel AS, Karan KR, et al.(2022) A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations. Sci Data 9: 751.
   https://doi.org/10.1038/s41597-022-01852-y
8. Monzel AS, Enríquez JA, Picard M (2023) Multifaceted mitochondria: moving mitochondrial science beyond function and dysfunction. Nat Metab5: 546–562.
   https://doi.org/10.1038/s42255-023-00783-1

Mitochondria have long been recognized for the production of energy within cells. But there is more than one type of energy. In a recent review, Jacobs et al. (2024)¹ described the results of their studies and that of others that show how mitochondria produce heat as well as chemical energy. Like many motors, mitochondria produce heat at the same time as performing ‘work’. Furthermore, they note that the heat produced by mitochondria might have been important in the evolution of eukaryotes and warm-blooded animals (e.g., birds, mammals).

Jacobs et al. used heat-sensitive dyes and fluorescent proteins to measure the temperature of mitochondria. They found that the temperature of the mitochondria was about 15°C higher than the environment.

They speculate that the heat energy had profound effects on life on Earth. First, eukaryotes resulted from an endosymbiotic relationship between a bacterium and another prokaryotic organism. The bacterium evolved into a mitochondrion. For some time, the assumption has been that the proto-mitochondrion provided additional chemical energy as ATP. However, Jacobs et al. point out that the most likely partner was an archaean that lived near a hydrothermal vent, as proposed originally by Dunn (2017)². By entering into a partnership, the proto-mitochondrion provided heat that allowed the hybrid organism to move away from the warm waters of the hydrothermal vent. The most compelling aspect is that the transfer of heat does not require the evolution of additional mechanisms for transfer that ATP does. Second, the heat from mitochondria might have allowed warm-blooded animals to evolve.

While still just a hypothesis, the involvement of heat in evolution is an intriguing possibility that suggests lots of additional experiments.

¹Jacobs HT, Rustin P, Bénit P, Davidi D, Terzioglu M (2024) Mitochondria: Great balls of fire. The FEBS Journal 291: 5327-5341. https://doi.org/10.1111/febs.17316

²Dunn CD (2017) Some liked it hot: A hypothesis regarding establishment of the proto-mitochondrial endosymbiont during eukaryogenesis. Journal of Molecular Evolution 85: 99-106. https://doi.org/10.1007/s00239-017-9809-5