The Mitochondrial Minefield of Three-Parent Babies

In September, reproductive endocrinologist John Zhang and his team at the New Hope Fertility Center in New York City captured the world’s attention when they announced the birth of a child to a mother carrying a fatal genetic defect. Using a technique called mitochondrial replacement therapy, the researchers combined DNA from two different women and one man to bypass the defect and produce a healthy baby boy — one with, quite literally, three biological parents. It was heralded as a stunning technological leap for in vitro fertilization, albeit one that the team was forced to perform in Mexico, because the technique has not yet been approved in the United States.

The boy was an astonishing gift for the birth mother. A mutation in the mitochondria in her eggs causes Leigh Syndrome, a progressive neurological disorder, and over a period of twenty years, that mutation was linked to four miscarriages and the eventual death of her two children. Mitochondria are the energy powerhouses inside our cells, and they carry their own DNA, separate from our nuclear genome. The procedure replaced defective mitochondrial DNA in the mother’s egg with healthy mitochondria from a donor woman’s egg, and the hybrid egg was then fertilized with the father’s sperm.

The technique is spreading quickly, including gaining official approval just two weeks ago by the Human Fertilization and Embryology Authority in the U.K. The move will allow clinics to apply for permission to carry out the treatment, with the first patients expected to be seen as early as next year.

But for all the accolades, the method also has some experts concerned — particularly after a landmark study published earlier this month in Nature. That analysis, led by Shoukhrat Mitalipov, head of the Center for Embryonic Cell and Gene Therapy at the Oregon Health and Science University in Portland, suggested that in roughly 15 percent of cases, mitochondrial replacement could fail and actually allow fatal defects to return, or even increase a child’s vulnerability to new ailments. The findings confirmed the suspicions of many researchers, and the conclusions drawn by Mitalipov and his team were unequivocal: The potential for conflicts between transplanted and original mitochondrial genomes is real, and more sophisticated matching of donor and recipient eggs — pairing mothers whose mitochondria share genetic similarities, for example — is needed to avoid potential tragedies.

“This study shows the potential as well as the risks of gene therapy in the germline,” Mitalipov says. “This is especially true of mitochondria, because its genome is so different than the nuclear genome.

“Slight variations between mitochondrial genomes,” he adds, “turn out to matter a great deal.”

A new study in the journal Nature suggests that in roughly 15 percent of cases, mitochondrial replacement could fail and actually allow fatal defects to return, or even increase a child’s vulnerability to new ailments.

The danger lies in the fact that mitochondria are in some ways like aliens inside our cells. Two billion years ago they were free-floating bacteria basking in the primordial soup. Then one such microbe merged with another free-floating bacterium, and over evolutionary time, the two formed a complete cell. The bacteria eventually evolved into mitochondria, migrating most of their genes to the nucleus and keeping just a few dozen, largely to help them produce energy.

Today, our nuclear genome contains around 20,000 genes, while a scant 37 genes reside in the mitochondria. And yet, the two genomes are intensely symbiotic: 99 percent of the proteins that mitochondria import are actually made in the nucleus.

Mitochondria also still divide and replicate like the bacteria they once were, and constant replication means that mutations arise 10 to 30 times more often than in nuclear genes. If too many mitochondria become dysfunctional, the entire cell suffers and serious health problems can result. Faulty mitochondria are implicated in genetic diseases, as well as many chronic conditions from infertility to cancer, cardiac disease and neurodegenerative diseases. That’s because when mitochondria falter, the bioenergetics of the cell itself is compromised.

A three-parent baby could solve the problem by overriding faulty mitochondria, but it also raises the stakes, because the procedure does not completely replace defective mitochondria with healthy ones. When the mother’s nucleus is transferred, it’s like a plant dug up out of ground — a bit of the original soil (in this case, the mother’s mitochondria) is still clinging to the roots. That creates a situation that never happens in nature: Two different mitochondrial genomes from two different women are forced to live inside the same cell. In most cases, a tiny percentage (usually less than 2 percent) of the diseased mitochondria remain — but that tiny percentage can really matter.

In his new study, Mitalipov crafted three-parent embryos from the eggs of three mothers carrying mutant mitochondrial DNA, and from the eggs of eleven healthy women. The embryos were then tweaked to become embryonic stem cells that could live forever and yet be multiplied and studied. (Embryonic stem cells can replicate indefinitely, and are pluripotent, meaning they are able to grow into each of the more than 200 cell types of the adult body.)

In three cases, the original maternal mitochondrial DNA in the embryonic stem cells returned.

“That original, maternal mitochondrial DNA took over,” Mitalipov says, “and it was pretty drastic. There was less than 1 percent of the original maternal mitochondrial DNA present after replacement with donor DNA and before fertilization, and yet it took over the whole cell later.” Mitalipov warns that this reversal might not only occur in the embryonic stem cells; it could also occur in the womb at some point during the development of a baby. Complicating things further, Mitalipov found that some mitochondrial DNA actually stimulates cells to divide more rapidly, which would mean that a subpopulation of cells containing maternal mitochondrial DNA could eventually dominate as the embryo developed.

What could cause a mere wisp of defective mitochondrial DNA to take over an entire cell, and kill off 99 percent of the new, healthy mitochondria? Some mitochondrial genomes replicate much faster than others, says University of California molecular biologist Patrick O’Farrell, who called the new research both impressive and in keeping with his own thinking on the matter.

He explains that a diseased genome could behave like a super-replicating “bully,” re-emerging and having a large impact on the three-parent baby at any time. “The diseased genome might stage a sneak comeback to afflict subsequent generations,” O’Farrell says. At the same time, he adds, such super-replicators could also act as “superheroes,” if they carry healthy, fit DNA that is able to out-compete a mutant genome.

Shoukhrat Mitalipov, head of the Center for Embryonic Cell and Gene Therapy at the Oregon Health and Science University in Portland, suggests that as with blood donations, the mitochondria of the mothers and donors ought to be matched. Visual: Oregon Health and Science University

Natural selection, of course, favors functional genes, but O’Farrell says the new nuclear genes donated by a father could also influence the behavior of the mitochondria in ways we cannot yet predict. For example, the father might introduce new genes that actually favor the replication rate of a defective bully genome, he said. Conversely, the father might introduce genes that help a “wimpy” healthy genome survive and thrive.

Mitalipov’s solution is to match the mitochondria of the mother and the donor, since not all mitochondria are alike. Our mitochondria, all over the earth, are in a sense a billion or more clones of their original mother, passed down in endless biblical begats from mother to child. Yet, even as clones, they have diverged over time into lineages with different characteristics. These are called haplotypes.

O’Farrell mentions blood types as a comparison. Just as you would not want to transfuse blood type A into someone with blood type B, you might not want to mix different lineages. And while he says he thinks the idea of matching lineages is brilliant, he suggests going a step further. “I say let’s … try to get a match with the dominating genome so that the defective genome will ultimately be completely displaced,” O’Farrell says.

In fact, he adds, the ideal would be to look for one superhero genome, the fastest replicator of all, that could displace any diseased genome.

To find out which branches are super replicators, O’Farrell hopes to collaborate with other laboratories and test the competitive strength of different haplotypes. For instance, his laboratory published work earlier this year showing that competition between closely related genomes tends to favor the most beneficial, while matchups between distantly related genomes favor super replicators with negative or even lethal consequences. There are, he says, at least ten major lineages that would be distinct enough to be highly relevant.

Mitalipov says that most of the time, matching haplotypes should ensure success. However, he cautions that even then, tiny differences in the region of the mitochondrial genome that codes for replication speed could cause an unexpected surprise. Even in mitochondria from the same haplotype, there could be a single change in a gene that could cause a conflict, he says.

In his study, Mitalipov zeroes in on the region that appears responsible for replication speed. In order to find out a mother’s haplotype, he says, full sequencing is necessary, and this region from the donor’s egg should also be looked at to be sure it matches the mother’s. Today, it costs a few hundred dollars to sequence a woman’s mitochondrial genome.

But battles between mitochondrial genomes are only one part of the emerging story. Some research suggests that nuclear genes can evolve to sync well with a mitochondrial haplotype, and that when the pairing is suddenly switched, health might be compromised. Research in fruit flies and in tiny sea creatures called copepods shows that when the “mitonuclear” partnership diverges too much, infertility and poor health can result. In some cases, however, the divergent pairs are above average and can actually lead to better health.

Swapping as little as 0.2 percent of mitochondrial DNA in laboratory animals “can have profound effects on the function of cells, organs, and even the whole organism, and these effects manifest late in life,” according to mitochondrial biologist Patrick Chinnery of the University of Cambridge, writing in the November issue of the New England Journal of Medicine. Mitalipov did not see any effect on the development of the embryos in the study, but he says “it is possible that miscommunication between certain combinations of nuclear and mitochondrial genomes may occur.”

Because of all these unknowns, a U.S. panel recommended last February that mitochondrial replacement therapy, if approved, implant only male embryos so that the human-altered mitochondrial germline would not be passed down through the generations. Most scientists approve of this advice, but biologist Damian Dowling of Monash University in Melbourne, Australia, has reservations about even this solution. His own research in fruit flies shows that males may actually be more vulnerable than females to impaired health from mitochondrial replacement. Since females pass on mitochondria, natural selection will help daughters sift out any mutations that might be harmful to them, and keep their nuclear and mitochondrial genes well matched. Males aren’t so lucky: If mutations don’t harm females but do harm males, the males may have to suffer impaired fertility and go to their graves earlier.

This is known as the “mother’s curse” — a term coined by geneticist Neil Gemmell of the University of Otago in New Zealand, to describe the biological baggage that mothers unwittingly pass down to their male babies.

The bottom line, according to biologist David Rand of Brown University, whose most recent research swapping mitochondrial genomes did not show males to be disadvantaged, is that when you swap mitochondria, the reaction is “highly unpredictable.” The child born might suffer more health and fertility problems, or might end up with superior fitness. We just don’t know.

And that’s why many experts are calling for caution even amid all the excitement following the three-parent Mexico trial — though there is reason to believe they aren’t being heard. A three-person baby has now been born in China, and two more may soon be born in Ukraine, according to Nature News. Dr. Zhang, meanwhile, continues to encourage potential patients in Mexico: “We have received interest both locally and abroad,” he told Undark, “and we invite people to learn more about the treatment.”

Doug Wallace, head of the Center for Mitochondrial and Epigenomic Medicine at the Children’s Hospital of Philadelphia, is among those calling for a more methodical approach to the technique, though he says he doesn’t think there’s any way to put the brakes on now. “I think what’s happened is we’re going to see more and more trials and some families are going to be exceedingly fortunate — and perhaps some will be an unfortunate part of the learning set,” Wallace adds.

Research on mitochondria has to catch up now, Wallace says, and he adds that while matching haplotypes is a good idea, it isn’t so easy to do in practice. “Finding women to be egg donors is going to be a major limitation,” he says — and you’d first have to survey a large group to find out what mitochondrial DNA they are carrying.

Still, for women desperate to conceive, this may seem reasonable, and Wallace adds that mitochondrial replacement therapy might well find receptive patients even outside those seeking to avoid fatal genetic mutations — including among older women simply facing reduced fertility. “There’s no proof that’s the case,” he says, but if in fact it is true, then we’re looking at a therapy that might change the DNA of tens of thousands, maybe hundreds of thousands of babies conceived by this method.

That would have a real impact on the long-term future of society, Wallace adds, and we don’t yet fully understand all of the implications.

“I think it’s an exciting possibility,” he says, “but also a little disconcerting.”

Jill Neimark is an award-winning science journalist and an author of adult and children’s books. Her most recent book is “The Hugging Tree: A Story About Resilience.”

CORRECTION: An earlier version of this article incorrectly referred to a variety of sea creature that has been used to study the impacts of mitochondrial replacement. They are copepods, not cephalopods.