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A family on the frontier of hyper-personalized medicine

Google programmer Mehmet Kuzu talked scientists and funders into treating his daughter’s rare genetic disorder with a novel, customized antisense drug

March 11, 2020

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Three-year-old Ipek Kuzu has an extremely rare genetic mutation that disrupts a protein needed for DNA repair, causing the loss of brain cells. Now she’s become only the second person in the world to receive a customized “antisense oligonucleotide” drug designed to compensate for the DNA mistake by allowing her cells to splice together a functional version of the protein. The drug took Boston-based pediatrician and geneticist Tim Yu only months to create, heralding a new era of individualized genomic medicine. But it cost $2 million to manufacture and test—leading to questions about how soon “hyper-personalized” treatments for rare genetic disorders can be made accessible and affordable. Journalist Erika Check Hayden got to know the Kuzu family, and in this episode she chronicles Ipek’s journey, with help from Ipek’s father Mehmet and Technology Review biomedicine editor Antonio Regalado.

Show notes and links:

If DNA is like software, can we just fix the code?, from the March/April 2020 print issue, p. 46

Hyper-personalized medicine, from the March/April 2020 print issue, p. 18

Two sick children and a $1.5 million bill: One family's race for a gene therapy cure, from the November/December 2018 print issue, October 23, 2018

Episode Transcript

Audio ID: This is MIT Technology Review.

Mehmet Kuzu: Around five to six months, they said she has something called ataxia telangectasia. And they said this doesn’t have any cure. The initial days were very tough. We were crying all the time. So then after a while, we started investigating what can be done.

Wade Roush: Mehmet Kuzu’s three-year-old daughter, Ipek, has a rare genetic mutation that could end her life by age 25. But now she’s getting a so-called antisense drug that her doctors engineered specifically for her. Which makes Ipek one of the first patients being swept up in a new wave of hyperpersonalized medicine. Journalist Erika Check Hayden wrote about the Kuzu family in the latest issue of Technology Review. And today, she helps us understand where this breakthrough came from, and how soon it might be scaled up. I’m Wade Roush, and this is Deep Tech.

[Theme music]

We’re right at the beginning of a revolution in individualized genomic medicine. And if you want to know what that revolution sounds like, this is a good place to start.

[Sound of Illumina sequencing machines]

That’s one of the hundreds of high-speed gene sequencing machines at the Broad Institute of MIT and Harvard. Here at the Broad’s genomics platform in Cambridge there are so many of these machines that the institute can read the equivalent of 30 whole human genomes every 10 minutes.

There aren’t a lot of research centers with that kind of power. But in many places around the world it’s now possible to scan a baby’s full genome for just a few hundred dollars, and locate DNA coding errors that can cause rare conditions like ataxia telangectasia.

That’s how doctors diagnosed Ipek Kuzu when she was just six months old. The mistake in her DNA means her cells can’t make a protein called ATM that’s essential for DNA repair. Over the long run that causes the loss of brain cells, which means Ipek has some trouble walking and doesn’t talk as much as a typical three-year-old.

Today Ipek is receiving an antisense drug made just for her. It’s designed to compensate for the DNA mistake and restore production of ATM. Which makes her only the second person in the world to get this kind of treatment. The first was another little girl named Mila Makovec. She has different genetic disorder called Batten disease that causes blindness, seizures, and other neurodegenerative problems. And Mila got her own customized antisense drug starting in 2018.

But to understand how her doctors came up with these two medicines,  and why this whole field of hyperpersonalized medicine is so hot that the editors of Technology Review decided to put it on this year’s list of 10 breakthrough technologies, we first have to jump back a few years, to 2016.

[CNBC Squawk Box news clip]

CNBC male anchor: Ionis Pharmaceuticals, in pre-market trading, is higher. The FDA has approved a drug called Spinraza. Spinraza.

CNBC female anchor: It’s not Spine-raza?

CNBC male anchor: Maybe it is. Because it’s for spinal muscular atrophy. It’s the first drug approved to treat the rare and fatal disease.

Wade Roush: Spinal muscular atrophy affects about 1 in 10,000 babies. So it’s not nearly as rare as Batten Disease or ataxia telangectasia. But Spinraza is literally the key to all of the more recent work to make customized antisense drugs for Mila and Ipek. So let’s take a minute to go over how it works.

What made Spinraza a big deal is that it was one of the first successful medicines made using an antisense oligonucleotide. In other words, a customized strand of RNA.

Antonio Regalado: If you can imagine, inside a cell, there's the DNA.

Wade Roush: This is Antonio Regalado, the editor for biomedicine at Technology Review.

Antonio Regalado: And it kind of sends out these messages into the nucleus made of RNA and those are used as the templates to make proteins. And so antisense is a drug that acts at the level of RNA. They're going to stick to that RNA message and they could block it.

Wade Roush: Keep it from being translated.

Antonio Regalado: Keep it from being translated, or modify the translation in some fashion.

Wade Roush: In the cells of healthy people, there’s a protein called SMN that helps motor neurons survive and grow. A gene called SMN1 carries the instructions for making that protein, and people with spinal muscular atrophy have a mutation that disables that gene. But it just so happens that human DNA also contains a second copy of the gene, called SMN2. This second copy is typically inactive, thanks to a small error that keeps the RNA message from being spliced together into a proper template. The Spinraza molecule contains a short segment of antisense RNA that prevents the splicing error. And that allows the body to start making the motor neuron protein.

Ionis Pharmaceuticals is the company that makes Spinraza, and they put a lot of work into figuring out how to get their molecule into cells in the brain and the nervous system, where it can do its work.

Antonio Regalado: And they finally mastered it and came up with pretty much kind of a miracle drug for one of these rare brain diseases that affects kids, spinal muscular atrophy. And so from that example, people then said, well, why can't we use antisense for other diseases that are similar?

And what we learned was that there was a doctor in Boston named Timothy Yu, who was an expert in sequencing genomes of sick children. And there was one girl named Mila Makovec. And her parents had come to him. He'd sequenced the genome. And then he just realized, ‘I don't have to stop here. Once I've identified this defect, I don't have to stop. I could potentially make a drug.’ And so that's exactly what he did.

Wade Roush: It turned out that Mila’s disease was caused by a splicing error very similar to the one that causes spinal muscular atrophy, except that in Mila’s case it disrupts a different protein called CLN7. Tim Yu’s idea was to take the backbone of the Spinraza molecule and attach a customized strand of antisense RNA. With this new business end, so to speak, the drug would enable Mila’s cells to start making functional copies of the CLN7 protein.

Antonio Regalado: That was probably at that point just the clearest, starkest, most stunning example of this hyper personalized medicine. Because in this case, it was really for one person. So we were very interested in this phenomenon, because it's a reflection of what technology can do. And then in the middle of last year, a pretty prominent journalist, Erika Check Hayden, came to us and she was also interested and wanted to do some work to find the cases, find the families and write more stories about it. And as it developed, we decided, well, let's put this on our list of breakthrough technologies, because it really is. And so Erika ended up writing the piece and she did a lot of work to find the patients. One of the great things she did was to find this Kuzu family, which happens to be right here in Cambridge.

Wade Roush: Erika, could you introduce yourself and tell us a little bit about you?

Erika Check Hayden: Sure. My name is Erika Check Hayden. I'm a journalist based in San Francisco. And I also run the science communication program at the University of California, Santa Cruz.

Wade Roush: When you set out to start reporting this piece, did you feel like it was important to go beyond the first sort of headline-making case of Mila Makovec and look for additional patients who were going through this process to see how broadly applicable the whole idea is?

Erika Check Hayden: I do think that while people have been very impressed by Mila's case and by the drug that Tim Yu made for her, which is called milasen, I think there's also been this question of are we gonna be able to do this for other patients? And if so, you know, who is going to be treatable via this method? And so if I'm going out and finding other families that are hopefully replicating that success, I think is a really important statement about how impactful this approach might eventually be.

Wade Roush: So this is where the Kuzu family comes in. So could you tell us a little bit about them and how you got in touch with them?

Erika Check Hayden: So the Kuzu family, they originally came from Turkey and the father in the family, Mehmet Kuzu, is now a software engineer at Google. And they were living in Silicon Valley when their daughter Ipek was born. And soon after she was born, she was diagnosed with this disease called ataxia telangectasia, which is also called A-T disease. And when that happened, they set about trying to understand if there was anything they could do to treat the disease or slow the disease. And that's what led Mehmet down this path that eventually led him to work with Tim Yu.

Mehmet Kuzu: I sent the genetic report of our daughter. Then he said, oh, there's a potential here, but there are two main problems. He said this might cost around like two million, and the insurance will not cover it. The second problem, it might cause damage because, we have a theoretical idea, but biology is complicated. So at the end of the day, it might be worse than what is expected.

Wade Roush: Right. So for the Kuzu family, while it was obviously bad news that your kid is getting diagnosed with A-T disease, there is this amazing foundation or non-profit led by Brag Margus, the A-T Children's Project, that has all this data and also apparently has some fundraising clout. And they wind up helping to finance a lot of this research and even finance Ipek’s treatment.

Erika Check Hayden: Right. And I think that's part of why this particular project was able to move so fast, because Brad Margus and the A-T Children's Project had done a lot of work over the years to fundraise and educate their community about the potential for treating this disease, so that when they found something that he actually thought could work, they were able to raise $1.4 million in a relatively short amount of time to fund the development of this unique drug.

Mehmet Kuzu: I think he understood to the promise of it. And then he agreed to financially support us. But the problem is this money in the pool is coming from many families. So we should have a fair selection. Then they found three kids that young in age, like three, two, two, three, four, with the right mutation type, and they got skin samples from all of them, and tested it. They were able to do it quickly.

Wade Roush: Mehmet can recount all these events pretty calmly. But I think it’s worth underscoring what a roller coaster the family’s been on. The backing of the AT Children’s Project opened a window for Tim Yu to design and manufacture an antisense drug. But the required safety testing is so expensive that only there was only enough money to do that for one patient. There was a two in three chance that Ipek would not be that patient. And even if she did get selected, there was no way to know whether the treatment would be effective. Mila Makovec had been having fewer seizures since she started getting her antisense treatment, but doctors still weren’t 100 percent sure that it was because of the medicine.  On top of all that, there was still the risk of unintended side effects.

Mehmet Kuzu: and then at the end of the day, Ipek’s cells responded the best among these three candidates. Now, once we know we are selected, now we concentrate on second issue: do we really want to take this risk of, like, making things worse? And then I thought, like, most probably something good will happen. Of course there is a probability of, a possibility [of failure]. But imagine if that happens: science will learn from this. And her kind of sacrifice, and that would help, too, many other people.

Erika Check Hayden: It's been just incredible over the past few years to meet these families, understand what they're doing, how they're doing it. I've just been really struck by everything they've been able to accomplish. And also the mindset that they bring to this where, you know, you'll talk to, or I will talk to, parents who are doing this for their kids and they've had scientists tell them, 'You've got to be prepared for the possibility that this isn't going to help your kid. You know, you might be doing all of this work on behalf of some other future child. This might not come in time to help your own child.' And they persist and are really driven.

Wade Roush: Ok. So in the same way that Tim Yu helped to create this unique drug called milasen for Mila Makovec, he's created a drug called atipeksen for Ipek. If that drug if that drug works, how will it help Ipek?

Erika Check Hayden: If this drug works, basically what it's going to do is correct the way that Ipek's cells interpret her genetic information so that she will make a functioning copy of the ATM protein. Now, how we will know if this is working is a bit of a tricky question. So, Tim Yu and other doctors are going to try a variety of methods to see if they can tell whether the drug is actually helping her. So, for instance, they will look at things like can they see evidence in Ipek's body that the drug is actually making corrected versions of the protein? They will look for evidence that she isn't declining in the ways that we might expect her to if she wasn't getting treatment to help control her disease. But it might be tricky to tell whether it actually works or not.

Mehmet Kuzu: She had three injections until this point because they are starting with very low dose and escalating it…And fortunately, we haven't seen any adverse effects in the first three. But like, of course, knowing if this is really working or not, they told us that it will take time. Maybe we need a year to understand if it's really working. But at least we have seen that no bad thing happened. At hospital she's going on the full anesthesia. They're putting on a mask. And after the injection they are taking bloods every four hours, three or four times. These are very stressful for her. She's fighting not to have this mask. She's crying a lot. Uh, but once discharge happens, once we come home, she forgets about everything. She just plays with her toys.

Wade Roush: Right. And this is one of the things you mentioned in your piece. Not only will it be tricky to see whether it's working or not, but we're talking about by definition an n of one study where there's only one patient. So you don't get the kinds of large numbers that help researchers feel more confident that a drug is safe and effective.

Erika Check Hayden: I think what we still don't know very well yet is which diseases are going to be helped most by this approach, or even if any of these individual customized treatments can cure a patient. So if you talk to Mila's mom, Julia Vitarello, she is very convinced that that drug has helped Mila. But I think accumulating that data to the level where we really know that this is a worthwhile approach, you know, that's probably going to take a while.

And to take a step back, I think that's part of the reason why these drugs are only being used right now in patients that have really severe progressive diseases, because you are taking a certain risk by giving a treatment to a patient when you haven't done the kinds of safety testing that we might be used to for a drug that would normally go through an FDA approval process. In fact, there are some people who object to even using the word treatment because we don't necessarily know that these drugs are going to cure the patients.

So in the meantime, I think everybody would like to see far more patients at least be able to try this. And so there's this question as to whether it's only going to be patients who have the resources to raise that money or access that money that are going to benefit. And I don't think anybody wants that to be the case.

Wade Roush: Are there any signs that the drug industry is looking at how to scale up some of these treatments? And, you know, maybe create a pipeline for hyper personalized drugs?

Erika Check Hayden: So we're seeing things like Ionis, their co-founder Stan Crooke has started a foundation called the n-Lorem Foundation that's going to try to develop these treatments for patients. The reason is that developing a drug for one patient that costs millions of dollars and doesn't really have a very large market is not something that's necessarily going to be attractive to a company. But I think people think there is a direction that could evolve where, you know, if the drug industry is better able to manufacture these drug templates or backbones and more easily switch out the part of the drug that's the business end that's doing the targeting of different genetic diseases to where that becomes much more large scale, much more customizable, much cheaper. You know, then you might see a model where this is much more economical, affordable, reimbursed by insurance companies, because right now this is not and obviously that's a major cost barrier.

Wade Roush: Do you think this is a time for patients with rare genetic disorders and families of those patients to feel more hopeful? Or is it just too early realistically for this to affect lots of people who are already suffering from these conditions?

Antonio Regalado: Right. It goes back to the question, should this be a breakthrough technology? Because right now, it's not helping that many people. We're talking about helping one person. Or we're talking about helping two or three very few people. Very few. And that's a strike against the idea, frankly. Like, why? Why should we invest resources into this when it helps so few people? Why should we call it a breakthrough technology? Well, the reason to is, it's sweet. Technically, it's sweet. And it paints a path towards a future where it like you can do a lot more with genetic drugs.

Wade Roush: So you can imagine a future not 100 years away, but maybe 10 years away, where this can be scaled up and broadened out to more patients.

Antonio Regalado: Yeah, absolutely. I mean, will the drugs work? How well will they work? It's kind of an open question. But yeah, we've already gone from one case to five cases next year no doubt it it'll be 10 and then a hundred and then thousands. Most likely. I want to raise something else, which this whole scenario is not fair. Because there's a lot of people with rare diseases and a lot of kids dying of rare disease in every neighborhood and every corner and every precinct of the country, of the world. So who has the opportunity to have this chance?

Wade Roush: Well, who does so far?

Antonio Regalado: Well, it is a very small subset of parents who for whatever reason have the ability to wrap their head around the science, to find where the opportunity is, and to raise quite a lot of money. And this is not bake sale money. This is two million dollars. Three million dollars. You have to really have a way to do that, and it favors people with a big network. That's why we're seeing people, you know, entrepreneurs from Silicon Valley or other people who just for whatever reason, manage to pull it off.

Wade Roush: If this kind of inequity persisted, it would definitely become a huge point of criticism around this whole area of therapy. But maybe you could look at these parents as the pioneers.

Antonio Regalado: Right. Exactly. A lot of the parents will say, well, in addition to trying to help my child, I also want to invest and try and create the process by which everybody else can be helped because they also have a lot of empathy for the next person. The idea is to help everybody. The pathway to doing that is not clear yet.

Wade Roush: All right. Well, whether this is a breakthrough or not, it raises so many interesting and thorny questions that it's perfect fodder for Technology Review.

Antonio: It's definitely a breakthrough, man. It's definitely a breakthrough.

Wade Roush: Okay. Thanks Antonio.

[Theme music]

That’s it for this edition of Deep Tech. This is a podcast we’re making exclusively for MIT Technology Review subscribers,to help bring alive some of the people and ideas you’ll find in the pages of our website and our print magazine. But the first four episodes cover our annual 10 breakthrough technologies issue, and we’re making those episodes free for everyone.

Deep Tech is written and produced by me and edited by Michael Reilly, with editorial help this week from Jennifer Strong. Our theme is by Titlecard Music and Sound in Boston. Special thanks this week to David Cameron, Howard Gelman, Erika Check Hayden, Mehmet Kuzu, Antonio Regalado, and Jane Wilkinson. I’m Wade Roush. Thanks for listening, and we hope to see you back here for our next episode in two weeks.