Credit: Center for iPS Cell Research and Application, Kyoto University

Shinya Yamanaka didn’t want to get ahead of himself the first time he looked at induced pluripotent stem cells (iPSCs) through a microscope. “Don’t be excited,” he told his colleague Kazutoshi Takahashi. “There’s a 99.9% chance this is a mistake,” said Yamanaka, now director emeritus of the Center for iPS Cell Research and Application (CiRA) at Kyoto University.

Researchers around the world were racing in the mid-2000s to figure out how to transform mature cells into stem cells, prompted by the practical and ethical challenges of embryonic stem cells. Yamanaka and Takahashi had treated cells with a combination of 4 factors dubbed OSKM — for Oct4, Sox2, Klf4 and c-Myc — that they thought might be important. But the lab was full of embryonic stem cells too, and a single errant cell could contaminate the experiment. “I asked him to repeat it, and repeat it and repeat it,” Yamanaka says.

In 2006, the pair co-authored a paper on the results of these experiments in Cell — providing a simple solution to make iPSCs in a Petri dish. Within months, other labs had replicated these findings and were embracing the reprogramming protocol for both basic and applied applications. In 2012, Yamanaka and Cambridge’s John Gurdon shared the Nobel Prize for discovering that mature cells can be transformed into pluripotent ones.

Twenty years on from Yamanaka’s landmark reprogramming publication, he is now celebrating the recent approvals of the first two iPSC-derived therapeutics in Japan. Amchepry, based on Jun Takahashi’s research at CiRA and made by Sumitomo Pharma and Racthera, consists of iPSCs that are re-differentiated into dopamine-producing neurons and injected into the brains of patients with Parkinson disease. ReHeart, made by Cuorips, consists of iPSCs that are grown up into sheets of heart muscle cells that are surgically implanted into patients with severe heart failure.

Both cell therapies were granted conditional approval on the basis of small single-arm phase I trials, and there are still big questions about whether they help patients and are safe. But Yamanaka is buoyed by the progress. “It was a big milestone, that’s for sure,” he says.

Scientific progress is a marathon rather than a sprint, adds Yamanaka, who recently completed his 49th marathon, in London. By being persistent, the field is also making progress with other potential applications of iPSC technologies. Companies including Altos Labs, where Yamanaka is a senior scientific advisor, and Life Biosciences are pushing forward with ‘partial reprogramming’ to rejuvenate cells for the treatment of various ageing-related diseases. Researchers are also working on chemically-induced reprogramming, and pushing the frontiers of iPSC-enabled drug screening and toxicity paradigms.

“This conditional approval is like passing the half way line,” says Yamanaka. “But we still have to run the remaining half, which is much harder.”

What did these first approvals of iPSC-based cell therapies mean for you?

I’m very happy about them. But at the same time, it is the beginning of the next step, so it’s no time to relax.

There are still questions about the efficacy and safety of both these therapies, which were tested in just a handful of patients, without a control arm. Some critics argue that the conditional approval pathway in Japan for regenerative medicines prematurely shifts the cost of drug development from companies to patients, insurers and governments. What do you make of those concerns?

Yes, the number of patients is small. But they do have lots of data in animals, including monkeys. It’s science as a whole that is important here, and we have good reason to believe that these cells have a high potential to be effective.

The cost of conducting clinical trials using cell therapies is also very high. For many companies, including start-up companies, it’s next to impossible to perform bigger-scale clinical trials by themselves. I think this system is reasonable because now they can have some financial support through insurance. This is a kind of financial aid from the government.

But they really have to perform much bigger clinical trials now to prove that these therapies work. That’s going to be an extremely important next step.

What’s your take on the need for control arms for these future trials?

Ideally speaking, it’s more scientific to run these with a placebo control. But it’s difficult to perform placebo controls in cell therapy trials, especially for Parkinson disease or heart disease. You’d still have to perform an operation, and instead of injecting real cells do a mock injection.

It’s easy to say, but very difficult to do.

What do you make of the pace of progress with iPSCs, 20 years on from your Cell paper?

I think it’s been very smooth, in a sense. Twenty years is around what we expected. We had COVID, which delayed us at least a few years. And there were some other incidents that delayed our progress. If everything had gone exactly right, it could have been a bit faster. But I think 20 years is a very reasonable timescale.

There are now over 115 trials ongoing of embryonic stem cell and iPSC-derived therapeutics, in everything from diabetes to cancer. Which of these are most exciting?

I’m excited about everything! But cancer immunotherapy is something I believe is very important. Cancer is the number one killer in many countries, so I really hope iPSCs can contribute here.

As a source for next-generation CAR Ts?

That’s right. And as other types of immune cells as well, such as NK, NDT cells and so on.

Earlier this year, Life Biosciences launched a first trial of Yamanaka factors as drugs, aiming with ER-100 to drive partial reprogramming and cell rejuvenation in vivo in the eye. What do you make of this kind of effort?

It has a very high potential. But to apply it to humans — especially in vivo — you have to be very careful, because you have to control the degree of reprogramming. Otherwise you can end up causing tumours. I don’t know detailed information about the clinical trial, but they have to have a very good strategy to avoid that.

They are delivering the OSK factors to the eye with an adenovirus, and using oral doxycycline for 8 weeks to drive OSK expression.

They are not using c-Myc, which makes it much safer. As long as they are not integrated into patients’ genomes, I think it should be okay. But c-Myc is very risky. It is a double-edged sword.

What other rejuvenation efforts are you watching?

We, at CiRA, have only a small project ourselves regarding rejuvenation. But there should be many ways of moving forward here. In addition to in vivo approaches, we can imagine ex vivo approaches with OSK or OSKM, like prior to cell transplantation or even during organ transplantation.

That kind of ex vivo application may be easier to control.

How about progress with small-molecule mimetics of Yamanaka factors?

We had a Keystone meeting earlier this year to celebrate the 20th anniversary of iPSCs, and Hongkui Deng, one of my friends in China at Peking University, presented his work on chemically induced iPSCs. I was surprised to see that they are already doing a clinical trial using their chemically induced autologous cells for patients suffering from type I diabetes. It is very, very exciting.

They have published many papers on their approach, but largely those papers are from their own group so we don’t yet know how reproducible they are. Judging from their publication, it’s a tedious process to use chemicals to induce pluripotent stem cells.

I don’t know how that will play out.

OSKM is so easy, and that’s why we are still using it.

The iPSC field has also embraced these cells for drug screening and disease modelling. Was this opportunity clear to you from the get go?

Yes and no. Cellular therapy was the main opportunity that was in in my mind at that time, but we already knew the potential of embryonic stem cells in disease modelling and drug discovery. Even before the publication of iPSCs in 2006, Austin Smith, a pioneer in embryonic stem cell research, had made it very clear that these cells could be used in drug screening. Probably drug screening was thought to be the most important application of human embryonic stem cells. Now I believe their use in disease modelling is even more important.

I wrote in 2015 about how iPSC-based disease models and screens were delivering small-molecule and antibody candidates for clinical trials. None of those panned out. How has the field matured since then?

Yes, it is true these haven’t worked out yet. But there are at least six clinical trials ongoing — in familial Alzheimer disease, Pendred syndrome, amyotrophic lateral sclerosis, fibrodysplasia ossificans progressiva and polycystic kidney disease — with drugs discovered with patient iPSCs that seem to be promising. So hopefully we’ll see more success in the near future.

What we have been learning is that iPSCs from different patients can be very different, even when the patients have the same disease. One of my colleagues, Haruhisa Inoue, has developed a panel of iPSC-derived motor neurons from around 30 patients. It’s like a clinical trial in a Petri dish. They have tested many, many drugs on that panel, and it is now very clear that each patient and cell line is very different in terms of drug responsiveness.

Now that we know that, I think we can be more precise and more personalized in our drug-screening efforts.

This variability is in both monogenic and polygenic diseases?

In monogenic diseases it’s a little simpler. But in polygenic diseases, cells from patients with the same identical mutations can have very different responses. We really have to think more carefully about how to predict which patients should be treated with which drugs.

In the US and EU regulators are signalling their intent to move away from animal models of toxicity testing, prioritizing instead ‘new approach methodologies’ like iPSC-derived organoid testing. What opportunities do you see here?

One of my friends, Takanori Takebe, has been generating 3D liver buds. These are really mini-livers that consist not only of hepatocytes but also of the many other cells that exist in the liver. By using that kind of system, I think we can get much better toxicity predictions.

Others are working on other assembloids, which are organoids consisting of multiple types of cells. I think these are a very important application of iPSCs. We cannot make moving mice from human iPSCs, but we can make organoids and assembloids that are much closer to our human system.

We’ve seen large pharmas dip into the stem cell space, mostly to exit it a few years later. What’s your take on industry’s willingness to invest — and stay invested — here?

I don’t know what they’re thinking.

Certainly cell therapy as a whole — not just with iPSCs — is a very attractive area. But it takes time and it is expensive. And drug developers have many other modalities they can work with, including mRNA and modified antibodies. It’s probably easier for them to focus on these modalities, so I can understand why they shift from cell therapies. But not all diseases can be treated by those other modalities. For some patients, cell therapies are required, so I really hope some companies will keep working on iPSCs.

It’s perhaps too early in the marathon for them?

Yes. Other sports maybe seem to be easier. You really have to love the marathon.

Marathon running and scientific research have lots in common. You have to be patient, and you have to work hard.

At the Keystone meeting earlier this year though, it was clear that iPSC research is making solid progress. I’m so happy to see that.