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Honorary Doctor Hans Clevers: Lab-made mini-organs, a growing success story
Depth interview

Honorary Doctor Hans Clevers: Lab-made mini-organs, a growing success story

Dutch molecular geneticist Hans Clevers developed a way to grow miniature versions of our organs outside the body.

21 minutes
18 January 2021

If Hans Clevers (63) had not become a researcher, he says that he would have liked to be a novelist. One can only wonder whether these novels would have been as fascinating as the scientific story that the Dutch molecular geneticist is writing. At the Hubrecht Institute in Utrecht, Clevers and his team developed a way to grow miniature versions of our organs outside the body. Such ‘organoids’ are now used in laboratories across the world – including in Leuven. Among other things, they enable scientists to study diseases and to predict how patients will react to medications.

“It was immediately clear that we were looking at something spectacular. In two or three months, those cells had produced an enormous amount of tissue.” The euphoria that he felt at the time comes straight back to the surface when Hans Clevers tells us about the great eureka moment – his second – that he experienced in 2008. Along with the Japanese postdoc Toshiro Sato, Clevers had made a plan to make a stem cell from the intestine of a mouse divide in a Petri dish. The prevailing dogma about stem cells claimed that this was impossible. But Clevers and Sato thought they could do it. It was just a question of providing the right growth factors, blocking the right processes, and creating an environment in which stem cells could thrive: a gel that acts like the connective tissue that envelops cells in the body. “They seem to enjoy being there, whatever that might mean,” Clevers says.

And enjoy profoundly, so it turned out. He saw this immediately when the modest Sato asked him to come and take a look. “Our intention was to use one stem cell to make many stem cells, but it was immediately clear that something else was happening.” The cells had formed a structure that looked like a mini-intestine and in many respects, it also seemed to work like a real intestine. The first organoid was born. “That is what they call serendipity,” Clevers says.


Our intention was to use one stem cell to make many stem cells, but it was immediately clear that something else was happening.

The right flag

Discovering something that you weren’t looking for: it is only possible if you keep your perspective wide open and are not afraid to stray off the path that you had set for yourself. This describes Hans Clevers to a T. He studied biology and medicine, appeared to be predestined for a career as a paediatrician, but ultimately decided that he was more of a researcher than a medical doctor. He went to Harvard to do a postdoc and then became a professor of immunology at Utrecht University and University Medical Centre Utrecht.

The focus of his research shifted to the intestine when he studied one of the chemical languages that cells speak, the so-called ‘Wnt pathway’. Many of our organs contain stem cells that repair damaged or worn-out parts by making new cells. The stem cells in the intestine are exceptionally active: they ensure that the epithelium – the inner layer of cells in the intestine – is renewed every five days. The Wnt pathway plays a crucial role in this process. “When we blocked it in mice, epithelium regeneration also stopped,” Clevers says. “On the other hand, an excess of Wnt pathway signals leads to the proliferation of cell division. This leads to polyps, a preliminary stage of cancer.”

These were important new insights into healthy and diseased intestines, but Clevers also wanted to know where precisely these stem cells are located. This requires markers – a little ‘molecular flag’ as Clevers calls it. “My British postdoc Nick Barker and I tried all kinds of little flags for two years, with no success. And that is no surprise because everyone thought those stem cells were in a different place than they ultimately turned out to be.”

Thanks to a little flag called LGR5, they eventually found the stem cell all the way at the bottom of the crypts, the pits in the intestinal wall. It was Clevers’ first eureka moment. “We had made a cell blue and we saw a blue stripe running upwards. Then you know that this cell made all of these daughter cells on its own in a week. That was the first time that someone really saw a stem cell in action.”

Black and white prediction

Two years later, it became the blueprint for the development of the organoid method. This technology has developed considerably over the past decade: from mouse to human tissue, from the intestine to a whole series of other organs. There are now miniature versions of the liver, the lungs, the stomach, the kidneys and the pancreas, among others. These are no longer only the work of Clevers and his colleagues in Utrecht. Researchers across the whole world are now using their recipes to create organoids.

The enthusiasm is understandable. These mini-organs are able to replace many forms of animal testing research and they offer unprecedented possibilities. For example, you can use an organoid to test whether a particular medication will be effective on an individual patient. This is an application that Jeffrey Beekman, a molecular biologist at the UMC Utrecht, developed with Hans Clevers for patients with cystic fibrosis, a hereditary condition that disrupts water and salt circulation in the body. This results in thick mucus that causes obstructions in the airways, the gastrointestinal tract and the liver. Cystic fibrosis is the most frequently occurring genetic disease in this region.

It has long been known which gene causes the problem, but there are more than two thousand mutations that can cause the disease. “An American company had been the first to bring a medication onto the market that corrected the workings of that gene,” Clevers says. “This as such is an incredible miracle. The medication was developed to treat a commonly occurring form of cystic fibrosis that affects about fifty percent of patients. The other half had no access to the medication, though it might also have helped some members of that group.”

“To test this with the patients themselves, you have to administer the medicine over a long period of time, to ascertain whether the condition of the lungs regresses further or not. With an organoid, you can do this much faster. In only a week, you can take some rectal tissue and make mini-intestines, and then see whether the medicine works. It provides a genuinely black and white prediction of whether the medication will work. We were thus able to ensure that all the patients with a positive organoid test would be reimbursed for the expensive medication.”

“There are now several more cystic fibrosis medications, which are currently in the test phase. Utrecht is coordinating a European trial to research whether these medications can be matched to individual patients.”

An organoid of the human liver. Thanks to the fluorescent colouring, researchers were able to study what goes wrong in cell division when the cancer gene TP53 is mutated.
An organoid of the human liver. Thanks to the fluorescent colouring, researchers were able to study what goes wrong in cell division when the cancer gene TP53 is mutated.
© Delilah Hendriks & Benedetta Artegiani – Hubrecht Instituut

Bullseye

In a similar way, it might be possible to adapt cancer treatments to specific patients, Clevers says. “If you are diagnosed with cancer now, you are put in a group of which the statistics are known: ‘the five-year survival rate is this or that percent, this is the best therapy, and this is the second best.’ But you don’t know whether that is actually true for you. Approximately forty percent of cancer therapies helps to a greater or lesser extent, sixty percent do not. But there are side effects in one hundred percent of cases, and they are considerable.”

It would thus be a major step forward to be able to test the therapy outside the patient first. An additional advantage is that you can offer the patient a working therapy immediately, Clevers explains. “You can treat the disease in an earlier stage than if you have to wait and see until the second or third medication works. And you avoid inflicting the damage that non-effective therapies can have.”

He is absolutely convinced of the potential of organoids for cancer treatment. “We can grow ninety percent of the cancers that occur in adults. Last year, about five articles were published showing that for intestinal cancer, organoids can correctly predict sensitivity to a medication in 80 to 90 percent of cases. This must all still be confirmed in large validation trials, of course. In the meantime, companies are working on equipment to make the tests faster and cheaper.”

Repapering

Organoids are not only very useful outside the body, but they can also be sent inside the body as reinforcements. Clevers’ research group – in cooperation with Mamoru Watanabe in Tokyo – demonstrated this in mice with inflamed intestines that function as models for inflammatory bowel disease in humans. “The inner coating of the intestine absorbs nutrients, but also keeps the content of your intestines out of your body,” he explains. “If there is a leak in the coating, such as if you suffer from Crohn’s disease or ulcerative colitis, bacteria try to escape, and this causes chronic inflammation.”

You can solve this problem by ‘repapering’ the intestinal coating, as Clevers describes it expressively. And this layer of ‘wallpaper’ is an organoid. “You need the organoids to stick, so there must be a blood supply immediately. Technically, this is not easy, but Toshi (Toshiro Sato – ed.) managed to find a stem cell in mice with which he made it work. We used it to make many mini-intestines, which we then froze and sent to Tokyo. They implanted the organoids in forty mice with inflammation of the large intestine. To our great surprise, the organoids spontaneously started grafting to the damaged sections of intestinal coating. They opened up and repaired the holes, almost like a band-aid.”

This technique is currently being tested in Japan with human organoids in patients with chronic intestinal inflammation. If this new step proves successful, organoids might make transplants of certain organs unnecessary in the future, Clevers predicts. “You could build a biobank with mini-organs made of tissue from living donors who let you take a section of organ and then just go home. That would allow you to help patients at a time when the diseased organ still has considerable structure. You wouldn’t need to build a whole lung or liver weighing a kilo and a half. And the patients wouldn’t need to wait for an organ from a road casualty. The organoids would just be ready in the freezer.”

Hans Clevers and researcher Joep Beumer discuss an organoid of the human intestine.
Hans Clevers and researcher Joep Beumer discuss an organoid of the human intestine.

Different kettle of fish

Fixing failing organs using organoids: it is music to the ears of people who want to live a few years longer. But Hans Clevers does not see this as the most important application of his work: “Ageing research is now an enormous field, but it doesn’t really interest me. Our stem cells are strong enough for us to reach eighty or ninety years old. It is like an old car. Things eventually start going wrong.”

“This might sound a little obvious, but it is better to do something to help somebody earlier in life. A seventy-year-old patient with lung cancer who has smoked their whole life: I wouldn’t wish it on anybody, but a three-year-old child with a neuroblastoma (malignant tumour – ed.) weighing a kilo is a different kettle of fish.”

Caring for sick children is thus a leitmotif in his career. For example, he was one of the driving forces behind the foundation of the Princess Máxima Centre for pediatric oncology, which is also in Utrecht. The basic premise for the centre is that all Dutch children with cancer should be able to receive treatment in one place. “It is unique in the world,” Clevers says. “It was politically very complicated to get this done. But we simply knew that there is a smaller chance of things going well in certain hospitals than in others. This centre brings together the best care with the best research. And you can take that quite literally: the coffee machines are placed in such a way that the doctors, nurses and researchers simply have to meet one another.”

Ageing research is now an enormous field, but it doesn’t really interest me. It is better to do something to help somebody earlier in life.

At the Hubrecht Institute, the most interesting conversations likewise occur around the coffee machine, as Professor Marc Ferrante knows from personal experience. He is a gastroenterologist at UZ Leuven, researcher at TARGID (Translational Research in GastroIntestinal Disorders) and one of the three nominators of the honorary doctorate that Hans Clevers will receive from KU Leuven. Ferrante spent a year in Utrecht as a postdoc. “Professor Paul Rutgeerts quickly realized that organoids could be useful for Leuven research into inflammatory bowel diseases, which he pioneered,” Ferrante says. “So I went and worked at Hans’ lab in 2010. At precisely the right time: until then, they had only made organoids from mouse tissue, and I was able to work on the first applications with human tissue. For a clinician, that is of course much more interesting.”

Following his research period in Utrecht, Ferrante brought the recipe for the organoids to Leuven. There was great interest in them, he says: “I think at least ten in-house research groups came to learn the technique. For research into cystic fibrosis, for example, I provided the knowhow and we still consult regularly with colleagues in paediatrics. I taught them how to take the biopsies and process them. The Leuven cystic fibrosis clinic has now used the organoid model for several years, in close cooperation with Jeffrey Beekman’s group in Utrecht. They use organoids to determine which patient is eligible for which therapy, and they participate in the larger European project that Hans mentioned.”

“For our own research into the mechanisms of the development of inflammatory bowel disease, the great advantage of organoids is that we can grow a lot of intestinal tissue in a short time. We can simply keep it in the freezer and use it when we need it. We distribute it on a ‘Transwell membrane’: on one side of the plate, we imitate the content of the intestines and on the other side we simulate what happens in the patient’s body, namely the immune system.”

Professor Marc Ferrante took the recipe for the organoids to Leuven and applies it in his own research into inflammatory intestinal diseases.
Professor Marc Ferrante took the recipe for the organoids to Leuven and applies it in his own research into inflammatory intestinal diseases.

Super-smart cells

Various research groups in Leuven that use organoids have founded a network for further interdisciplinary cooperation. One of the driving forces is the group of Professor Hugo Vankelecom at the Department of Development and Regeneration, which developed organoids of the endometrium in 2017. This breakthrough opens new perspectives for research into (in)fertility and into diseases of the endometrium, such as endometriosis and endometrial cancer. The organoid models that the group derived from diseased tissues will help to understand the pathological conditions better and develop new medications. The KU Leuven technology is currently being tested for applications in reproductive medicine, which a start-up will eventually use in practice.

“We also worked on the endometrium in Utrecht, but we had to let Leuven get the scoop,” Hans Clevers says. “I actually think it is brilliant that our technology is applied across the world and that some researchers do things better and more quickly than we do. Incidentally, Matteo Boretto, the first authors of those Leuven papers, now works in my lab.”

When you hear ‘stem cells’ and ‘Leuven’, you of course also think of Catherine Verfaillie. Her ground-breaking research focuses on embryonal and pluripotent stem cells, which can make everything, while Hans Clevers works with adult and organ-specific stem cells. Nevertheless, his insights have also given an extra dimension to the research at the Stem Cell Institute Leuven, says Verfaillie, who is likewise nominator of the honorary doctorate. “If we try to make liver cells from pluripotent cells, for example, we see that things happen in a three-dimensional system like an organoid that we cannot imitate in the classical two-dimensional Petri dish. You end up with cells that look much more like liver cells. In other words, you might say that Hans Clevers has demonstrated that the cells are smarter than we are.”

The organoids of the endometrium made by the group led by Professor Hugo Vankelecom at the Department of Development and Regeneration opened new perspectives for research into (in)fertility and illnesses of the endometrium.
The organoids of the endometrium made by the group led by Professor Hugo Vankelecom at the Department of Development and Regeneration opened new perspectives for research into (in)fertility and illnesses of the endometrium.
© Indra Van Zundert en Hugo Vankelecom

Organoids and COVID-19

The question that many scientists are asked these days: can your research contribute to the fight against COVID-19? “Chinese scientists with whom we cooperate have made organoids of the horseshoe bat, the species that is linked to the virus,” Hans Clevers says. “The virus appears to grow incredibly well on bat intestines. This means that it is very likely that it originated there.”

Along with colleagues in Rotterdam, Amsterdam and Maastricht, Clevers’ team demonstrated with organoids that the corona virus can infect intestinal cells and can multiply there. Scientists in Leuven are also researching what the virus does in the intestines. “We have made organoids of healthy people and of patients with a chronic inflammatory disease of the large intestine,” Marc Ferrante says. “Among the latter group, we saw that the ‘entryways’ for the virus became more prominent if we caused inflammation in the organoid, while that did not happen when we did the same with the organoids of healthy people. Experiments in which organoids are infected with the coronavirus itself may confirm that patients with such a chronic inflammatory disease have a higher risk of more serious symptoms if they contract COVID-19.”

In their search for powerful viral blockers, virologists at the Leuven Rega Institute also use organoids. “Before we test a therapy on laboratory animals, we first verify whether it works in human organoids,” Professor Johan Neyts says. “Among other things, we use organoids of tissue from the airways, which we infect with the virus. On the outside, they make contact with the air, just like our airways do, and on the inside, there is a growth medium, which functions like blood. To this we add the antiviral substances and we then analyse how they impact the proliferation of the virus. We applied this method successfully, for example, when we researched the effectiveness of Favipiravir, a Japanese flu drug. In the next step, we demonstrated that it has an antiviral effect in hamsters that are infected with SARS-CoV-2. In several countries clinical studies are now being conducted to study whether the medication also protects humans against COVID.”

According to Hans Clevers, organoids can also play a role in preventing future epidemics: “Thirty to forty coronaviruses have been found in bats alone. You can barely research them because they don’t yet grow on human cells. If these viruses make you sick, it is already too late, so we would like to research them in advance. Organoids are a good way to do this. The question is whether the world is ready to make the funds available.”

Furthermore, the bat is not the only animal of which organoids have been made. Researchers in Hans Clevers’ group developed a method to grow the venom glands of snakes in the lab. They actually managed to make the glands produce and secrete venom. This offers new perspectives for the development of antidotes and medications that are based on components in the venom.

Oiled chaos

Just like a stem cell needs the right growth factors and environment to make an organoid, a laboratory also needs the right stimulants to be successful. This is one of the strengths of Hans Clevers, Marc Ferrante says. “His lab is a well-oiled machine: it is organized so well that it could only produce brilliant results. He encourages his researchers to propose new ideas and ensures that they have the necessary time and financial means to develop them.”

“I think of it more as organized chaos than a well-oiled machine,” Clevers says. “But it is true that I have always ensured that there is a lot of money for my people, and especially for research on the margins because that is where all of the important discoveries are made. We make an artform of trying things out all the time without turning them into longer-term projects. I tell my researchers: ‘Keep an open vista and do as many tests as you can. If you see a pattern, we will all look at it together.’ That is the philosophy of the lab.”

The human mind controls an enormous amount of what you think you know and see, Clevers says. If you start from a hypothesis, you will simply try to prove it. “You hammer away in one single direction and close your eyes to anything you might find along the way. During my postdoc in the United States, I learned how to ask really fundamental questions: you barely understand the content of the question yourself, let alone what the answer will look like.”

He is therefore also very concerned about the direction in which science seems to be going, with an increasing emphasis on research that yields results quickly. He says that developing a career like his would probably very difficult for young researchers today. “If I were to start over, and I only did the things of which I could promise that I would have the appliance or test in two years… That is called translational research, but if you make no new discoveries, there will soon not be anything left to translate.”

Of course, he looks with particular interest at the situation in his own country, which he knows like the back of his hand, in part because from 2012 until 2015, he was president of the KNAW, the Royal Netherlands Academy of Arts and Sciences. “Unbound research is under pressure across the world, but in the Netherlands the shift is enormous,” Clevers says. “During the last financial crisis, the Ministry of Finance managed to redirect significant portions for the education and science budgets to industry research. Your ideas are irrelevant if there is no immediate corporate interest.”

I have always ensured that there is money for research on the margins because that is where all of the important discoveries are made.

Meaningful book

Fortunately, his own scientific achievements have by no means gone unnoticed. The list of his awards is long and ranges from the Breakthrough Prize in Life Sciences to the title of Chevalier de la Légion d'Honneur. And he will soon also be a doctor honoris causa, for the first time. This is also a great honour for KU Leuven, says Professor Séverine Vermeire, who heads research into inflammatory bowel diseases in Leuven and is the third nominator of the honorary doctorate. “People who are not afraid to explore new avenues and who are open to surprises, those are the people who innovate and inspire. Hans Clevers will no doubt continue to do this over the coming years.”

Indeed, Clevers does not intend to rest on his laurels. “I have resigned my administrative responsibilities and have returned to the lab full time,” he says. “We are doing amazing things. For example, we are working hard to acquire permission to launch our own biotech company focused on an application of our organoid technology for metabolic diseases such as diabetes and fatty liver disease. We think that we can really make a difference there too.”

What about that alternative dream career as a novelist? Is it still a latent presence somewhere? “I don’t know if there is any certainty that I would be very good at it, but I would very much like to write a real book, yes. Doing something meaningful outside my own scientific world would give me great pleasure.”

An intestinal organoid of a mouse, with cells that secrete substances in colour: the red cells produce hormones, the blue cells make antimicrobial substances, and cells that regulate the immune system are coloured green.
An intestinal organoid of a mouse, with cells that secrete substances in colour: the red cells produce hormones, the blue cells make antimicrobial substances, and cells that regulate the immune system are coloured green.
© Joep Beumer – Hubrecht Instituut

Virtuoso with video

“There is nobody else who makes such beautiful animations (see example below) to convey his message,” says Séverine Vermeire. “These videos present his results in an accessible and incredibly clear way, while this is extremely complex matter.”

“They were initially intended for scientific conferences, not for the general public,” Hans Clevers himself says. “But when I was chair of the KNAW (Royal Netherlands Academy of Arts and Sciences), I often had to speak to politicians and journalists, and they also immediately understood what they were seeing.”

“The man who makes the animations for me, his name is Jeroen Huijben, does so brilliantly. I write a screenplay and provide figures, and he uses them to illustrate the videos. He sometimes sends me reactions like: ‘This cell is here and it cannot go there because I cannot animate that.’ This shows me that there is a transition in my story that is not completely clear, or two things I need to separate. If it doesn’t work in a video, it won’t work in a Nature article.”

The videos are now a permanent fixture of his presentations. “You see people sit back in their chair: they are entertained and they understand what they are seeing and hearing. I used to make the mistake of giving my complicated presentation and then showing the video. Now I start with the video, so everyone is already convinced and can understand my presentation perfectly.”