Professor Johan Den Dunnen is at the Leiden University Medical Center (LUMC), where he is currently working on the latest technologies of DNA sequencing and developing new assays to apply in the hospital. His current focus is on two things: reading the entire DNA code of a patient and measuring the activity of all genes. In Den Dunnen’s opinion, at some point the hospital will decide to offer a full genome sequence for every patient. What you can learn from that is whether there is a genetic component in the health problem of the patient thereby improving the proper diagnosis and the best treatment for the problem is. After all, everybody has genes that influence how you, your body, is built and how you cope with the drugs that you take. It is not very difficult to read that information and then to start with the best drug and its optimal dose, explains Den Dunnen.
Professor Den Dunnen is also working with technology which examines the activity of all genes as blood is taken from a patient. Through sequencing the ribonucleic acid (RNA) you can see what exactly goes on in a body at the time the blood sample is taken. It will be very helpful to combine that with how the patient feels, as there will be measurements from throughout the body which can also be compared with those of other patients and the diagnosis and treatment they received. When the disturbances are identified, and a proper treatment is commenced, all the measurements should return to normal values, and can therefore determine whether or not the treatment that is given is effective.
Johan Den Dunnen is a molecular biologist who worked with DNA sequencing during his entire career. His main reason for dedicating his life to biology was due to his interest in DNA when he was young. “I was fascinated by the fact that such a small molecule more or less determines who I am and what I do in life,” he says.
After graduating from a Bachelor and MSc of Biology, he commenced his PhD at Nijmegen University in the Netherlands, where he worked on proteins in the eye lens. At this time, it was the early days where it became possible to read the DNA sequence, and also to clone pieces of human DNA in bacteria so that you could make enough to study it and read the DNA code. “I sequenced specific sets of genes which are expressed in the eye lens,” he says. “And while reading these four letters in a row where you could recognise these genes and the code to make the proteins expressed in the eye lens I realised I was the first ever to see this.”
After his PhD, he wanted to apply what he learned to find the cause of genetic diseases. He then moved to Leiden University where he commenced work on a project to find of the gene for Duchenne Muscular Dystrophy (DMD), a progressive neuromuscular disorder occurring in childhood that mainly affects boys. It affects 1 in 3500 live male births throughout the world. Working in a hospital, as soon as the gene was identified, his project team designed diagnostic tests so that when a family came to the hospital, they could diagnose whether or not the problems in the child were caused by mistakes in the DMD gene.
His work then split a little. First he studied in detail the gene itself, in the hope that they could identify exactly what the disturbance was and think of a potential therapy. He also applied the same technology to find the cause of many other diseases, first limb girdle muscular dystrophy then any muscular dystrophy, and finally on very rare diseases, particularly intellectual disabilities in young children. Here with the latest technologies, looking in one experiment at all the genes in our body, it becomes feasible to find the cause.
When it became possible to read a DNA sequence, more and more data was coming out of the machines, which meant that a new type of expertise was required: bioinformatics. Den Dunnen’s role was to promote the exchange of expertise by organising meetings and (international) courses, setting up a local (LUMC) and national expertise centre and developing bioinformatics as a new specialisation that young people could study. “You had biology and you had computer science or informatics and the combination of these two opposite expertises was a challenge. Initially it was quite difficult to find people who could work on the combination. My role was more initiating that these types of studies became possible and I organised a lot of conferences in Holland where this type of information was shared,” said Professor Dunnen. Around 1995 Den Dunnen met the late Professor Dick (Richard) Cotton who was active in collecting information on variants found in people and their consequences with causing a disease or just being a variation that you can have without problems. Professor Cotton firstly involved Professor Den Dunnen in a group which designed recommendations regarding when a change in DNA is found and how to then express that on paper, so that when information is reported or published everybody will immediately understand. These recommendations are now known as HGVS (Human Genome Variation Society) nomenclature and used as a standard world-wide (see www.HGVS.org/varnomen).
“Another shared interest with Professor Cotton were the gene variant databases, freely accessible databases collecting all reported observations of variants and their potential consequences, associated with disease or not. Prof Cotton pushed me to work with him on these databases, develop standards and software to allow people to start such databases. The software that den Dunnen build with his team in Leiden, LOVD, is freely available and developed into a world-standard. “Our frustration was that although everybody agreed that it is important to have that information available on the Internet and, although few people actively contribute, everybody expects that the information gets into the database by itself and for free” he says.
“Inspired by Professor Cotton I became one of a group of a people that was always promoting that people should share their research and diagnostic data,” says Den Dunnen.
“Professor Cotton invited me many times to come to Melbourne to work on this shared project, especially after the Human Variome project was initiated in 2006 in Melbourne. Last year (May) I finally accepted his invitation, but unfortunately in the summer Professor Cotton died. This was a big loss but I still decided to go to Melbourne to work on the subject. I was sure that he wanted me to do so because it was for a good cause.”
His contributions to the field, and dedication to research, includes studies towards a potential therapy for Duchenne Muscular Dystrophy. His team developed a specific technology in Leiden called exon skipping which is being tested now in phase three clinical trials. The idea of exon skipping, he explains, is now applied widely because it might also work for other diseases.
While exon skipping for DMD worked in cultured cells (mouse and human) and in a mouse model for DMD, in the end you need to work with patients. That is highly specialised work a little too much for a small research group in the hospital. The group filed for a patent, received it, and used the patent to collaborate with the company that could perform all the analyses in patients (phase I, II and III clinicaltrials). Although his influence on the project slowly disappeared, the work continued and patients in hospitals worldwide receive the potential treatment to determine whether the treatment is effective.
“At that time, I focused more on my research to finding causes of genetic diseases and I started to make databases which everyone could use through the Internet. The idea of the databases was when you find something on a patient, you put that result in the database so that others can see when they find the same variant, whether or not it has been seen before, supporting the conclusion of the researcher for that specific change in the DNA – is it related to the disease or not?” he explained.
With so many successes through his great contributions to his field, he surely must have a strategy for success. “That’s difficult to say,” he admits. “First, when you have a really good idea and believe in it then you should never give up. Try to find money to prove that it works and to apply it,” he says.
He shares a personal example during his time as head of the LUMC’s Leiden Genome Technology Centre, following the purchase of a new expensive instrument. After checking what type of research you could do with it he tried to interest people to use that new technology. The main problem was that a lot of people were apprehensive to look into new technology. “Why should I try something new when I know that for sure with this old trick I have the answer in two or three weeks, while the new technology might fail and then I have nothing,” colleagues would say. “And that is a big problem when you have an innovation that needs a lot of convincing for people to try it. They always want you to prove that it works, before they are going to start to use it. I think that’s a Catch-22. You need the opportunity to show and a real-life example that it works,” he said. “And it’s quite difficult to find money to do so, through research grants, and that again means to try, try, try until you are successful,” he urges. “Although everybody now is very fond of our Exon Skipping technology, when we first applied for money to do it, people said it was a ridiculous idea, it will never work.”
In the world of biology, genetics and its associated research, finding money to progress your ideas can be hard – probably like most fields. But what Den Dunnen found most difficult for himself, was making the change from the laboratory to the desk. Den Dunnen, is at heart, a researcher. He likes to be in the laboratory. “At some point you start to make a career and the consequence is that you end up doing something that you are not trained for,” he says. “I was trained to do experiments in the lab and research and then I ended up behind the desk. I have to look at finances, I have to guide people, I have to go through all kinds boring meetings, and the most difficult part for me was to learn to like that as a job,” he says. “It took me many years. I still find it a little bit strange that you get very expensive training to do something and then after 10-20 years when you are successful in that you end up doing something more or less completely different.”
Despite the challenges, Den Dunnen is certainly an advocate for biology, and is especially keen to promote and extol its values to younger people and graduates. He explains that young people today have many options in life, and consequently, it can be hard to make a decision. He sees this in his own children who struggle with what kind of choices to make in the present, that will more than likely profoundly affect their lives in the future. Looking towards DNA is one answer. “I try to interest people in my field of research by explaining to them that what drives you is your DNA as well,” he says.
“It is already possible to read the entire code and based on that have an analysis of who you are, and what talents or risks are hidden inside you. That is a topic that immediately interests everybody. Everybody is interested to know about all possible talents but at the same time everybody is afraid of mistakes which might be in the DNA and the uncertainty about how far the influence of the DNA is. And you cannot change your DNA.” he adds.
“I’m convinced that when we read the entire DNA code of somebody you learn a lot. In the DNA code of a person, you find roughly 4 million differences with the reference in the database. We still do not know yet for every of these 4 million variants what they mean,” he explains. But a lot is known and that information is very valuable. One of the things you can see for instance, is what type of blood group that somebody has, whether you can taste bitter, what your eye colour is, etc. It can also offer deeply invaluable information when a child is born: DNA sequencing can be used to replace the heel prick where after a few days a few drops of blood are taken to test for some very specific diseases. This way, of course, you can identify what kinds of diseases or health issues that child may have, and treat them. Looking at DNA can identify whether or not people have a high risk for certain cancers. And as the risk is known, conducting regular check-ups to see whether or not the cancer is present in the person means that it can be detected early, and therefore the patient has a higher chance of timely and effective treatment.
“You can read all that information from the DNA code, and the cost of that at the moment is €1k-2k. I think that’s a lot of very valuable information that helps you to guide people through the rest of their life for health risks they may have,” he says. And with the power of technology, the information that can be gleaned from such tests is only getting more prolific.
In 2003 the entire human genome was sequenced to an accuracy of 99.99 per cent, by Cambridge Scientists in a global consortium with laboratories from the US, France, Germany, China and Japan. At the time, Director of the Sanger Institute, Allan Bradley, told The Guardian that the sequencing of chromosome 20 – just one part of the work – has already accelerated the search for genes involved in diabetes, leukemia and childhood eczema. The work costed £150 million. Today it only costs around £1000, purports Den Dunnen, and the only difference there is technology. Every time, these new machines produce more data for roughly the same price or even less. Combined with the power of computers to analyse all that data, and of course the internet, the future of having reliable knowledge about our health and wellbeing is looking good.
“I have to work still for another 10 years, I think that I can easily fill that time by developing this technology further so we get knowledge in databases behind every variant we encounter because in the end we need that to understand a DNA sequence,” he says. “And what I’ve been working on a lot lately also is explaining to lay people what you can do with a DNA sequence because people don’t have a very good understanding of genetics, and also of what you can and cannot see when you analyse DNA.”
He continues, “I think it’s very important that before the hospital starts offering this service – research into your entire genome and what you want us to tell you – that people know what it’s about and know exactly what is to be looked for because the DNA code is partly determining your life. Improving education on the topic of DNA and what you can and cannot do with that.”
As Professor Den Dunnen’s work takes him around the world, from hospital to hospital, university to laboratory, and yes, even to desk, he looks back at his time at Graduate House fondly. “I liked the time in Melbourne a lot,” he says. “I also liked the environment at Graduate house. It was great to meet people from all over the world.” We look forward to seeing you again Professor Den Dunnen!
photos, supplied by Johan Den Dunne. Photo 1 © Hannie Melisse, 2016.