"Our success is based on scientific curiosity"
12 research groups with different focus work at the Department of Gene Technology. The common denominator is their way of working with method development, mainly in medical problems.
”One of the reasons for us being a top department is that we ourselves decide what we are going to research," says Peter Savolainen, Head of Deparment at Gene technology.
The Department of Gene Technology is situated in the premises of SciLifeLab in Solna. Around 70 employees work here, of which 50 work within research. The remaining employees work for the national research infrastructure National Genomics Infrastructure (NGI) as well as for Clinical Genomics, a collaboration between KTH and KI that conducts gene sequencing for hospitals.
Peter Savolainen says that the research is centered around nucleic acids, that is DNA and RNA, as well as to some extent proteins. The orientation of the research varies between the 12 different research groups.
As an example of two really successful professors, Peter Savolainen mentions Joakim Lundeberg and Tuuli Lappalainen, who came from the US last year.
”They are two real star researchers that we have. According to measurements from the KTH Library, we are the best department at KTH when it comes to research publications. We have a high impact factor for the journals we publish in and a high citation rate,” he says.
Population geneticist reinforcement
Professor Tuuli Lappalainen’s group, Functional Population Genomics, uses medical population statistics to discover medically important variations through the study of human populations.
”We haven’t had a population geneticist before, so it is a reinforcement to the department. You want to find out what genetic variants that have medical importance. By extension, the knowledge is used for treatments and for the development of new medicines,” says Peter Savolainen.
Recently, professor Joakim Lundeberg has been noticed for his method Spatial Trancsriptomics, a method for analysing gene activity in tissue that has been chosen as Method of the Year in the prestigious scientific journal Nature Methods.
”You get to know what genes are active in different tissues, in parts of the tissues and even in the different cells of the tissues. Most recently, they have looked at cancer tumours and surrounding tissue and discovered that what looks like healthy tissue around the tumour already contains mutations that lead to cancer. This could make it possible to discover cancer cells even before they have developed to cancer,” says Peter Savolainen.
In order to show the breadth of the research, Peter Savolainen mentions one additional research group at the department – Environmental Genomics, led by Professor Anders Andersson. The group analyses microbes in different ways with specialisation in mikrobe populations in the Baltic Sea, plankton and bacteria.
”Partly, it is to identify what species are there, to map their genome. It is also a way of monitoring the development of the biological environment in the Baltic Sea, which is the basis for fish etcetera. It is possible to see how the environment is affected by changes in oxygen level, nutrients and temperature over time. The group has also looked att human intestinal bacteria, that is the bacterial flora of the intestine,” says Peter Savolainen.
Method development for all
What is common for the researchers at Gene Technology is that they all perform method development. Since most of them are basically engineers it is their strength.
”We identify a societal problem, perform a needs’ analysis and if an analysis method is lacking, we develop one and apply it on the problem in question. To a great extent, we develop methods to analyse medical problems, we have a lot of collaboration with mediacl research att Karolinska Institutet. The same applies to Anders Andersson and the other groups, method development for both lab analysis and data analysis is central. We both generate and analyse massive data sets and need to be innovative through this whole process.”
What is it like working with these questions?
”It is very exciting. These are important questions, we usually say that this is really ”curiosity driven science”. We are pretty independent and it is we who decide what we want to research. This is perhaps a reason for our success as a department. It is based on scientifical curiosity and it has been going well for us. It is all about getting grants, it is a good circle, we receive grants which makes it possible for us to continue. Then, I generally think that we are quite competitive, we strive to perform at the highest level and publish in the best journals.”
Peter Savolainen himself has chosen a quite different path, where it is harder to receive grants. He does research on dogs – their origin, history and evolution, as well as "dog forensic science".
”We have identified that the domestic dog originates from wolves who were tamed in South East Asia, but there is still an academic battle around this where not everyone agrees. We have also identified the origin of the Australian dingo, which is commonly accepted.”
Aiding the police
The work on developing better methods for analysing DNA from strands of hair has led to Peter Savolainen having helped the police in several criminal cases, among other the so called Helén murder.
”We have contributed to the police investigations, mainly by giving the police reconnaissance material. If you have found hair from the same dog on two victims, it is probably the same murderer. We have also made analyses where we have established that the hair strands did not come from the suspect’s dog. So we have acquitted suspects, but never put anyone in jail,” says Peter Savolainen.
What remarks did you receive in KTH’s research assessment exercise (RAE)?
“Not that many, they were actually quite exuberant. They wrote that it seems to be a department where there does not seem to be hardly any problems. They think we should expand the cooperation with Protein Science and other departments, in particular when it comes to large-scale data analyses and artificial intelligence. We have the same problems and work with similar things. We really agree with this. With radically increased data sets, large-scale data management and analysis become increasingly important within our research, and there is extensive expertise at KTH which we could use better.”
How do you see the future?
”It is hard to get any better, haha. We have many high-class studies going on, mainly within medicine. As the RAE evaluation points out, there is an increasing importance of data management and analysis. An important aspect of this is that the education at KTH has to be able to prepare our students for this future, with an increased training within bio related data analysis.”
Text: Sabina Fabrizi