Meet Katleen De Preter

Katleen joins the VIB-UGent Center for Medical Biotechnology as new PI

December 7, 2022

By Milton Antwi and Nick Deploey, both PhD students at the lab of Karolien De Bosscher.

As we say goodbye to 2022, we welcome Katleen De Preter as a new PI at the VIB-UGent Center for Medical Biotechnology (CMB). With her Lab of Translational Oncogenomics and Bio-informatics (TOBI lab), she develops analytical and bioinformatic pipelines for diagnostic, prognostic, and predictive analysis, which enables more precise cancer management.

Good morning, Katleen! Tell us, what inspired you to get into science?

“In high school, I developed an interest in most science courses, including physics, mathematics, and biology (and to be honest: to a lesser extent in chemistry) which, together with good grades, led me to decide to study bioscience engineering at Ghent University. I felt like this education would provide me with a broad basis in science. As I was more interested in the medical side of cell and gene biotechnology, I decided to do a Master’s thesis at the university hospital (UZ Gent) campus in the Center for Medical Genetics (CMGG).”

What was your thesis about?

“My Master’s thesis was about neuroblastoma, which is a rare pediatric cancer that begins in cells of the developing sympathetic nervous system called neuroblasts. Using the first qPCR machine installed on the campus, I was involved in the development of a qPCR test to quantify DNA copy numbers of the MYCN gene, an oncogene in neuroblastoma. After my thesis, I obtained an FWO grant for a PhD that allowed me to stay and continue my neuroblastoma research. The main goal during my PhD was to isolate neuroblastoma progenitor cells (neuroblasts) from fetal adrenal glands and use these as a reference for transcriptome analysis of neuroblastoma tumors. During the last year of my PhD thesis, I managed to isolate and profile those cells, which was a unique and unprecedented achievement in those times.”

During your PhD and postdoc did you have any favorite (or not so favorite) experiments?

“Honestly, I was not always the biggest fan of wet lab work. It requires a great deal of patience during experimental optimizations and if it fails, you have to repeat (and repeat and repeat) an experiment. During my thesis, I tried to isolate neuroblasts while avoiding RNA degradation, which was very challenging and frustrating when one after the other experiment failed. Both for my Master’s and PhD thesis it became clear that I was mostly enjoying the analysis of the data that resulted from the experimental work. Playing around with the data and visualizing them was more rewarding for me. So, I acquainted myself with R and bioinformatics during my PhD and post-doctoral fellowship.”

How do you see your research field evolve in the coming decade?

“I’m currently working on the analysis and understanding of tumor heterogeneity using single-cell sequencing. At the moment, single-cell sequencing is not implemented in clinical practice for several reasons, but I expect that this is something that might happen in the future. The technology is evolving rapidly, prices are decreasing, and computational approaches improve daily.

However, to perform single-cell sequencing, tumor tissue samples are needed, while in clinical practice nowadays mostly small needle biopsies are taken, which limits access to the tumor material. A tumor biopsy is also an invasive and, in some patients, even a risky procedure. In the past years, liquid biopsies (like blood or urine samples) have proven to be a valuable alternative to analyze the genomic characteristics of the tumor. A few years ago, we started collaborating with the team of Nico Callewaert at CMB to use their cfRRBS method on liquid biopsy samples to improve the diagnosis of cancer patients. While we and others have shown the potential of liquid biopsies in the diagnostic and therapeutic management of cancer patients, assay sensitivity is still a big challenge. I believe that further improvement in the technology and bioinformatics can be expected towards more sensitive liquid biopsy assays.”

Do you have a favorite paper or project to which you contributed?

“Beyond the ERC consolidator grant that I obtained beginning of this year, I’m also very proud of a study that we published in the Journal of the National Cancer Institute a few years ago. Neuroblastoma is a rare disease and therefore it is difficult to access large numbers of patient samples that are needed for biomarker studies. By setting up an international collaboration we succeeded to collect DNA copy number data of more than 500 high-risk neuroblastoma tumors. This helped us to identify two types of copy number aberrations that are associated with extremely poor outcomes in those patients. I pick this study because it shows the power of working in an international setting as well as the strength of mining large datasets.”

Do you have any tips for young researchers to build a career in science?

“A first tip: ‘Never give up.' Some PhD students tend to lose some of their initial enthusiasm because they start to realize that the research is not progressing as fast as they had expected and a first publication is not yet there. Most of these students do not always understand that they have already evolved significantly as a researcher and have learned a lot (and also, you sometimes learn more from a failed experiment). For example, during my PhD, neuroblast isolations only started to be successful during the 2 last years.”

“A second tip: ‘Communication is key.' Communicate as much as possible openly about your research with colleagues and collaborators (of course you need a certain level of prudence...). Equally important, if you are doubting, struggling, panicking, hesitating, … about your trajectory as a researcher, talk about it with your colleagues, including your PI.”

Which parts of your work give you the most satisfaction and which ones 'not so much'?

“The part of my job that gives me the most satisfaction is supporting and supervising PhD students in the team. I enjoy the brainstorming meetings on their research, but experiencing their journey as a PhD candidate is also very satisfying: having evolved from a young graduate student to a more confident and proud researcher with a PhD diploma.”

“My job comes also with some administrative work which I like the least. While I like and learn a lot by reviewing papers and projects and participating in review boards, it sometimes takes too much of my time. Now and then I have to say no to certain jobs to keep the right balance.”

How do you deal with stressful situations and what are your go-to ways of coping/releasing stress?

“I’m very passionate about my work and tend to work a lot. However, I regularly need to step back from my work to charge my batteries: “disconnect to reflect”. Spending time with my three children, family and friends is vital to me. I also try to find time for 2-weekly runs with friends in the neighborhood of my home in Sint-Niklaas. In addition, I like doing some functional training as well as yoga. Going to a concert or a theatre play is also an ideal way to relax for me.”

What do you hope to achieve while being at VIB CMB?

“I’m looking forward to delving into this new environment and meeting all CMB researchers and their unique expertise. While our research primarily focuses on genomics and transcriptomics analyses, I’m confident that learning more about the protein-focused research at CMB will certainly lead to novel research ideas and collaborations.”

Do you have a hobby you want to share?

“I like baking and cooking, but prefer easy recipes with lots of surprising flavours. Big fan of the recipes of Ottolenghi!”

If you were an animal what animal would you be and why?

“I would definitely be a cat(leen)! No explanation needed, I guess. I used to be allergic but a few years ago it miraculously went away and now I even have a cat at home, called ‘Leen’.”