Professor at TUD – Kavli Institute of Nanoscience
Nynke Dekker has been a group leader in the Faculty of Applied Sciences at TU Delft
since 2002 and Full Professor (chair of “Single molecule nanoscale biophysics”) since
2008. She graduated with a BSc cum Laude from Yale (with majors in both physics and in
applied mathematics), an MSc cum laude in physics from Leiden University, and a
prestigious PhD in physics from Harvard University. This was followed by a postdoctoral
period at the Ecole Normale Supérieure in Paris in which she transitioned into biological
Prof. Dekker has contributed seminal advances at the top of her field of biological physics. Her research focuses on fundamental biological topics such as transcription, replication, and topology that have also a strong link to biomedical research. In order to understand these critical biological processes, she quantitatively probes the dynamics of single molecules of DNA, enzymes, and molecular motors, thus generating a precise and mechanistic biophysical perspective. Her successful research efforts have included realtime studies of processive molecular motors (e.g. polymerases) on DNA and RNA, experiments that probe the mechanisms of DNA-binding proteins involved in DNA compaction (e.g. nucleosomes, tetrasomes) and the termination of replication, and groundbreaking experiments on the understanding of chemotherapeutic inhibitors in clinical use, thus uncovering a new mechanism through which they influence the activity of topoisomerase enzymes. Her research at the single-molecule level was also extended to the context of live bacterial cells, which places her research group in the unique position of being able to quantitatively compare the behavior of individual biological molecules both in vitro and in vivo.
In recent years, Prof. Dekker has concentrated her research efforts in the study of the dynamics of the complete eukaryotic replication fork at the single-molecule level. This builds on the ability of many biochemists, which culminated in the reconstitution of the eukaryotic replication fork in bulk in 2015. Her novel single-molecule studies examine the dynamic aspects of the loading of the yeast replisome using state-of-the-art instrumentation. Understanding the mechanisms that underlie eukaryotic replication provides a key that will link to our understanding of disease development such as genetic disorders and cancer.
Adventures in DNA replication using single-molecule biophysics
Many transactions on the DNA that forms our genome are carried out by molecular machines that operate at the nanometer-scale, and how they do so effectively is a question of long-standing interest. We are particularly interested in studying the dynamics of these molecular machines, and do so using single-molecule techniques. I will briefly highlight how the field of single-molecule biophysics has been able to advance such techniques over the past few decades, so that the dynamics of diverse sets of motor proteins can now be accurately followed. I will next describe how single-molecule techniques are now sufficiently mature that they can be used to undertake an exciting new challenge, namely the probing of complex molecular machines built up from many different components, such as the replisome that carries out accurate DNA replication in eukaryotes such as ourselves. While the overall outline of replisome assembly is understood, little is known about the dynamics of the individual proteins on the DNA and how these contribute to proper complex formation. I will show that using integrated optical trapping and confocal microscopy, one can dissect how protein binding, diffusion, sequence recognition, and protein-protein interactions play important roles in the first steps of replisome assembly, and discuss the biological implications thereof.
Professor at Leiden UMC – Department of Cell and Chemical Biology
Head Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
Neefjes is studying the molecular and cell biology of antigen processing and presentation by MHC class I and MHC class II molecules. Neefjes’ team has solved many steps in our current understanding of the MHC class I and MHC class II cell biology. This work is broadly applied in modern immunotherapy approaches. He is now combining that with genetic and chemical screens to find new targets and new leads for manipulation.
Neefjes has developed a number of unique lines of research with implications for cancer. These include the molecular basis for radio-immunotherapy and drug development for chemo-immunotherapy in cancer. Other lines of research include the relationship between bacterial infections and cancer. Neefjes showed the link between Salmonella Typhi infections and gallbladder carcinoma and most recently the link between another Salmonella serovar, Salmonella Enteritidis and colon cancer risk.
His research at the interphase of these disciplines resulted in a cell biological study on the activities of doxorubicin, a heavily used anti-cancer drug. Although reported in over 100,000 publications as a topoII poison that generates DNA breaks, Neefjes identified a second activity; histone eviction at defined sites in the genome. This work was extended to identify variant drugs that are active in oncology but lack the different side effects, including cardiotoxicity. The re-analysis of old drugs with new technologies offers the opportunity of modifying compounds to alter their activities and remove (some of) the therapy-limiting side effects, as will be presented.
What to do with a Spinoza premium?
It is fairly unusual that you get a call with a question whether you would like to receive an award worth 2.5 million Euro. This happened to me last year and was highly welcome! I will explain in this short presentation why and how then to spend this award. My work over the years moved from Immunology to Oncology and Cell Biology to Chemistry. We made exciting contributions to all these fields. The Spinoza premium will however be used for one direction in my research. Some 10 years ago, we discovered a new activity of an old anti-cancer drug called doxorubicin. This drug is effective but also toxic (it is also called Toxorubicin by clinicians). We wondered how important this new activity was for the anti-cancer activities and also for the toxicity of doxorubicin. We synthesized variants of doxorubicin and chemically separated the old from the new activity. Testing these variants in mice, cardiomyocyte cultures and tissue culture showed that the doxorubicin variants containing only the new activity are still active anti-cancer drugs but lack the toxic effects of doxorubicin. These variants can then be used for cancer patients that already received their maximal dose of doxorubicin but also for old cancer patients with a poor heart function that are now excluded from doxorubicin containing cancer treatments. These old cancer patients in fact represent most cancer patients! This variant drug should thus be made for patients. There is only one problem. The compound had been reported in the late 1980’s implying that there is no patent position and… that Pharma will not be interested in making this compound for clinical studies. In fact, such compounds then have to be made by Academia. But how to finance this? Here Spinoza comes in. I will present the steps that we have taken since October last year to bridge the gap between bench and bedside in the generation of a non-toxic doxorubicin variant for cancer patients. Spinoza is critical in bridging this gap!