Associate Professor

Research Areas
Structure-Function analysis DNA repair proteins, post-translational modification enzymes and cytosolic Sulfotransferases, Mechanism of Action of proteins and drugs (chemotherapeutics), Drug development for novel therapeutic targets, Post-translational modification by Ubiquitin, SUMO (Small Ubiquitin-like MOdifier), Sulfonation of small molecules and proteins, Protein-Protein interactions

Biography

I obtained my Ph.D. in medical oncology from the University of Groningen, the Netherlands, in the group of Drs. Nanno Mulder and Elisabeth de Vries. My first postdoctoral fellowship was at the Netherlands Cancer Institute, with Dr. Jan Schellens and collaborator Dr. Jaap Brouwer (University of Leiden, the Netherlands). My second postdoctoral fellowship was at St. Jude Children’s Research Hospital in Memphis, Tennessee, in the group of Dr. Mary-Ann Bjornsti, where I collaborated with Dr. Brenda Schulman and Dr. Stephan White. As a research associate at St. Jude, I developed my interest in tyrosyl-DNA phosphodiesterase I (Tdp1), as both an enzyme and a potential therapeutic target.

Research Interests

In the van Waardenburg Lab, we are interested in the response of cells to treatment with chemotherapeutics, specifically DNA damaging agents. To investigate this response, we use yeast and human genetic technologies, biochemistry, and collaborate with structural biologists to resolve small-angle x-ray/crystal structures to analyze the structure-function relations and mechanisms of action of proteins and anti-cancer drugs.

We study the eukaryotic DNA repair enzyme Tyrosyl-DNA phosphodiesterase I (Tdp1), which belongs to the phospholipase D superfamily. Tdp1 comprises a very interesting catalytic cycle that consists of two active site histidines, one that functions as nucleophile and the other one as general acid/base. Using this histidine couple, Tdp1 is able to remove DNA adducts from the 3’- and 5’-end of a DNA strand break, and transfers the DNA end to its nucleophilic catalytic histidine. The interaction between Tdp1 and its substrates is very adaptable given that Tdp1 hydrolyses a wide variety of substrates that differ in size and complexity. Tdp1 removes small adducts such as a damaged nucleotide to a large and complex protein-DNA adduct. We use two clinically relevant model substrates: DNA topoisomerase I (Top1) to study 3’DNA-adducts, and DNA topoisomerase II (Top2) for 5’ DNA- adducts. Thus, Tdp1 is a unique DNA repair protein. It removes a DNA adduct via the formation of another one (Tdp1-DNA adduct); moreover, cells with low Tdp1 activity are hypersensitive to chemotherapeutics or other agents that induce DNA adducts, yet elevated expression, such as observed in almost all cancers, induces chromosome instability. It is unclear and understudied how cells regulate Tdp1 activity. Using these known protein-DNA substrates, we are able to study Tdp1 function in vivo/cell and in vitro biochemical assays. We are interested in the structure-function analysis of catalytic residue substitutions to investigate their catalytic function, determine mechanism of action (induction of cellular toxicity), and study Tdp1 cellular function/interaction with substrates and other proteins. We specifically focus on Tdp1 interactions with its protein-DNA substrates, e.g. Top1-DNA adducts in cells, biochemically and in structural analysis. In addition, we study the effects of post-translational modification, such as SUMOylation (SUMO conjugation) of Tdp1, on catalytic activity and protein-protein interactions in both the yeast and human cell model. SUMOylation has been shown to translocate Tdp1 within the nucleolus, while phosphorylation stimulates Tdp1 binding to other DNA repair proteins to be translocated to damaged nucleotides. We on the other hand study Tdp1 cellular distribution and translocation-stimuli; Tdp1 is found in the cytosol, nucleus and mitochondria. For the latter location, no obvious localization signals have been identified, so one of our focuses is to elucidate Tdp1 mitochondrial function and translocation signals/ pathways. These studies will reveal Tdp1 physiological function and Tdp1’s role in the etiology of human diseases. Furthermore, these studies revealed an alternative strategy to use Tdp1 as a therapeutic target for cancer treatment, which we are actively pursuing in the lab and are funded in part Alabama Drug Discovery Alliance (ADDA), Faculty development grants from ACS and UAB CCC and Department of Defense.

Besides cancer, Tdp1 is also involved in neurodegeneration. A mutation of the general acid/base histidine to arginine was identified in patients with the autosomal recessive disease spinocerebellar ataxia with axonal neuropathy (SCAN1). The mechanism by which this Tdp1-mutant only affects cerebellar neuronal cells is unknown. We are interested in elucidating this interesting phenotype by studying the role of Tdp1 in genome stability and the involvement of Tdp1’s mitochondria function. Interestingly, these SCAN1 patients are not prone to other genetic diseases, such as cancer or immune-deficiencies, suggesting that the cellular conditions of these cerebellar neurons play an important role in disease development.

Another subject the lab is interested in is the role of post-translational modification of proteins by ubiquitin and ubiquitin-like proteins, specifically SUMO (Small Ubiquitin-like MOdifier), in response to DNA damage. We focus on the effects of SUMOylation of proteins stimulated by SUMO E3-ligase and the effects of SUMO modification on protein-protein. Unlike the ubiquitin pathway, the SUMO pathway only uses a limited amount (10 to 20) of E3-ligases, which specifically stimulates SUMO conjugation to a sub-set of proteins (substrates). We are interested in identifying those proteins that are modified and play a role in the response to DNA damage in human cells.

Education

Graduate School
Ph.D., University of Groningen, the Netherlands

Postdoctoral Fellowship
Postdoctoral Fellow, The Netherlands Cancer Institute, Amsterdam, the Netherlands
Postdoctoral Fellow, St. Jude Children's Research Hospital

Contact

Office Location
Volker Hall 155

Phone
205-934-4572 (Office)
205-934-4513 (Lab)

Email
rvanwaar@uab.edu