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.

Cuya S.M., Bjornsti M.-A., and van Waardenburg R.C.A.M. DNA Topoisomerases Targeting Chemotherapeutics: What’s New? Invited by Cancer Chemotherapy and Pharmacology, in Press, 2017.

Cuya S.M., van Waardenburg, R.C.A.M. TDP1(Tyrosyl-DNA phosphodiesterase I). In: Choi, S. (ed.) Encyclopedia of Signaling Molecules, 2nd Edition, Springer International Publishing AG (In press, 2017).

Cuya S.M., Comeaux E.Q., Wanzeck K.C., Yoon K.J., and van Waardenburg R.C.A.M. Dysregulated human Tyrosyl-DNA phosphodiesterase I acts as cellular toxin. Oncotarget, 7(52): 86660-86674, 2016.

van Waardenburg R.C.A.M. Tyrosyl-DNA Phosphodiesterase I a critical survival factor for neuronal development and homeostasis. J. Neurol. Neuromed. (5) 25-29, 2016.

Comeaux E.Q., Cuya S.M., Kojima K., Jafari N., Wanzeck K.C., Mobley J.A., Bjornsti M.-A., and van Waardenburg R.C.A.M. Tyrosyl-DNA Phosphodiesterase I Catalytic Mutants Reveal an Alternative Nucleophile that can Catalyze Substrate Cleavage. J Biol Chem 290(10): 6203-6214, 2015.

Feduska J.M., Aller S.G., Garcia P.L., Cramer S.L., Council L.N., van Waardenburg R.C.A.M., Yoon K.J. ICAM-2 confers a non-metastatic phenotype in neuroblastoma cells by interaction with α-actinin. Oncogene 34(12): 1553-1562, 2015.

van Waardenburg R.C.A.M. and Bjornsti M-A. Ubiquitin Proteasome Pathway in Cancer in Molecular Oncology, edited by Gelmann EP, Sawyers CL 3rd and Rausher FJ. (eds). Cambridge University Press, New York, 2014. ISBN: 9780521876629.

Comeaux E.Q. and van Waardenburg R.C.A.M. Tyrosyl-DNA Phosphodiesterase I Resolves both Natural and Chemically Induced DNA Adducts and its Potential as a Therapeutic Target. Drug Metab Rev 46: 494-507, 2014.

Gajewski S., Comeaux E.Q., Jafari N., Bharatham N., Basford D., White S.W., van Waardenburg R.C.A.M. Analysis of the active-site mechanism of tyrosyl-DNA phosphodieasterase I: A member of the phospholipase D superfamily. J Mol Biol 415: 741-758, 2012.

He, X.#, van Waardenburg, R.C.A.M.#, Babaoglu, K., Price, A.C., Nitiss, K.C., Nitiss, J.L., Bjornsti, M.-A. and White, S.W. Mutation of a conserved active site residue converts Tyrosyl-DNA phophodiesterase I into a DNA topoisomerase-dependent poison. J. Mol. Biol., 372, 1070-1081, 2007. # Co-first authors, F1000 citation.