I received a PhD in Biochemistry and Molecular Biology at the University of Maryland School of Medicine and completed postdoctoral training at the Johns Hopkins University School of Medicine and the University of Maryland Center for Advanced Research in Biotechnology (CARB; currently known as IBBR). I joined the Department of Biochemistry and Molecular Biology at the University of Maryland School of Medicine in 2005. Our research has been supported continuously by grants from the NIH since 2005.
Our research centers on two areas, DNA repair and epigenetic regulation. The nucleobases of DNA are amenable to a broad range of chemical alterations, a feature that enables enzyme-mediated modifications but also allows for threatening DNA damage. We study enzymes that find and repair DNA lesions, thereby maintaining genomic integrity and protecting against cancer and other diseases. We also investigate enzymes that perform essential functions in epigenetic regulation, by acting on modified DNA bases. We use a broad range of biochemical, biophysical, structural, and molecular approaches, and collaborate with many other research groups. Some of our current research interests are summarized below.
DNA Repair – Avoiding mutations caused by mC deamination
Often termed the “5th base” in DNA, 5-methylcytosine (mC) is a key epigenetic mark in eukaryotes, and it functions in restriction modification systems of archaea and bacteria. However, mC also threatens genetic and epigenetic integrity. Deamination of mC to T generates G/T mispairs, and, upon replication, CàT transitions. Through this process, mC deamination causes many point mutations in cancer and genetic disease. Two human glycosylases remove T from G/T mispairs, TDG (thymine DNA glycosylase) and MBD4 (methyl binding domain IV). Like other glycosylases, they flip a damaged base into their active site and cleave the base-sugar bond; follow-on base excision repair (BER) enzymes complete the repair process. While most glycosylases excise bases that are foreign to DNA (e.g., uracil), these mismatch enzymes remove a canonical base, thymine, from rare G/T mispairs but not from the vast background of A:T pairs. Because aberrant action on A:T pairs can be mutagenic and cytotoxic, specificity is critical for these enzymes, and we are studying how it is attained. We also study how TDG and MBD4 recognize other damaged bases, including uracil and 5-fluorouracil (5FU), among others. TDG excision of 5FU contributes to the antitumor effects of 5FU, which is used to treat cancer.
Epigenetic Regulation - Base Excision Repair in active DNA DemethylationMethyltransferases are known to convert C to mC, but the process for reversing this epigenetic modification had remained unclear. One mechanism involves DNA replication without subsequent remethylation. Recent studies establish a pathway for active DNA demethylation, involving TET (ten-eleven translocation) enzymes and TDG-initiated BER (Fig. 1). TET enzymes catalyze stepwise oxidation of mC, to give 5-hydroxymethyl-C (hmC), then 5-formyl-C (fC), and 5-carboxyl-C (caC). TDG excises fC and caC, and subsequent BER steps restore cytosine. This central function in epigenetic regulation likely explains findings that TDG is essential for embryonic development. We study the role of TDG and other BER enzymes in active DNA demethylation.
Protein Regulation by SUMO binding and SUMO conjugation
TDG can be covalently modified by SUMO (small ubiquitin-like modifier) proteins, and it also features a SUMO interacting motif (SIM) that binds non-covalentlyto SUMO domains. The SIM can bind free SUMO, a SUMO domain that is tethered to another protein, and intramolecularSUMO (tethered to TDG). We are investigating the effect of SUMO binding and SUMO conjugation on TDG function(s), and testing the current paradigm that SUMO modification of product-bound TDG is needed to relieve product inhibition and allow for efficient catalytic turnover. We are also studying how SUMO modification of TDG is regulated in cells.
DNA repair by endonuclease-exonuclease-phosphatase (EEP) enzymes
Enzymes of the EEP superfamily catalyze phosphate ester hydrolysis and mediate a broad range of important biological reactions. Abundant in all three domains of life, EEPs are required for processes such as apoptosis, cell-cycle regulation, DNA repair, intracellular signaling, and transposition, among others. While many crystal structures of EEPs are available and the essential catalytic residues are known, the mechanism of these enzymes remains unresolved. We are interested in two EEPs that function in DNA repair, AP endonuclease 1 (APE1) and tyrosyl-DNA-phosphodiesterase 2 (TDP2). APE1 is essential for BER and strand break repair; it cleaves DNA at abasic sites and removes 3 ´-blocking groups at strand breaks, enabling follow-on repair. TDP2 removes the 5’-tyrosyl moiety from DNA strand breaks caused by aborted topoisomerase reactions; these toxic lesions arise naturally and are generated by topoisomerase-directed anti-tumor agents. TDP2 is also a host factor for viruses that cause human disease (e.g., hepatitis B). APE1 and TDP2 are considered important targets for new agents to treat human diseases, including cancer. They repair lesions generated by anti-tumor agents and their suppression sensitizes cells to such agents.