Research
Experimental Systems
The Gartner lab has a track record focused on using the nematode worm Caenorhabditis elegans as a model for understanding basic aspects of germ cell apoptosis, genome maintenance, and meiotic recombination. C. elegans is the simplest genetically tractable animal to study genome maintenance at an organismal level. Studies on C. elegans take advantage of the fast generation time of fewer than 4 days, the ease of its maintenance, vast strain collections, the feasibility for conducting forward genetic screens, and a rich repertoire of RNAi and advanced genome editing procedures. The C. elegans germline affords advanced cytological staining procedures and worm embryos are amenable to sophisticated real-time imaging, with one cell cycle occurring in less than 20 minutes. The small genome size of 100 million base pairs allows for high coverage of whole-genome sequencing at a cost of less than ~US$50.
We also use mammalian TK6 lymphoblastoid cells as a second model to study DNA damage response mechanisms and mutagenesis. These cells have a normal karyotype and can be easily manipulated. Furthermore, a large number of TK6-derived DNA repair defective isogenic knockout lines are available. We are interested in the basic mechanism of DNA damage signaling, genome maintenance, and mutagenesis.
Studying new fail-safe mechanisms that ensure faithful genome maintenance just before cells divide.
On average, only one mutation occurs in a C. elegans generation, and only ~20 germline mutations occur in a human generation. The question of how such high fidelity is achieved is still the subject of many research efforts, and redundant DNA repair pathways appear to be a key mechanism. For example, branched DNA structures that arise as intermediates in DNA metabolism can be processed by the Mus81, Slx1, and Gen1 nucleases. Nevertheless, some branched molecules persist into mitosis and result in DNA bridges in a large fraction of dividing cells. The processing of those DNA bridges is important to prevent aneuploidy and disease. We recently discovered that the conserved LEM-3/Ankle1 nuclease resolves these bridges using C. elegans. We will elucidate the mechanisms by which LEM-3/Ankle1 acts and study this process in more detail and now also use mammalian cells.
Understanding the basic mechanism of mutagenesis and exploiting our insight to find modalities that specifically target DNA repair defective cancer cells.
The acquisition of mutations is an intrinsic feature of all cells despite the vast majority of primary DNA lesions being removed by repair pathways. Although DNA damage and repair pathways have been extensively studied, there is limited understanding of mutational processes operating in eukaryotic cells in vivo. The advent of next-generation sequencing provides the power to detect and characterize large sets of mutations and to determine mutational patterns, providing a new opportunity to understand mutagenesis and various DNA repair processes that mend damaged DNA as well as the interplay between them. Mutational patterns associated with known mutagens, DNA repair deficiencies, or a combination thereof can be compared to mutational signatures derived from cancer genomes, and provide the opportunity to explain the mutagenic processes that drive cancer progression. Paradoxically, the majority of chemotherapeutic anti-cancer agents act by inflicting DNA damage to kill cancer cells. Systematically deciphering mutagenic processes triggered by exposure to genotoxic agents has the potential to improve cancer treatment.