Genome Maintenance Research Program
Program Leaders: David Cortez, Ph.D., and William Tansey, Ph.D.
The mission of the Genome Maintenance (GM) program is to understand the mechanisms that govern genome integrity, stability, expression, and the relationships between them. This program was established in January 2007 with the intention of providing a well-defined intellectual framework for Cancer Center members studying DNA-based processes. With this perspective in mind, the GM program has two broad Specific Aims:
- To foster interactions among GM members, providing them with a forum to exchange ideas and expertise, and to identify emerging areas of connectivity between different facets of DNA biology.
- To serve as a common intellectual resource for the Cancer Center, providing members of other programs with access to contemporary understanding of the mechanisms and technologies that relate to DNA and DNA-dependent transactions.
Twenty-six faculty, representing eleven departments across the Vanderbilt campus, form the GM program, and establish a research base that extends from control of DNA replication and mitosis through to mechanisms of DNA damage, the DNA damage response, and the regulation of gene activity. Members of the GM program provide expertise in biochemistry, cell biology, genetics, molecular biology, mouse model systems, proteomics, and structural biology. Assembling this vibrant group of researchers, connected by the common thread of DNA homeostasis, not only strengthens individual research programs, but—critically—creates unique opportunities for synergy that did not exist before GM was created. Given that some of the most fundamental unresolved questions in cancer biology relate to the processes that connect different aspects of DNA homeostasis, this synergy provides our Cancer Center with the means to meet the future challenges of basic cancer research head on.
Program Focus to Meet Scientific Goals
The GM program is organized around the central theme of DNA homeostasis. It has long been recognized that alterations in the quality or expression of the genetic material lie at the heart of cancer, and that understanding mechanisms through which these alterations occur, are remedied, or impact the cell is critical for any basic understanding of the disease. Importantly, however, the rubric of genome maintenance is also recognized as one offering great potential for the development of tools and strategies to detect, prevent, and treat human malignancy. It is this central role of genome maintenance, and the quality of the investigators that work within the program, that makes GM an important part of the basic research initiatives within the Cancer Center.
Interactivity is key to developing and maintaining the success of the GM program. The leadership of this program organizes a series of defined activities to promote such interaction. Highly focused intra-programmatic events allow GM to function as a coherent entity, whereas inter-programmatic exchanges permit the program to contribute in a meaningful way to the progress of research across the Cancer Center.
The processes that led to the development and implementation of this new program are described below. The GM program leaders at the time, David Cortez, Ph.D. and Earl Ruley, Ph.D., were anxious to establish a strong identity for this program from its onset. To launch GM, a retreat was held January 2007 in which seven GM program members presented their ideas about the “most important questions in mutagenesis and genome maintenance.” The goal was to start a discussion about how genome maintenance is important in cancer biology, identify the most important research questions in the field, outline the research expertise in these areas within the VICC, and identify opportunities for interactions that would drive new scientific discoveries relating to genome maintenance and cancer. Titles of presentations included: “To die or repair—what determines the response of cells to DNA damage?” by Sandra Zinkel, M.D., Ph.D.; “How are the successive activities of proteins coordinated in genome maintenance machines?” by Walter Chazin, Ph.D.; “What cellular processes regulate genome stability?” by Dr. Cortez; and “Do stem cells possess specialized mechanisms to suppress mutations?” by Dr. Ruley. To begin encouraging inter-programmatic interactions and translational research, we also invited Dennis Hallahan, M.D. (HT) to talk about “Therapeutic DNA-PK inhibitors.” This retreat was overwhelmingly successful, and not only defined the areas of research focus of the program, but also established an important tone for interactivity and collaborative research.
Figure GM 1. Focus of Research Activities within the Genome Maintenance Program.
Program Membership Criteria
Program membership was initially determined in January 2007 based on shared interest in the area of genome maintenance, including carcinogen metabolism, DNA damage, nucleic acid metabolism, cell cycle control, and chromatin structure and function. VICC Research Program membership is evaluated on a regular basis by the Research Program Leader's Committee. The most recent evaluation occurred in the spring of 2009. Recent VICC recruits or faculty who are interested in VICC membership submit a brief application, along with their current curriculum vitae and other support information for review and consideration. Applicants are evaluated for suitability as program members based on three criteria: 1) scientific interest and relevance of research to cancer and to the GM mission; 2) scientific excellence as judged by peer-reviewed publications and extramural grant support; and 3) level of scientific interaction as indicated by participation in VICC activities, as well as co-authorship and co-investigator status.
Faculty who do not meet all criteria but who have the potential to do so (i.e., junior faculty without current grant support) may be granted program membership privileges but are re-evaluated at least annually to determine progress in meeting our membership criteria.
About the Program Leaders
David Cortez, Ph.D., has been co-leader of this program since its inception in 2007, and is instrumental in defining the program and providing leadership continuity. As co-leader of GM, Dr. Cortez has been principally responsible for organizing the program’s activities, including monthly meetings, seminar series, and retreats.
Dr. Cortez is a Professor of Biochemistry and Ingram Professor for Cancer Research. Dr. Cortez was chosen as a co-leader of the GM program because of his research expertise and demonstrated leadership in genome maintenance at Vanderbilt. He has organized and led the DNA Repair, Replication and Damage Response interest group since 2005. This group’s monthly meetings continue as one of the GM programmatic activities. Dr. Cortez’s research focuses on the cellular responses to DNA damage. He is a leader in the field of DNA damage signaling by the ATM/ATR kinases, which regulate DNA repair, cell cycle transitions, DNA replication, and apoptosis. Dr. Cortez’s laboratory uses a variety of experimental systems, including yeast genetics, human cell culture, mass spectrometry, and structural biology; this places him in an ideal position to understand and integrate the various research activities in the GM program. Dr. Cortez also serves as Director of Graduate Studies in the Department of Biochemistry, has served as an ad hoc member of several study sections, including Molecular Genetics A, and serves on the editorial board of Journal of Biological Chemistry.
William Tansey, Ph.D., joined the Department of Cell and Developmental Biology (CDB) in the Vanderbilt University School of Medicine in June 2009. As described above, his recruitment was a joint effort between CDB and VICC, the latter of which provided much of the start-up package and provides Dr. Tansey with an Ingram Professorship of Cancer Biology. Dr. Tansey was actively recruited to the VICC with the express purposes of strengthening, and co-leading, the GM program, filling the co-leader role left open when Dr. Ruley decided to focus his efforts on research. Dr. Tansey's research is focused on understanding the mechanisms of regulation of Myc, an oncoprotein transcription factor that features prominently in human cancer. Dr. Tansey pioneered understanding of how Myc levels and activity are controlled by the ubiquitin–proteasome system, and how this process is deregulated in blood-borne cancers. Prior to joining the Vanderbilt faculty, Dr. Tansey was a Professor at Cold Spring Harbor Laboratory (CSHL) in New York, where he had worked for 17 years. During his time at CSHL, Dr. Tansey gained significant administrative experience, and was Director of Graduate Studies for the Watson School of Biological Sciences, as well as Scientific Head of the Flow Cytometry Shared Resource within the CSHL Cancer Center. He is currently an Associate Editor for Molecular Biology of the Cell. Dr. Tansey has also served as an ad hoc member of NCI Program Project review panels, and was a permanent member—and chair—of the Molecular Genetics A Study Section.
Areas of Research Program Expertise
Research activities of the Genome Maintenance Program are focused in the following areas:
- Carcinogen metabolism and the biochemistry of DNA adducts
- Cellular responses to DNA damage, including signaling, checkpoints and apoptosis
- DNA metabolism including replication, repair and recombination
- Cell Cycle Control
- Chromosome and chromatin structure and function
Since the mechanisms controlling genome maintenance are highly evolutionarily conserved, program members use multiple model systems and approaches in their research, including:
- E. coli and archaebacteria genetics and biochemistry
- Saccharomyces cerevisiae and Schizosaccharomyces pombe
- D. melanogaster
- Xenopus laevis
- Structural biology, including X-ray crystallography and NMR
- Human and mouse cell culture
- Mouse models of human cancer
Below is a brief synopsis of our research activities:
Carcinogen metabolism and the biochemistry of DNA adducts
A research strength at Vanderbilt, and now a strength of the GM program, is in the area of carcinogen metabolism and mutagenesis. Fred Guengerich, Ph.D. studies how cytochrome P450 enzymes metabolize carcinogens into active compounds that produce DNA adducts leading to mutation. Dr. Guengerich has studied the catalytic mechanisms of these enzymes in detail, leading to an understanding of which P450 enzymes are critical in the activation of specific environmental carcinogens. He has defined the mutagenicity of many compounds, including halogenated hydrocarbons. Finally, he is interested in how the carcinogen-modified DNA interacts with polymerases to generate mutations. Dr. Guengerich uses a biochemical approach with human and bacterial enzymes. Micheal Stone, Ph.D. and Dr. Egli collaborate with Dr. Guengerich in these research activities. In particular, Dr. Stone studies the chemistry of the carcinogen-DNA adduct and Dr. Egli uses X-ray crystallography to define the structures of polymerases bound to damaged DNA. This research defines how mutations are generated by the DNA adducts during replication.
Lawrence Marnett, Ph.D. has had a long interest in cyclooxygenase and DNA damage. Cyclooxygenase-2 catalyzes the production of prostaglandins and is the molecular target of non-steroidal anti-inflammatory drugs. These drugs are being investigated in the cancer clinic. Dr. Marnett is also interested in the chemistry and biology of DNA damage caused by oxidative stress. By incorporating relevant DNA lesions into bacterial or viral genomes, he is able to perform in vivo mutagenesis experiments and identify the human DNA repair proteins required to remove these lesions. As the leader of the Vanderbilt Institute for Chemical Biology (VICB), Dr. Marnett also brings a unique set of tools to the GM program. His interactions within the program are beginning to influence other members’ activities. For example, both Drs. Oltz (former member of GM) and Cortez have initiated drug discovery programs with the collaboration of the VICB and financial support of VICC pilot project funding (detailed below).
Cellular responses to DNA damage
Dr. Cortez’s laboratory is dedicated to understanding how the cellular DNA damage responses coordinate genome maintenance activities, including DNA repair, replication, and cell cycle control. In particular, he studies the signaling cascades that are controlled by the ATM/ATR/DNA-PK family of protein kinases, including multiple tumor suppressors such as p53 and BRCA1. Dr. Cortez’s research in both human cell culture and S. cerevisiae systems has discovered how these kinases recognize DNA damage, the kinase activation mechanisms, and the downstream signaling events leading to cell cycle checkpoints.
Brian Wadzninski, Ph.D. and Dr. Zinkel are also interested in DNA damage responses. Dr. Wadzinski is investigating how protein phosphatases regulate the checkpoint signaling cascades. Dr. Zinkel studies the cell cycle arrest or apoptosis decision point. Using reagents generated in Dr. Cortez’s laboratory, Dr. Zinkel was recently able to show that the apoptotic protein BID also functions upstream in the ATR signaling pathway. These experiments were facilitated by the interactions within the GM program. In particular, Dr. Zinkel presented her ideas at a monthly meeting of the DNA Replication, Repair, and Damage Response Interest Group and this presentation, in turn, initiated the collaboration with the Cortez laboratory.
Dr. Eischen utilizes mouse models to study the influence of tumor suppressors and oncogenes on apoptosis, proliferation, chromosomal stability, and cellular transformation. She recently discovered that Mdm2 promotes genetic instability and cellular transformation independently of p53.
Michael Freeman, Ph.D. is interested in cancer drug development. In particular his laboratory is developing sensitizers to ionizing radiation and chemopreventive agents. He is using defined DNA substrates, cultured human cells, and animal models in these efforts.
DNA metabolism including replication, repair and recombination
A strength of the GM program is the investigators studying nucleic acid metabolism in several experimental systems. Several investigators study different aspects of DNA replication. Dr. Fanning studies replication origin control and primer synthesis by DNA Pol alpha. One of her model systems is the SV40 tumor virus, as its replication can be reconstituted in vitro. Dr. Cortez studies the replication checkpoint and the connections between DNA damage signaling and replication proteins. Dr. Chazin studies the replication apparatus with a view of it as a molecular machine. His structural studies on replication protein A (RPA) impact both Drs. Fanning and Cortez’s research because RPA is a key protein in replication and checkpoint control. Drs. Kaplan and Eichman are junior investigators that study the biochemistry of replication initiation and elongation. Daniel Kaplan, Ph.D. is focusing on the mini-chromosome maintenance proteins 2-7 (MCM2-7) that act as the replicative helicase. He is reconstituting helicase activity in vitro and determining how post-translational modifications catalyzed by the cell cycle kinases regulate their activity. Dr. Eichman has recently solved the structure of another mini-chromosome maintenance protein MCM10 that functions in origin initiation. Niel Osheroff, Ph.D. has a long-standing program in the enzymology of topoisomerase II, which is a major target of chemotherapeutic agents (i.e., etoposide).
Drs. Eichman and Chazin also have research programs in the area of DNA repair. Dr. Chazin is using the nucleotide excision repair system as a model to study how dynamic protein-protein and protein-DNA interactions accomplish excision and repair. Dr. Eichman has determined the structure of several DNA glycosylases that function in base excision repair. Dr. Guengerich has an active research program studying the mechanisms of DNA lesion bypass by specialized polymerases.
Finally, Dr. Ruley is interested in the mechanisms of DNA recombination, especially those that lead to loss of heterozygosity. He has developed a gene-trap library of embryonic stem cells that allows him to do genome-wide studies of spontaneous and carcinogen-induced loss of heterozygosity studies. His work underscores the importance of genome maintenance in stem cells that serve as the cellular precursors to cancer.
Cell cycle control
An important mechanism controlling genome stability is cell cycle control. In particular, chromosome instability and aneuploidy is caused by defects in mitotic control. Dr. Gould is a Howard Hughes Investigator with an interest in the mechanisms controlling chromosome segregation and cell division. Using the S. pombe model system, Dr. Gould has made many contributions to our understanding of mitotic control, including a recent low-resolution structural determination of the 13-subunit anaphase promoting complex (APC). This ubiquitin ligase complex controls chromosome segregation and mitotic exit through the regulated destruction of multiple cell cycle regulatory proteins. The structural studies of the APC were initiated as collaboration with Melanie Ohi, Ph.D. when she was a post-doctoral fellow, and this collaboration continues now that Dr. Ohi has been recruited to Vanderbilt as an Assistant Professor
Laura Lee, M.D. is also interested in chromosome segregation and uses D. melanogaster as a model system. She has isolated a series of fly mutants that have chromosome instability due to defective mitotic control. She is studying the mechanisms that these genes use to control chromosome stability and is extending her research into the human system, as most of the genes are conserved.
Chromatin structure and function
All nucleic acid metabolism works within the context of chromatin. Chromatin regulation is critical for DNA repair and DNA damage responses. For example, a histone variant, H2AX, is phosphorylated at sites of DNA damage by the checkpoint kinases ATM and ATR. In addition, epigenetic marks in the chromatin must be preserved during cell division; failure of this process can lead to aberrant gene expression patterns that promote tumorigenesis. Dr. Hiebert studies the molecular mechanisms of acute leukemia. He is particularly interested in how chromatin-modifying enzymes, including histone deacetylases (HDACs), regulate transcription and DNA repair. He recently published a collaborative study with Dr. Cortez that demonstrated the role of HDAC3 in regulating genome stability.
Finally, Dr. Tansey’s laboratory studies the mechanisms of ubiquitin-mediated proteolysis as they relate to the control of chromatin function and gene expression. Ubiquitylation controls multiple aspects of nucleic acid metabolism, including transcription and DNA repair. In particular, Dr. Tansey has studied how the Myc oncoprotein is controlled by proteolysis.
- Chazin, Walter J., Ph.D.
Chancellor's Professor of Biochemistry, Physics; Professor of Chemistry; Director, Vanderbilt University Center for Structural Biology; Researcher
- Cortez, David K., Ph.D.
Ingram Professor of Cancer Research; Professor of Biochemistry; Researcher
- Egli, Martin, Ph.D.
Professor of Biochemistry; Associate Professor of Biological Sciences; Researcher
- Eichman, Brandt F., Ph.D.
Associate Professor of Biological Sciences; Researcher
- Eischen, Christine Marie, Ph.D.
Associate Professor of Cancer Biology; Associate Professor of Pathology, Microbiology, and Immunology; Researcher
- Freeman, Michael L., Ph.D.
Professor of Radiation Oncology; Researcher
- Friedman, Katherine L. (Kathy), Ph.D.
Associate Professor of Biological Sciences; Researcher
- Gould, Kathleen L., Ph.D.
Louise B. McGavock Professor and Chair; in Cell & Developmental Biology; Researcher
- Guengerich, F. Peter, Ph.D.
Professor of Biochemistry; Researcher
- Hiebert, Scott W., Ph.D.
Associate Director for Basic Research; Hortense B. Ingram Professor of Cancer Research; Professor of Biochemistry; Associate Professor of Medicine; Researcher
- Khabele, Dineo, M.D.
Assistant Professor of Cancer Biology; Obstetrics and Gynecology; Gynecological Oncologist
- Lee, Laura A., M.D., Ph.D.
Associate Professor of Cell and Development Biology; Researcher
- Marnett, Lawrence J., Ph.D.
Mary Geddes Stahlman Professor of Cancer Research; University Professor of Biochemistry and Chemistry; Professor of Pharmacology; Director, Vanderbilt Institute of Chemical Biology; Director, A.B. Hancock Jr. Memorial Laboratory; Director, Vanderbilt Institute; Researcher
- Ohi, Melanie D., Ph.D.
Assistant Professor of Cell and Developmental Biology; Researcher
- Ohi, Ryoma, Ph.D.
Assistant Professor of Cell and Developmental Biology; Cell Biology Researcher
- Osheroff, Neil, Ph.D.
John Coniglio Professor of Biochemistry; Professor of Medicine; Researcher
- Porter, Ned A., Ph.D.
Stevenson Professor of Chemistry; Professor of Biochemistry; Researcher
- Rizzo, Carmelo J., Ph.D.
Professor of Chemistry; Director of Graduate Studies; Researcher
- Stone, Michael P., Ph.D.
Professor of Chemistry; Chair of the Department of Chemistry; Researcher
- Tansey, William P., Ph.D.
Ingram Professor of Cancer Research; Professor of Cell and Developmental Biology; Researcher
- Venters, Bryan J., Ph.D.
Assistant Professor of Molecular Physiology & Biophysics
- Wadzinski, Brian E., Ph.D.
Associate Professor of Pharmacology; Researcher
- Zinkel, Sandra, M.D., Ph.D.
Assistant Professor of Medicine, Cancer Biology, Cell & Developmental Biology; Medical Oncologist, Hematologist