We are applying genome-scale approaches to derive and test network models of cancer and the eukaryotic DNA damage response. Failure of cells to respond to DNA damage is a primary step in the onset of cancer and is also a major way in which environmental toxins diminish human health. Consequently, cells have evolved complex repair and stress responses that are highly conserved across the eukaryotic kingdom, from yeast to humans. The DNA damage response network has multiple layers, including genetic, transcriptional, and protein interactions. To elucidate the genetic network layer we have used an approach called differential epistasis mapping (dE-MAP) to map widespread interaction changes among yeast kinases, phosphatases, and transcription factors as the cell responds to DNA damage [Bandyopadhyay et al. Science 330(6009):1385-1389 2010]. The differential interaction mapping approach has been very effective at identifying DNA repair pathways, highlighting new damage-dependent roles for the Slt2 kinase, Pph3phosphatase, and histone variant Htz1.
To explore the transcriptional response, we have used genome-wide chromatin immunoprecipitation (ChIP-chip and ChIP-seq) to systematically map transcriptional interactions [Workman et al. Science312(5776):1054-1059 2006]. We have examined the genome binding profiles of over 30 transcription factors before and after DNA damage is applied resulting in thousands of dynamic TF-target interactions. We have also interrogated the transcriptional circuits that govern the process by which cells adapt to stress by reactive oxygen species [Kelley and Ideker, PLoS Genetics 5(5):e1000488 2009]. Reactive oxygen species (ROS) are a natural byproduct of metabolism that can also result in significant damage to cell structures. We have implicated a network involving the TF Mga2 as central for adaptation to hydrogen peroxide.
Finally, we have integrated protein-protein interaction networks with DNA damage sensitivity measurements for all yeast gene knockouts to identify protein interaction complexes that are essential for the response to DNA damaging agents [Begley et al. Molecular Cell 16(1):117-25 2004, Molecular Cancer Research1:103-112 2002
] including arsenic [Haugen et al.Genome Biology 5(12):R95 2004
DNA damage response: Genetic interaction view [Bandyopadhyay et al. Science 2010].
DNA damage response: Transcriptional network view [Workman et al. Science2006].
To build and interpret these maps we have enjoyed significant collaborations with the laboratories of Nevan Krogan (UCSF), Richard Kolodner (UCSD), and Leona Samson (MIT). These projects are funded by grant ES014811 from the National Institute for Environmental Health Sciences.