CORE 2: DRIVING BIOLOGICAL PROJECTS DBP 1. Identifying Hox protein-specific DNA-binding sites and probing their shapes Background: The Hox genes encode a set of homeodomain-containing transcriptional regulators that play critical roles in the development of all metazoans. Mutations in Hox genes and in their DNA-binding cofactors underlie several human diseases and birth defects, most notably, leukemias (54, 55). Hox genes in humans all encode proteins with nearly indistinguishable binding specificities, despite having distinct functions in vivo, raising the question of how these factors achieve specificity (56, 57). A partial answer to this paradox is that Hox proteins only achieve specificity when binding cooperatively to DNA with various cofactors (58, 59). As further discussed in DBP 1, while a number of crystal structures exist for ternary complexes of DNA and the DNA-binding homeodomains of a Hox protein and one of its cofactors, until recently they did not provide insights as to the source of specificity. Part of the problem was that the crystal structures had been determined with non-specific DNA. Our studies of a site that is specific to a single Hox protein revealed that, in addition to the major groove binding pattern common to all Hox proteins, specificity is achieved, at least in part, through the recognition of sequence-specific minor groove shape. However, we do not yet have an understanding of how other Hox family members use this readout mechanism. Acquiring such information is critical to eventually solving the Hox specificity problem and at the same time providing critical insights into the general problem of DNA recognition by many TFs thus providing a paradigm for how other TF families achieve specificity. DBP 2. Probabilistic dynamic modeling of the ErbB signaling pathways Background: ErbB pathways, involved in cell proliferation, survival and motility, are among the best studied mammalian signaling networks (60). Dysregulation of the ErbB signaling has been implicated in a variety of human cancers (61, 62). ErbB receptors and downstream targets are also a major focus of current pharmaceutical research (63, 64). The combinatorial complexity of the pathway, both at the level of ErbB1-4 receptors and at the level of their multiple downstream targets, makes computational modeling essential in understanding ErbB-related signaling (65). Kinetic models of ErbB pathways are usually based on ordinary differential equations, where core interactions are represented as elementary reactions with appropriate rate laws (66-70). Although helpful, the predictive power of these models is limited by the presence of a large number of unmeasured and uncalibrated parameters. Currently, there is no principled way to account for parameter uncertainty in existing models. DBP 3. Master regulators of tumorigenesis and drug sensitivity in prostate cancers Background: We have recently demonstrated that unbiased analysis of a genome-wide molecular-interaction network (interactome), inferred from a large collection of molecular profiles of GBM patients, could elucidate the genetic determinants of the most aggressive subtype of the disease (5). Such networks, assembled from naturally occurring phenotypic variability in patients, while highly informative on disease etiology fail to capture the tumor response to specific therapeutic agents. Similarly, while extensive molecular profiles produced by chemical perturbation of cell lines have been assembled (38), these fail to capture compound activity in vivo. To address these issues the Abate-Shen, Shen, and Califano labs were recently funded by the Mouse Model of Human Cancer Consortium (MMHCC) to assemble and interrogate a prostate cancer interactome by perturbing several genetically engineered mouse models with perturbagens targeting key pathways in the disease. Such a mouse Prostate Cancer interactome (mPCi) will provide valuable information on drug-related pathway activity in vivo and would be ideally complemented by an equivalent in vivo human Prostate Cancer interactome (hPCi). This combination would provide tremendous insight into compounds whose pathways activity is conserved in both organisms, allowing a truly informed use of the mouse as a model to test compounds and biomarkers for translation into humans. Unfortunately, performing these studies in human subjects in not viable because of the complexity of the protocols and because many of the probes that can perturb relevant pathways may be too toxic to be used in human subjects.