Chromatin Landscaping of TGF-P/SMAD Signaling Targets

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The TGF-beta/SMAD signaling network plays an important role in growth inhibition of normal epithelia. In neoplastic processes, genetic and epigenetic losses of TGF-beta/SMAD signaling can result in outgrowth and invasion of transformed cells. In ovarian cancer, it has recently been reported that TGF-beta/SMAD signaling can become non-responsive to activators of TGF-beta, despite the fact that upstream regulators, such as TbetaRII, remain genetically intact and functional. Thus, it appears that other aberrant events, perhaps affecting co-activators or co-repressors of this growth inhibitory pathway, trigger epigenetic perturbations in TGF-beta/SMAD downstream targets. These as of yet un-explored perturbations have the potential to gradually alter chromatin structure in and around promoters of target genes and may be somatically heritable. We hypothesize that epigenetic deregulation TGF-beta/SMAD signaling may alter transcriptional profiles of TGF-beta/SMAD target genes, resulting in the initiation and promotion of neoplastic outgrowth of the ovarian surface epithelium. To test our hypothesis, we will comprehensively survey and compare regional chromatin profiles (active or repressed state) of TGF-beta/SMAD target promoters in ovarian cancer versus normal epithelia. Relative to this epigenetic phenomenon, SMAD-mediated transcription regulation also depends on other mechanisms, such as tissue-specific factors, promoter sequences, and cooperative interaction with other DMA-binding transcription factors. We will use computational tools to identify putative TGF-beta/SMAD target sequences and determine their functional relationship with local chromatin structure in ovarian epithelia. A novel microarray-based ChlP-on-chip assay will be developed to experimentally determine whether chromatin remodeling (i.e., histone modifications) of these predicted promoters occurs in ovarian cancer. Statistical approaches will be proposed to model the interaction between SMAD complexes and altered chromatin structure and to define unique epigenetic signatures in ovarian cancer cells. Specifically, we will 1) develop KbTSMAD (Knowledge base of TGF-beta/SMAD signaling pathway), an information resource of the TGF-beta/SMAD signaling pathway and its direct target gene promoters; 2) determine profiles of chromatin remodeling in these downstream loci in ovarian cancer cells; and 3) develop statistical approaches for modeling the synergistic interaction between TGF-beta/SMAD complex and altered chromatin structure and for defining unique epigenetic signatures in ovarian cancer cells.