All cells in an organism, with a few exceptions, bear the same genome, yet they specialize to give rise to tissues with diverse morphology and function. This diversity arises due to the differences in sets of genes that are expressed in a programmed manner during development and cellular differentiation. The recent decoding of the human genome, coupled with genome-wide expression profiling, is clarifying the relationship between specific gene expression patterns and cell fate. Gene expression patterns are controlled by a host of transcription regulatory factors. In many types of cancers it is often malfunctioning transcriptional regulators that produce aberrant patterns of gene expression that are at the heart of the ailment. In this context, it is critical to identify regulatory targets of oncogenic transcriptional regulators and develop synthetic molecules that can control their expression. Ideally, such synthetic molecules or artificial transcription factors (ATFs) would be engineered to positively or negatively regulate targeted genes within regulatory networks. Such molecules would serve as powerful tools for functional genomics as well as for unraveling key transcriptional events at specific genes that govern cell fate. In the long term, ATFs have significant potential as chemotherapeutic agents. A major goal of this proposal is to define the DNA regulatory sites of two oncogenic transcription factors, E2a- Pbx1 and HoxA9. E2a-Pbx1 is implicated in the onset of 25% of all diagnosed pediatric pre B-cell leukemias (B-ALL) and the misregulation of HoxA9 is linked to the etiology of Acute Myeloid Leukemia (AML). The identification of genome-wide DNA regulatory sites of the two proteins will serve as the basis for understanding the gene regulatory networks that govern the onset of these cancers. The second major goal of the current proposal is to develop synthetic molecules to target and inactivate the human oncogene E2a-Pbx1. This effort builds on our success in targeting homologous transcription factors from Drosophila and the up-regulation of eukaryotic gene expression with rationally designed artificial transcription factors. The proposed studies will provide the framework to develop ATFs that target and regulate the transcriptional and oncogenic properties of other oncogenic transcription factors. We will thus develop a general approach to building sophisticated ATFs that act in concert with endogenous transcription factors to regulate genes in response to cellular signals. Together, our work will generate powerful tools that can be used to study intractable mechanistic features of transcriptional regulation, dissect genome-wide transcriptional networks, serve as guides to trigger desired transcriptional cascades and control the fate of cells and organisms.

Public Health Relevance

This grant is focused on understanding and controlling the gene networks that govern the onset of leukemia by utilizing genomic and chemical strategies to target the oncogenic protein E2a-Pbx1. The modular design principle of our small molecule inhibitors permits enormous breadth and are broadly applicable to a variety of transcriptional regulators that have been implicated in many different cancers. In addition, the genome location and expression studies as well as the cognate site identification platform that we invented have direct utility in elucidating the nature of gene networks that cause specific forms of cancer due to misregulation of a broad swath of transcription regulators.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Drug Discovery and Molecular Pharmacology Study Section (DMP)
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Fu, Yali
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University of Wisconsin Madison
Schools of Earth Sciences/Natur
United States
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Erwin, Graham S; Grieshop, Matthew P; Bhimsaria, Devesh et al. (2016) Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin). J Vis Exp :e53510
Xiong, Kan; Erwin, Graham S; Ansari, Aseem Z et al. (2016) Sliding on DNA: From Peptides to Small Molecules. Angew Chem Int Ed Engl 55:15110-15114
Erwin, Graham S; Grieshop, Matthew P; Bhimsaria, Devesh et al. (2016) Synthetic genome readers target clustered binding sites across diverse chromatin states. Proc Natl Acad Sci U S A 113:E7418-E7427
Mead, Matthew E; Stanton, Brynne C; Kruzel, Emilia K et al. (2015) Targets of the Sex Inducer homeodomain proteins are required for fungal development and virulence in Cryptococcus neoformans. Mol Microbiol 95:804-18
Eguchi, Asuka; Lee, Garrett O; Wan, Fang et al. (2014) Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers. Biochem J 462:397-413
Erwin, Graham S; Bhimsaria, Devesh; Eguchi, Asuka et al. (2014) Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites. Angew Chem Int Ed Engl 53:10124-8
Campbell, Zachary T; Bhimsaria, Devesh; Valley, Cary T et al. (2012) Cooperativity in RNA-protein interactions: global analysis of RNA binding specificity. Cell Rep 1:570-81
Tietjen, Joshua R; Donato, Leslie J; Bhimisaria, Devesh et al. (2011) Sequence-specificity and energy landscapes of DNA-binding molecules. Methods Enzymol 497:3-30
Ansari, Aseem Z; Peterson-Kaufman, Kimberly J (2011) A partner evokes latent differences between Hox proteins. Cell 147:1220-1
Peterson-Kaufman, Kimberly J; Carlson, Clayton D; Rodríguez-Martínez, José A et al. (2010) Nucleating the assembly of macromolecular complexes. Chembiochem 11:1955-62

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