Histone deacetylases (HDACs) play important roles in cancer, and the FDA approved HDAC inhibitor, suberoylanilide hydroxamic acid (SAHA), is used for the treatment of advanced and refractory cutaneous T-cell lymphoma in patients with progressive, persistent, or recurrent disease. SAHA is part of more than 225 clinical trials. Inhibition of HDAC activity results in altered acetylation of core histones and other proteins that cause changes in gene expression, resulting in cell growth arrest and apoptosis. However, despite the massive investment the United States has made into the study of SAHA as a drug for human disease treatment, it is routinely stated that the mechanism of action of SAHA remains poorly understood. Recent findings from our lab suggest that SAHA and HDAC inhibitors actually have broader, noncatalytic effects on HDAC complexes. Here we will use innovative biochemical, quantitative proteomic, computational, and genomic technologies to further elucidate the mechanism of action of SAHA. In particular, we will analyze the SAHA induced disruption of a human HDAC protein interaction network and determine which fraction of SAHA induced gene expression changes can be accounted for by disrupting this network.
In specific aim 1 we will complete our assembly of the protein interaction network and biochemically dissect the multiple complexes present in this network. Furthermore, we will develop novel computational approaches for protein interaction network assembly and determine the strength of interactions in this network.
In specific aim two, we will finalize our analysis of the SAHA induced dynamics of the network and dissect the gene expression changes resulting from network disruption. In the third specific aim, we will carry out focused studies on a breast cancer cell line and compare these results to the standard cell line used in specific aims 1 and 2. By comparing and contrasting these results, we will determine the cell specific effects of SAHA on this human HDAC network. Upon completion of this application, we will have a detailed understanding in multiple cell types of the effects of SAHA on a histone protein interaction network and the resulting gene expression changes mediated by the disruption of this network. This information will yield novel insights into the mechanism of action of SAHA and facilitate future development of novel HDAC inhibitors.
Currently, we have a poor understanding of the mechanism of action of the cancer therapeutic suberoylanilide hydroxamic acid. We have strong evidence to suggest that disrupting a protein interaction network mediates a significant portion of the effect of this drug on gene expression. By applying innovative genomics and quantitative proteomics analyses, we will generate fundamental biological insights regarding the mechanism of action of this important human therapeutic.
|Banks, Charles A S; Miah, Sayem; Adams, Mark K et al. (2018) Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly. Sci Rep 8:13712|
|Banks, Charles A S; Thornton, Janet L; Eubanks, Cassandra G et al. (2018) A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry. Mol Cell Proteomics 17:1432-1447|
|Sardiu, Mihaela E; Gilmore, Joshua M; Groppe, Brad et al. (2017) Identification of Topological Network Modules in Perturbed Protein Interaction Networks. Sci Rep 7:43845|
|Eubanks, Cassandra G; Dayebgadoh, Gerald; Liu, Xingyu et al. (2017) Unravelling the biology of chromatin in health and cancer using proteomic approaches. Expert Rev Proteomics 14:905-915|
|Miah, Sayem; Banks, Charles A S; Adams, Mark K et al. (2016) Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer. Mol Biosyst 13:42-55|
|Washburn, Michael P (2016) There is no human interactome. Genome Biol 17:48|
|Banks, Charles A S; Boanca, Gina; Lee, Zachary T et al. (2016) TNIP2 is a Hub Protein in the NF-?B Network with Both Protein and RNA Mediated Interactions. Mol Cell Proteomics 15:3435-3449|
|Washburn, Michael P; Zhao, Yingming; Garcia, Benjamin A (2016) Reshaping the Chromatin and Epigenetic Landscapes with Quantitative Mass Spectrometry. Mol Cell Proteomics 15:753-4|