Suberoylanilide Hydroxamic Acid (SAHA)-Induced Dynamics of a Human Histone Deacetylase Protein Interaction Network

Mihaela E Sardiu,Karen T Smith,Brad D Groppe,Joshua M Gilmore,Anita Saraf,Rhonda Egidy,Allison Peak,Chris W Seidel,Laurence Florens,Jerry L Workman,Michael P Washburn

doi:10.1074/mcp.m113.037127

Abstract

Histone deacetylases (HDACs) are targets for cancer therapy. Suberoylanilide hydroxamic acid (SAHA) is an HDAC inhibitor approved by the U.S. Food and Drug Administration for the treatment of cutaneous T-cell lymphoma. To obtain a better mechanistic understanding of the Sin3/HDAC complex in cancer, we extended its protein-protein interaction network and identified a mutually exclusive pair within the complex. We then assessed the effects of SAHA on the disruption of the complex network through six homologous baits. SAHA perturbs multiple protein interactions and therefore compromises the composition of large parts of the Sin3/HDAC network. A comparison of the effect of SAHA treatment on gene expression in breast cancer cells to a knockdown of the ING2 subunit indicated that a portion of the anticancer effects of SAHA may be attributed to the disruption of ING2's association with the complex. Our dynamic protein interaction network resource provides novel insights into the molecular mechanism of SAHA action and demonstrates the potential for drugs to rewire networks.

Highlights

The identification of proteins that change in response to a drug perturbation can shed light on the molecular mechanisms of the drug and its potential use in therapies
The number of spectra identified for each protein was used to calculate distributed normalized spectral abundance factor (dNSAF) values; this is an established spectral-counting-based approach in which shared peptides are distributed, data are normalized to the length of individual proteins, and data are normalized to the total intensity of a given multidimensional protein identification technology (MudPIT) run [25]
The human Sin3/Histone deacetylases (HDACs) network consists of several different sub-networks, of which one was more tightly associated with the Sin3/HDAC core; this subsequently was verified via reciprocal purifications using a newly identified interaction partner, forkhead box k1 (FOXK1)

Summary

Introduction

The identification of proteins that change in response to a drug perturbation can shed light on the molecular mechanisms of the drug and its potential use in therapies. We characterized the global effects triggered by SAHA in the context of a Sin3/ HDAC protein interaction network in order to provide insights into SAHA’s molecular mechanism. The human histone deacetylase Sin3/HDAC is a multiprotein complex well known for its role in diverse biological and cellular processes including transcription, chromatin structure, cell-cycle progression, genomic stability, and embryonic development (9 –13), and it was most recently found to be implicated in suppressing cell migration [14]. More recent findings suggest that SAHA and HDAC inhibitors may have broader noncatalytic effects on HDAC complexes [15, 17]. HDAC1 and HDAC2 are part of several complexes, as was recently demonstrated in an elegant protein interaction network analysis using the 11 human HDACs as baits [18]. We present a focused study on the Sin3a complex and describe a strategy to determine the effect of SAHA on an Molecular & Cellular Proteomics 13.11

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Conclusion