Quantitative Proteomic Analysis Identifies Targets and Pathways of a 2‑Aminobenzamide HDAC Inhibitor in Friedreich’s Ataxia Patient iPSC-Derived Neural Stem Cells

• Published in: Journal of proteome research Vol. 13; no. 11; pp. 4558 - 4566
• Main Authors: Shan, Bing, Xu, Chunping, Zhang, Yaoyang, Xu, Tao, Gottesfeld, Joel M, Yates, John R
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 07.11.2014
• Subjects: Friedreich Ataxia - metabolism; Histone Deacetylase Inhibitors - metabolism; Humans; Induced Pluripotent Stem Cells - metabolism; Mass Spectrometry; Molecular Probes - metabolism; Molecular Probes - pharmacology; Neural Stem Cells - metabolism; Nuclear Proteins - metabolism; ortho-Aminobenzoates - metabolism; Proteomics - methods; Pyrazoles - metabolism; Pyrazoles - pharmacology; Pyridinium Compounds - metabolism; Pyridinium Compounds - pharmacology; RNA Processing, Post-Transcriptional - physiology; HDAC inhibitor; FRDA; MudPIT; dimethyl labeling
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/pr500514r

Members of the 2-aminobenzamide class of histone deacetylase (HDAC) inhibitors show promise as therapeutics for the neurodegenerative diseases Friedreich’s ataxia (FRDA) and Huntington’s disease (HD). While it is clear that HDAC3 is one of the important targets of the 2-aminobenzamide HDAC inhibitors, inhibition of other class I HDACs (HDACs 1 and 2) may also be involved in the beneficial effects of these compounds in FRDA and HD, and other HDAC interacting proteins may be impacted by the compound. To this end, we synthesized activity-based profiling probe (ABPP) versions of one of our HDAC inhibitors (compound 106), and in the present study we used a quantitative proteomic method coupled with multidimensional protein identification technology (MudPIT) to identify the proteins captured by the ABPP 106 probe. Nuclear proteins were extracted from FRDA patient iPSC-derived neural stem cells, and then were reacted with control and ABPP 106 probe. After reaction, the bound proteins were digested on the beads, and the peptides were modified using stable isotope-labeled formaldehyde to form dimethyl amine. The selectively bound proteins determined by mass spectrometry were subjected to functional and pathway analysis. Our findings suggest that the targets of compound 106 are involved not only in transcriptional regulation but also in posttranscriptional processing of mRNA.