Lysine deacetylases inhibitors (KDACIs) are used in basic research, and many are being investigated in clinical trials for treatment of cancer and other diseases. However, their specificities in cells are incompletely characterized. Here we used quantitative mass spectrometry (MS) to obtain acetylation signatures for 19 different KDACIs, covering all 18 human lysine deacetylases. Most KDACIs increased acetylation of a small, specific subset of the acetylome, including sites on histones and other chromatin-associated proteins. Inhibitor treatment combined with genetic deletion showed that the effects of the pan-sirtuin inhibitor nicotinamide are primarily mediated by SIRT1 inhibition. Furthermore, we confirmed that the effects of tubacin and bufexamac on cytoplasmic proteins result from inhibition of HDAC6. Bufexamac also triggered an HDAC6-independent, hypoxia-like response by stabilizing HIF1-α, providing a possible mechanistic explanation of its adverse, pro-inflammatory effects. Our results offer a systems view of KDACI specificities, providing a framework for studying function of acetylation and deacetylases.
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- Supplementary Text and Figures (3,709 KB)
Supplementary Figures 1–14, Supplementary Table 1 and Supplementary Notes 1 and 2
- Supplementary Table 2 (7,078 KB)
All identified acetylation sites
- Supplementary Table 3 (510 KB)
Comparison of short- and long-term Nicotinamide treatment in HeLa cells
- Supplementary Table 4 (565 KB)
Nicotinamide upregulated acetylation sites
- Supplementary Table 5 (407 KB)
List of acetylation sites quantified in MV4-11 cells treated with nicotinamide
- Supplementary Table 6 (674 KB)
Comparison of Nicotinamide treatment and SIRT1KO in MEF Cells
- Supplementary Table 7 (586 KB)
Comparison of Nicotinamide treatment and SIRT6KO in MEF Cells
- Supplementary Table 8 (401 KB)
Comparison of Sirtinol treatment and SIRT2KO in MEF Cells
- Supplementary Table 9 (451 KB)
Comparison of AGK2 treatment and SIRT2KO in MEF Cells
- Supplementary Table 10 (664 KB)
EX-527 treatment in HeLa cells
- Supplementary Table 11 (119 KB)
Overview of bufexamac and tubacin upregulated acetylome
- Supplementary Table 12 (624 KB)
Comparison of Bufexamac and Tubacin treatment and HDAC6KO in MEF Cells
- Supplementary Table 13 (1,837 KB)
High and low dose bufexamac proteome