Acetylation site specificities of lysine deacetylase inhibitors in human cells

Journal name:
Nature Biotechnology
Volume:
33,
Pages:
415–423
Year published:
DOI:
doi:10.1038/nbt.3130
Received
Accepted
Published online

Abstract

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.

At a glance

Figures

  1. Quantitative profiling of the KDACI-regulated acetylome.
    Figure 1: Quantitative profiling of the KDACI-regulated acetylome.

    (a) An overview of the 19 KDACIs used for cell-based acetylome analysis and their reported specificities for human deacetylases based on cell-free assays. KDACs shown in dark gray background have been shown to be expressed in HeLa cells50. (b) The experimental design. SILAC-labeled HeLa cells were treated for 16 h with KDACIs or vehicle control. Subsequently, proteins were extracted and proteolyzed using Lys-C and trypsin. Acetylated peptides were enriched with anti-acetyllysine antibodies and fractionated by strong-cation exchange (SCX) chromatography. Peptides were analyzed by MS and data were used for downstream bioinformatic analyses. (c) The number of acetylation sites quantified and the fraction of acetylation sites regulated by individual KDACIs. The left part of the figure shows total number of quantified acetylation sites for each inhibitor. The bar chart shows the fraction of upregulated sites (>2-fold increase, shown in red) and the fraction of downregulated sites (>2-fold decrease, shown in blue). The numbers next to the bars indicate percent of up- or downregulated sites, and the number of up- or downregulated sites for each KDACI is indicated within parentheses. IP, immunoprecipitation. AcK, lysine acetylation.

  2. Specificity of KDACIs and subcellular distribution of KDACI-upregulated acetylated proteins.
    Figure 2: Specificity of KDACIs and subcellular distribution of KDACI-upregulated acetylated proteins.

    (a) Site-based specificity analysis of KDACIs in HeLa cells. SILAC ratios of KDACI-upregulated sites were used to calculate pair-wise Pearson correlation coefficients for all KDACIs, and the inhibitors were grouped based on their correlation values using average linkage clustering approach (see Supplementary Fig. 14 for pair-wise correlations). Node-size reflects number of upregulated sites, and line thickness corresponds to the degree of correlation. (b) Subcellular distribution of proteins with KDACI-upregulated acetylation sites. The bar plot shows the fraction of KDACI-upregulated acetylated proteins annotated with the indicated GO cellular compartment (GOCC) terms. As a reference, the first bar indicates subcellular distribution of all acetylation sites identified in this study. The dendrogram at the top of the plot shows similarity of KDACIs for upregulated subcellular acetylomes. Sirtinol, JQ12 and PCI34051 were excluded from this analysis owing to insufficient number of upregulated sites. (c) Profile of KDACI-regulated histone acetylation sites. The heatmap shows quantified histone acetylation sites and their regulation by KDACIs. The dendrogram illustrates similarity of KDACIs for histone acetylation sites. Black matrix areas show sites not identified for an individual inhibitor. (d) Overlap of acetylation sites upregulated in cells treated with broad-range KDACIs nicotinamide, tenovin-6, tubacin and PCI24781. The diagram displays the number of upregulated sites in response to each KDACI, as well as the number of sites found in two, three or all four of these inhibitors. AcK, lysine acetylation.

  3. Nicotinamide increases acetylation of nuclear proteins.
    Figure 3: Nicotinamide increases acetylation of nuclear proteins.

    (a) Functional annotation of proteins containing nicotinamide-upregulated acetylation sites in HeLa cells. Significantly enriched GO biological process (GOBP) terms associated with nuclear processes are indicated. Gray bars: all sites identified; black bars: upregulated sites. (b) The scatter plot shows the correlation between nicotinamide-regulated acetylation in MV4-11 and HeLa cells. Correlation was determined with Pearson correlation coefficient. (c) The scatter plots show the correlation between acetylation sites quantified in biological replicate experiments for nicotinamide-treated WT MEFs, Sirt1/ MEFs, as well as between these two conditions. Correlation was determined with Pearson correlation coefficient. (d) Functional annotation of proteins with nicotinamide- or SIRT1-upregulated acetylation sites in MEF cells. Significantly enriched GO terms are indicated. Heatmap represents P-values for each term in comparison to whole mouse proteome. The numbers within boxes indicate hyperacetylated proteins covering the percent of proteins associated with the indicated GO terms.

  4. Tubacin- and bufexamac-mediated increase in protein acetylation is likely mediated by HDAC6.
    Figure 4: Tubacin- and bufexamac-mediated increase in protein acetylation is likely mediated by HDAC6.

    (a) The scatter plot shows the correlation between acetylation sites quantified in tubacin- and bufexamac-treated HeLa cells. Correlation was determined with Pearson correlation coefficient. (b) Verification of Hdac6 deletion in knockout MEFs. Expression of HDAC6 and acetylation of tubulin were analyzed by immunoblotting. (c) The scatter plots show the correlation between acetylation sites identified in biological replicate experiments of tubacin- or bufexamac-treated MEF cells and Hdac6/ cells, as well as between each condition. Correlation was determined by Pearson correlation coefficient. (d) Functional annotation of proteins with upregulated acetylation sites in bufexamac- or tubacin-treated MEFs or in Hdac6/ MEFs. Significantly enriched GO terms are indicated. Heatmap represents P-values for each GO term in comparison to whole mouse proteome. The numbers within boxes indicate percent of hyperacetylated proteins associated with the indicated GO terms. n.d., not determined.

  5. Bufexamac inhibits KDACs at lower concentrations and causes hypoxia-like responses at higher concentrations.
    Figure 5: Bufexamac inhibits KDACs at lower concentrations and causes hypoxia-like responses at higher concentrations.

    (a) Treatment of HeLa cells with 1 mM bufexamac results in the induction of HIF1-α, as determined by immunoblotting. The known hypoxia mimetics CPX and DFX were used as positive controls; vinculin served as loading control. (b) Verification of bufexamac-specific upregulation of HIF1-α. HIF1-α protein expression was analyzed 4 h after treatment of cells with the indicated compounds. Ac, acetylated. (c) Time-course analysis of HIF1-α induction by bufexamac. The induction of HIF1-α protein was analyzed by immunoblotting. The graph shows rapid stabilization of HIF1-α upon bufexamac treatment with half-maximal intensity I1/2 of about 75 min. Error bars represent s.d. of three independent experiments. (d) HIF1-α is stabilized only at higher concentrations of bufexamac and accumulates in the nucleus. Induction of endogenous HIF1-α and its nuclear accumulation was analyzed using immunofluorescence microscopy; scale bar, 10 μm. (e) Bufexamac increases transcriptional activity of HIF1-α. Luciferase activity was measured in HeLa cells transfected with HRE-luciferase reporter upon treatment with CPX, DFX or bufexamac. Error bars represent s.d. of three independent experiments. (f) Bufexamac treatment increases expression of HIF1-α target vascular endothelial growth factor A. Vegfa mRNA levels were assessed by real-time PCR and the data were normalized to Gapdh. Error bars represent s.d. of two independent experiments. (g) Dose-response curves of bufexamac-treated cells and the corresponding immunoblots are shown (HIF-1α and acetyl-tubulin were visualized simultaneously by using a mixture of anti–HIF-1α and K40-acetyl-tubulin antibodies). Error bars represent s.d. from three independent experiments. Lower panel shows immunofluorescence images of HeLa cells treated with 50 μM and 250 μM bufexamac and immunostained for acetylated tubulin. Scale bar, 10 μm. (h) Dose-response plot showing HIF1-α protein levels and a representative corresponding immunoblot. Cells were treated with 250 μM bufexamac and with the indicated concentrations of FeCl3. Data were normalized to the maximal HIF1-α expression; error bars represent s.d. from three independent experiments. (i) Iron supplementation dose-dependently inhibits bufexamac-induced HIF1-α transcriptional activity. Cells were transfected with a HRE-luciferase reporter plasmid, and luciferase activity was measured after treatment with 250 μM bufexamac and different concentrations of FeCl3, as indicated. Error bars represent s.d. of three independent experiments. CPX, ciclopirox olamine; DFX, deferoxamine; HRE, hypoxia response element; Gapdh, glycerol aldehyde 3-phosphate dehydrogenase.

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Author information

  1. Deceased.

    • Anna R McCarthy

Affiliations

  1. Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

    • Christian Schölz,
    • Brian T Weinert,
    • Sebastian A Wagner,
    • Petra Beli &
    • Chunaram Choudhary
  2. Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

    • Yasuyuki Miyake &
    • Patrick Matthias
  3. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.

    • Jun Qi &
    • James E Bradner
  4. Department of Protein Science and Technology, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.

    • Lars J Jensen
  5. Department of Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.

    • Werner Streicher
  6. Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.

    • Anna R McCarthy &
    • Sonia Lain
  7. School of Chemistry and Biomedical Sciences Research Complex, EaStCHEM, University of St. Andrews, St. Andrews, Scotland, UK.

    • Nicholas J Westwood
  8. Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany.

    • Jürgen Cox &
    • Matthias Mann

Contributions

C.S. performed most of the experiments and collected data. B.T.W. performed initial experiments, and obtained data in MV4-11 cells, S.A.W. helped with bioinformatic analyses, P.B. assisted with immunofluorescence microscopy, Y.M. provided HDAC6 knockout cells, L.J.J. performed average linkage clustering analysis of KDACIs, W.S. performed UV/VIS spectroscopy, J.Q. synthesized JQ12 and performed in vitro KDAC enzymatic assays for this compound, A.R.M., N.J.W. and S.L. provided tenovin-6, J.C. helped with computational analysis of MS data, P.M. provided critical research reagents, M.M. was involved in the planning of the tenovin-6 experiments and provided infrastructure for initial test experiments, J.E.B. designed experiments, provided pandacostat and JQ12, C.C. planned the project, C.C. and C.S. wrote the manuscript; all co-authors provided input for writing the paper.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

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Supplementary information

PDF files

  1. Supplementary Text and Figures (3,709 KB)

    Supplementary Figures 1–14, Supplementary Table 1 and Supplementary Notes 1 and 2

Excel files

  1. Supplementary Table 2 (7,078 KB)

    All identified acetylation sites

  2. Supplementary Table 3 (510 KB)

    Comparison of short- and long-term Nicotinamide treatment in HeLa cells

  3. Supplementary Table 4 (565 KB)

    Nicotinamide upregulated acetylation sites

  4. Supplementary Table 5 (407 KB)

    List of acetylation sites quantified in MV4-11 cells treated with nicotinamide

  5. Supplementary Table 6 (674 KB)

    Comparison of Nicotinamide treatment and SIRT1KO in MEF Cells

  6. Supplementary Table 7 (586 KB)

    Comparison of Nicotinamide treatment and SIRT6KO in MEF Cells

  7. Supplementary Table 8 (401 KB)

    Comparison of Sirtinol treatment and SIRT2KO in MEF Cells

  8. Supplementary Table 9 (451 KB)

    Comparison of AGK2 treatment and SIRT2KO in MEF Cells

  9. Supplementary Table 10 (664 KB)

    EX-527 treatment in HeLa cells

  10. Supplementary Table 11 (119 KB)

    Overview of bufexamac and tubacin upregulated acetylome

  11. Supplementary Table 12 (624 KB)

    Comparison of Bufexamac and Tubacin treatment and HDAC6KO in MEF Cells

  12. Supplementary Table 13 (1,837 KB)

    High and low dose bufexamac proteome

Additional data