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. 2017 Jan 17;18(3):647-658.
doi: 10.1016/j.celrep.2016.12.055.

Acetate Recapturing by Nuclear Acetyl-CoA Synthetase 2 Prevents Loss of Histone Acetylation during Oxygen and Serum Limitation

Vinay Bulusu  1 , Sergey Tumanov  1 , Evdokia Michalopoulou  1 , Niels J van den Broek  2 , Gillian MacKay  2 , Colin Nixon  2 , Sandeep Dhayade  2 , Zachary T Schug  2 , Johan Vande Voorde  2 , Karen Blyth  2 , Eyal Gottlieb  2 , Alexei Vazquez  2 , Jurre J Kamphorst  3
Affiliations

Acetate Recapturing by Nuclear Acetyl-CoA Synthetase 2 Prevents Loss of Histone Acetylation during Oxygen and Serum Limitation

Vinay Bulusu et al. Cell Rep. .

Abstract

Acetyl-CoA is a key metabolic intermediate with an important role in transcriptional regulation. The nuclear-cytosolic acetyl-CoA synthetase 2 (ACSS2) was found to sustain the growth of hypoxic tumor cells. It generates acetyl-CoA from acetate, but exactly which pathways it supports is not fully understood. Here, quantitative analysis of acetate metabolism reveals that ACSS2 fulfills distinct functions depending on its cellular location. Exogenous acetate uptake is controlled by expression of both ACSS2 and the mitochondrial ACSS1, and ACSS2 supports lipogenesis. The mitochondrial and lipogenic demand for two-carbon acetyl units considerably exceeds the uptake of exogenous acetate, leaving it to only sparingly contribute to histone acetylation. Surprisingly, oxygen and serum limitation increase nuclear localization of ACSS2. We find that nuclear ACSS2 recaptures acetate released from histone deacetylation for recycling by histone acetyltransferases. Our work provides evidence for limited equilibration between nuclear and cytosolic acetyl-CoA and demonstrates that ACSS2 retains acetate to maintain histone acetylation.

Keywords: acetate; acetyl-CoA synthetase 2; cancer metabolism; enzyme localization; histone acetylation; histone deacetylation; hypoxia; lipogenesis; metabolite compartmentalization; stable isotope tracing.

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Figures

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Graphical abstract
Figure 1
Figure 1
ACSS2 Controls Acetate Incorporation Into Lipogenic Acetyl-CoA (A) Schematic of lipogenic AcCoA production. (B) Steady-state 13C labeling (percent) of lipogenic AcCoA from 90 μM U-13C-acetate (Ac) in normoxia or hypoxia (1% O2). (C) Steady-state 13C labeling (percent) of lipogenic AcCoA from U-13C-glucose (Gluc), U-13C-glutamine (Gln), and 90 μM U-13C-acetate. (D) Western blot of ACSS2 from cells transfected with scrambled RNA (SCR) or two independent ACSS2 siRNAs. The normalized ratio is relative to the SCR control. (E) Steady-state 13C labeling (percent) of lipogenic AcCoA from 90 μM U-13C-Ac in hypoxic SCR or ACSS2 siRNA-treated cells. (F) Steady-state 13C labeling (percent) of lipogenic AcCoA from U-13C-Gluc and U-13C-Gln in hypoxic SCR or ACSS2 siRNA-treated cells. The medium contained 90 μM 12C-acetate. (G) ACSS2 western blot from multiple human cancer cell lines under hypoxia (48 hr). Tubulin was used as the loading control. (H) Steady-state 13C labeling (percent) of lipogenic AcCoA from 500 μM U-13C-Acetate. (B–F) Experiments were done in MDA-MB-468 cells. All data are mean ± SD (n = 3); ∗p < 0.05, ∗∗p < 0.01. See also Figure S1.
Figure 2
Figure 2
Cancer Cells Take up and Release Acetate, and ACSS2 Expression Dictates Net Exchange (A) Time course of U-13C-Ac (90 μM) uptake by MDA-MB-468 cells in normoxia and hypoxia. (B) Time course of unlabeled (12C) Ac release into the medium. (C) Time course of total Ac (U-13C-Ac + 12C-Ac) concentration in medium. (D) Estimated acetate release, uptake, and exchange fluxes in normoxic (blue) and hypoxic (red) MDA-MB-468 cells for multiple concentrations of U-13C-Ac in the medium. The open bars represent the 5% quantile of the acetate release flux (i.e., with 95% confidence, the release flux is higher than the bar height). The filled bars represent the 5% quantile of the acetate uptake flux (i.e., with 95% confidence, the uptake flux is higher than the bar height). The dashed bars and error bars represent the median and 95% confidence intervals of the acetate exchange flux. (E) Net acetate exchange for the panel of cell lines in hypoxia and 10% or 1% dialyzed serum. Cell lines are ordered based on increasing ACSS2 expression from left to right. All data are mean ± SD (n = 3). See also Figure S2.
Figure 3
Figure 3
High Mitochondrial and Lipogenic Demand for Acetate Limits Its Use for Histone Acetylation (A and B) Steady-state labeling of TCA cycle intermediates from U-13C-Ac (500 μM) in (A) MDA-MB-468 cells and (B) BT-474 cells. (C and D) Effect of ACSS1 knockdown on net acetate uptake in (C) MDA-MB-468 and (D) BT474 cells. (E and F) Lipogenic AcCoA demand for de novo fatty acid synthesis as determined by kinetic flux profiling (Supplemental Experimental Procedures) for (E) MDA-MB-468 and (F) BT-474 cells. (G and H) Steady-state labeling of histone-bound acetate from U-13C-Gluc, U-13C-Gln, and U-13C-Ac for (G) MDA-MB-468 and (H) BT-474 cells. (I) Effect of free fatty acid supplementation on fatty acid biosynthesis in MDA-MB-468 cells. (J) Effect of free fatty acid supplementation on steady-state, histone-bound acetate labeling from U-13C-Ac in MDA-MB-468 cells. For (A)–(D), (I), and (J), data are from cells in hypoxia (1% O2) and low serum (1%). All data are mean ± SD (n = 3); ∗p < 0.05, ∗∗p < 0.01. See also Figure S3.
Figure 4
Figure 4
ACSS2 Localizes to the Nucleus during Oxygen and Serum Limitation and Is Prominently Nuclear in Tumors (A) Representative images of DAPI (nuclear) and ACSS2 staining (separately and merged) in MDA-MB-468 cells in normoxia and 10% serum or hypoxia and 1% serum. Scale bar, 20 μm. (B) Quantification of the nuclear fraction of ACSS2 (percent) in MDA-MB-468 cells cultured under different conditions. Data are mean ± SD of three independent experiments (seven or more images per experiment). (C) Immunohistochemical staining of serial sections from a representative tumor of the MMTV-PyMT mouse model for carbonic anhydrase 9 (CAIX, a hypoxic marker), CD31 (a marker for blood vessels), ACSS2, and H&E staining. (D) Scoring of ACSS2 nuclear intensity in normoxic and hypoxic tumor regions. Ten different ROIs were selected for normoxic and hypoxic regions of two tumors (five ROIs each), and the percentages of cells with weak, moderate or strong nuclear ACSS2 staining were scored. Data are mean ± SD (n = 10 ROIs). See also Figure S4.
Figure 5
Figure 5
ACSS2 Recaptures Endogenously Produced Acetate (A) Plot of the ratio of 12C-acetate released/13C-acetate consumed to ACSS2 expression in cancer cells in hypoxia and 10% or 1% dialyzed serum. Statistics are from Pearson’s correlation analysis using GraphPad Prism software. (B) Medium 13C-acetate consumption by siRNA-treated MDA-MB-468 cells exposed to hypoxia and 1% dialyzed serum. (C) Medium 12C-acetate production in the same experiment. (D) Total acetate in medium of the same experiment. (E) Ratio of 12C-acetate released to/ 13C-acetate consumed by MDA-MB-468 cells treated with SCR or ACSS2 siRNAs. (F) The same for BT-474 cells. All data are mean ± SD (n = 3); ∗p < 0.05, ∗∗p < 0.01. See also Figure S5.
Figure 6
Figure 6
ACSS2 Recaptures Acetate Released from Histone Deacetylation (A) Western blot of AcH3 and AcH4 in MDA-MB-468 cells upon transfection with SCR or ACSS2 siRNAs. Cells were cultured under the indicated conditions for 48 hr after transfection under either condition. (B) Bar plot of the same data, with AcH3 normalized to histone H3 and AcH4 to histone H4, with normalized values expressed relative to the scrambled RNA. (C) Acetate release by MDA-MB-468 cells transfected with SCR or ACSS2 siRNAs and with or without 50 μM panobinostat for 6 hr in low oxygen and serum. (D) The same for BT-474 cells but with 8-hr incubation. (E) Schematic of acetate metabolism in oxygen- and serum-limited cancer cells. For (B)–(D), data are mean ± SD (n = 3); ∗p < 0.05, ∗∗p < 0.01. See also Figure S6.
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