HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models
Trang Thi Thu Nguyen, … , Peter Canoll, Markus D. Siegelin
Trang Thi Thu Nguyen, … , Peter Canoll, Markus D. Siegelin
Published April 21, 2020
Citation Information: J Clin Invest. 2020;130(7):3699-3716. https://doi.org/10.1172/JCI129049.
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Research Article Oncology

HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models

Abstract

The Warburg effect is a tumor-related phenomenon that could potentially be targeted therapeutically. Here, we showed that glioblastoma (GBM) cultures and patients’ tumors harbored super-enhancers in several genes related to the Warburg effect. By conducting a transcriptome analysis followed by ChIP-Seq coupled with a comprehensive metabolite analysis in GBM models, we found that FDA-approved global (panobinostat, vorinostat) and selective (romidepsin) histone deacetylase (HDAC) inhibitors elicited metabolic reprogramming in concert with disruption of several Warburg effect–related super-enhancers. Extracellular flux and carbon-tracing analyses revealed that HDAC inhibitors blunted glycolysis in a c-Myc–dependent manner and lowered ATP levels. This resulted in the engagement of oxidative phosphorylation (OXPHOS) driven by elevated fatty acid oxidation (FAO), rendering GBM cells dependent on these pathways. Mechanistically, interference with HDAC1/-2 elicited a suppression of c-Myc protein levels and a concomitant increase in 2 transcriptional drivers of oxidative metabolism, PGC1α and PPARD, suggesting an inverse relationship. Rescue and ChIP experiments indicated that c-Myc bound to the promoter regions of PGC1α and PPARD to counteract their upregulation driven by HDAC1/-2 inhibition. Finally, we demonstrated that combination treatment with HDAC and FAO inhibitors extended animal survival in patient-derived xenograft model systems in vivo more potently than single treatments in the absence of toxicity.

Authors

Trang Thi Thu Nguyen, Yiru Zhang, Enyuan Shang, Chang Shu, Consuelo Torrini, Junfei Zhao, Elena Bianchetti, Angeliki Mela, Nelson Humala, Aayushi Mahajan, Arif O. Harmanci, Zhengdeng Lei, Mark Maienschein-Cline, Catarina M. Quinzii, Mike-Andrew Westhoff, Georg Karpel-Massler, Jeffrey N. Bruce, Peter Canoll, Markus D. Siegelin

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Figure 4

HDAC inhibitors drive oxidative energy metabolism.

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HDAC inhibitors drive oxidative energy metabolism. (A) Isobolograms show...
(A) Isobolograms show the results for U87, NCH644, GBM12, and LN229 cells that were treated with Pb in the presence of oligomycin (Oli) for 72 hours. (B) PCE analyses of U87 and LN229 cells treated with Pb for 24 hours. (C) Western blots of the OXPHOS complex from parental U87 and LN229 GBM cells and U87 and LN229 GBM cells chronically exposed to Pb (PbR). (D) Western blots of the OXPHOs complex from U87 cells treated with Pb for 24 hours. (E) U87 cells were transduced with a c-Myc construct, treated with Pb for 24 hours, and analyzed for OXPHOS complexes. (F and G) OCR and OXPHOS-driven ATP production rates in U87 and LN229 cells chronically exposed to Pb (n = 3). (H) Electron microscopic images of parental U87 cells and U87 cells chronically Pb. Arrows highlight mitochondria. Scale bar: 500 nm. (I) Parental U87 and LN229 cells and U98 and LN229 cells chronically exposed to Pb were stained with MitoTracker and analyzed by flow cytometry (n = 3). (J and K) NCH644 and U87 cells were treated with Pb, stained with MitoTracker, and analyzed by flow cytometry (n = 3). (L) c-Myc construct–transduced U87 cells were treated with Pb for 24 hours, stained with MitoTracker, and analyzed by flow cytometry (n = 3). (M) TCA cycle metabolites in parental U87 cells or U87 cells chronically exposed to Pb (n = 3). (N) Parental U87 cells or U87 cells chronically exposed to Pb were cultured in DMEM media (25 mM U-13C-glucose, 4 mM glutamine) for 24 hours (n = 3). (O) U87 parental cells or U87 cells chronically exposed to Pb were cultured in DMEM media (25 mM glucose, 4 mM U-13C-glutamine) for 24 hours (n = 3). (P) Parental U87 cells or U87 cells chronically exposed to Pb were cultured in DMEM media (5 mM glucose, 1 mM glutamine, 100 μM U-13C-palmitic acid) for 24 hours (n = 3). Data represent the mean ± SD. Statistical significance was determined by 2-tailed Student’s t test (F–I and L–P) or 1-way ANOVA (J and K). *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001.