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 6

HDAC inhibitors drive lipid catabolism with activation of β-oxidation in a manner dependent on the transcription factor PPARD.

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HDAC inhibitors drive lipid catabolism with activation of β-oxidation in...
(A) Heatmap (mRNA) of NCH644 cells treated with 0.5 μM Pb for 24 hours, GBM43 (G43) cells treated with Pb (in vivo), and parent U87 cells and U87 cells chronically exposed to Pb. (B) GSEA plots of NCH644 cells treated with 0.5 μM Pb for 24 hours. (C) PPARD mRNA levels in GBM cells treated with 0.2 μM Pb for 24 hours (n = 3). (D) PPARD mRNA levels in parent U87 cells or U87 cells chronically exposed to Pb (n = 3). (E) PCE analysis of NCH644 cells and U87 cells treated with Pb for 24 hours (except for CPT2 and 14-3-3 [loading control] in NCH644 cells, which is standard Western blotting). (F) OCR in U87 GBM cells treated as indicated for 24 hours (n = 3). (G) OCR in U87 cells treated with 0.2 μM Pb in the presence of palmitate (n = 6). (H) U87 cells transfected with a siRNA against PPARD and treated with Pb for 24 hours. (I) U87 cells were transfected with siRNA against HDAC1, HDAC2, or a combination of both and analyzed by protein capillary electrophoresis. (J) ChIP-qPCR of the PPARD gene from the indicated cell lysates with either anti–c-Myc antibody or anti-H3K27ac antibody (n = 3). (K) ChIP-qPCR of the PPARD gene from the indicated cell lysates with anti-HDAC2 antibody (n = 3). (L) U87 cells were transduced with c-Myc and treated with 0.1 μM Pb for 24 hours. (M) mRNA levels in U87 cells transduced with c-Myc and treated with 0.1 μM Pb or 2.5 nM Ro for 24 hours (n = 3–4). (N) Isobolograms of NCH644, U87, GBM12, and GBM43 cells treated with Pb, with or without etomoxir, for 72 hours. Data represent the mean ± SD. Statistical significance was determined by 2-tailed Student’s t test (C, D, and G) or 1-way ANOVA (F, J, and K). *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001. Eto, etomoxir.