HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models
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
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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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 2

HDAC inhibitors reverse the Warburg effect.

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HDAC inhibitors reverse the Warburg effect. (A) Real-time PCR analysis o...
(A) Real-time PCR analysis of genes related to glycolysis from stem-like NCH644 GBM cells treated with 0.5 μM Pb or 2 nM Ro for 24 hours (n = 3–4). (B) Real-time PCR analysis of genes related to glycolysis from established U87 GBM cells treated with 0.5 μM Pb or 5 nM Ro for 24 hours (n = 3–4). (C) Analysis of protein lysate from NCH644 cells treated with the indicated concentration of Pb (LDHA, c-Myc, vinculin [loading control]: protein capillary electrophoresis [PCE]; HK2, actin [loading control]: standard Western blot gel; Ace-H3, H3 [loading control]: standard Western blot) or Ro for 24 hours (LDHA, c-Myc, HK2, vinculin [loading control]: PCE; Ace-H3, H3 [loading control]: standard Western blot). (D) U87 GBM cells were treated with 0.5 μM Pb for 24 hours and analyzed by LC/MS followed by metabolite (Met) pathway analysis. (E and F) Quantifications of glycolysis-related metabolites from NCH644 and U87 cells treated with 0.5 μM Pb for 24 hours (n = 3–4). GLU, glucose; G-6P, glucose-6-phosphate; F1,6BP, fructose-1,6-bisphosphate; 3-PGA, glyceraldehyde-3-phosphate; 3-PG, 3-phosphoglycerate; PEP, phosphoenolpyruvate; PYR, pyruvate; LAC, lactate. (G and H) NCH644 and U87 cells were exposed to 0.2 μM Pb, and the OCR and ECAR were recorded (n = 3). (I) U87 cells were treated and harvested as in E and F. Shown are the levels of ATP (determined by LC/MS). (J) PCE analysis of lysates from U87 cells treated with the indicated concentrations of Pb for 7 hours. (K) Quantifications of the relative abundances of the indicated 13C isotopologs from U-13C-glucose in U87 GBM cells treated with 0.5 μM Pb for 24 hours (n = 3). Data represent the mean ± SD. Statistical significance was determined by 2-tailed Student’s t test. *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001.