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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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 5

Pan- and selective HDAC inhibitors upregulate PGC1α in a partially c-Myc–dependent manner to drive respiration.

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Pan- and selective HDAC inhibitors upregulate PGC1α in a partially c-Myc...
(A) GBM cells were treated with Pb or Ro or chronically exposed to Pb or Ro (n = 3–4). (B) PCE analyses of U87 cells transfected with Myc siRNA and treated with Pb or Ro for 24 hours. (C) PCE analyses of U87 cells transfected with siRNA HDAC1, HDAC2, or a combination of both. (D and E) Real-time PCR analysis of U87 cells transfected with HDAC1 siRNA, HDAC2 siRNA, or a combination of both (n = 3–4). (F) ChIP-Seq profile of parental U87 and LN229 cells or U87 and LN229 cells chronically exposed to Pb with an antibody against H3K27ac or Rpb1. Shown are the respective tracks around the desert of the PPARGC1A (PGC1α) locus. (G) ChIP-qPCR (with anti-HDAC2 antibody) of the PGC1α promoter (c-Myc–binding region) from the indicated cell lysates (n = 3). (H) ChIP-qPCR of the PGC1α promoter (c-Myc–binding region) from the indicated cell lysates with either anti–c-Myc antibody or anti-H3K27ac antibody (n = 3). (I) PCE analysis of U87 cells transduced with a c-Myc construct and treated with 2.5 nM Ro for 24 hours. (J) Mitochondrial stress test of parental U87 cells or U87 cells chronically exposed to Pb and transduced with an shRNA against PGC1α (n = 4–5). O, oligomycin; F, FCCP; R/A, rotenone and antimycin A. (K) Maximal respiration data from the experiment in J. (L) Mitochondrial stress extracellular flux analysis of parental U87 cells or U87 cells chronically exposed to Pb and transduced with PGC1α sgRNAs (n = 4). (M) Maximal respiration data from the experiment in L. U87-KO-NT, nontargeting KO U87 cells; U87PbR-KO-NT, nontargeting KO U87 cells chronically exposed to Pb; U87-KO-PGC1A-2, PGC1A-2–KO U87 cells; U87PbR-KO-PGC1A-2, PGC1A-2–KO U87 cells chronically exposed to Pb. (N) PCE analysis of U87 cells transduced with an shRNA against PGC1α or PGC1α sgRNAs. Data represent the mean ± SD. Statistical significance was determined by 2-tailed Student’s t test (A) or 1-way ANOVA (D, E, G, H, K, and M). *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001.