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 3

HDAC inhibitors suppress c-Myc protein levels and thereby reduce survival and glycolysis in GBM cells.

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HDAC inhibitors suppress c-Myc protein levels and thereby reduce surviva...
(A) The top 9 pathways identified by GSEA of NCH644 cells treated with 0.5 μM Pb for 24 hours (transcriptome analysis). (B) GSEA plot. (C) Graphical representation of the FDR Q values versus NES derived from the analysis in A and B. (D) GBM cells were treated with Pb or were chronically exposed to Pb (n = 3). (E) GBM cells were treated with Ro or were chronically exposed to Ro (n = 4). (F) U87 GBM cells were transfected with HDAC1 siRNA (siHDAC1), HDAC2 siRNA (siHDAC2), or a combination of both (siHDAC1+2) (n = 3–4). (G) PCE analysis of lysates from U87 cells transfected with HDAC1 siRNA, HDAC2 siRNA, or a combination of both. (H) U87 cells were treated with the indicated concentrations of Pb, Ro, or Vr for 72 hours, and cellular viability was determined. (I) U87 cells expressing a c-Myc construct were treated with 0.2 μM Pb for 24 hours, and a glycolysis stress test was performed (n = 5). (J) ChIP-qPCR of different locations around the HK2 gene (promoter and exon 1) from the indicated cell lysate with either a c-Myc or IgG antibody (n = 3). (K) PCE analysis of U87 cells that were transfected with an siRNA against Myc-1 or Myc-2, treated with the indicated concentration of Pb for 24 hours, and analyzed for the indicated protein. (L) PCE analysis of lysates from U87 cells that were transduced with a c-Myc construct, treated with 0.5 μM Pb or 5 nM Ro for 24 hours, and analyzed for HK2. Data represent the mean ± SD. Statistical significance was determined by 2-tailed Student’s t test (F, I, and J) or by 1-way ANOVA (G and H). *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001. Ctrl, control; EV, empty vector; NES, normalized enrichment score; OE, overexpression; siNT, nontargeting siRNA .