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Garrett M, Sperry J, Braas D, Yan W, Le TM, Mottahedeh J, Ludwig K, Eskin A, Qin Y, Levy R, Breunig JJ, Pajonk F, Graeber TG, Radu CG, Christofk H, Prins RM, Lai A, Liau LM, Coppola G, Kornblum HI. Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type-specific vulnerabilities. Cancer Metab 2018; 6:4. [PMID: 29692895 PMCID: PMC5905129 DOI: 10.1186/s40170-018-0177-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background There is considerable interest in defining the metabolic abnormalities of IDH mutant tumors to exploit for therapy. While most studies have attempted to discern function by using cell lines transduced with exogenous IDH mutant enzyme, in this study, we perform unbiased metabolomics to discover metabolic differences between a cohort of patient-derived IDH1 mutant and IDH wildtype gliomaspheres. Methods Using both our own microarray and the TCGA datasets, we performed KEGG analysis to define pathways differentially enriched in IDH1 mutant and IDH wildtype cells and tumors. Liquid chromatography coupled to mass spectrometry analysis with labeled glucose and deoxycytidine tracers was used to determine differences in overall cellular metabolism and nucleotide synthesis. Radiation-induced DNA damage and repair capacity was assessed using a comet assay. Differences between endogenous IDH1 mutant metabolism and that of IDH wildtype cells transduced with the IDH1 (R132H) mutation were also investigated. Results Our KEGG analysis revealed that IDH wildtype cells were enriched for pathways involved in de novo nucleotide synthesis, while IDH1 mutant cells were enriched for pathways involved in DNA repair. LC-MS analysis with fully labeled 13C-glucose revealed distinct labeling patterns between IDH1 mutant and wildtype cells. Additional LC-MS tracing experiments confirmed increased de novo nucleotide synthesis in IDH wildtype cells relative to IDH1 mutant cells. Endogenous IDH1 mutant cultures incurred less DNA damage than IDH wildtype cultures and sustained better overall growth following X-ray radiation. Overexpression of mutant IDH1 in a wildtype line did not reproduce the range of metabolic differences observed in lines expressing endogenous mutations, but resulted in depletion of glutamine and TCA cycle intermediates, an increase in DNA damage following radiation, and a rise in intracellular ROS. Conclusions These results demonstrate that IDH1 mutant and IDH wildtype cells are easily distinguishable metabolically by analyzing expression profiles and glucose consumption. Our results also highlight important differences in nucleotide synthesis utilization and DNA repair capacity that could be exploited for therapy. Altogether, this study demonstrates that IDH1 mutant gliomas are a distinct subclass of glioma with a less malignant, but also therapy-resistant, metabolic profile that will likely require distinct modes of therapy.
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Affiliation(s)
- Matthew Garrett
- 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA
| | - Jantzen Sperry
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Daniel Braas
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,3UCLA Metabolomics Center, UCLA, Los Angeles, USA
| | - Weihong Yan
- 4Department of Chemistry and Biochemistry, UCLA, Los Angeles, USA
| | - Thuc M Le
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,5Ahmanson Translational Imaging Division, UCLA, Los Angeles, USA
| | - Jack Mottahedeh
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Kirsten Ludwig
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Ascia Eskin
- 7Department of Human Genetics, UCLA, Los Angeles, USA
| | - Yue Qin
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Rachelle Levy
- 8Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Joshua J Breunig
- 8Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA USA.,9Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA USA.,10Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Frank Pajonk
- 11Department of Radiation Oncology, David Geffen School of Medicine at UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Thomas G Graeber
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,3UCLA Metabolomics Center, UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Caius G Radu
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,5Ahmanson Translational Imaging Division, UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Heather Christofk
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,3UCLA Metabolomics Center, UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,14Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Robert M Prins
- 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA.,2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Albert Lai
- 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,13Department of Neurology, UCLA, Los Angeles, USA
| | - Linda M Liau
- 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Giovanni Coppola
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,13Department of Neurology, UCLA, Los Angeles, USA
| | - Harley I Kornblum
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,14Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
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Smida J, Xu H, Zhang Y, Baumhoer D, Ribi S, Kovac M, von Luettichau I, Bielack S, O'Leary VB, Leib-Mösch C, Frishman D, Nathrath M. Genome-wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma. Int J Cancer 2017; 141:816-828. [DOI: 10.1002/ijc.30778] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/19/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jan Smida
- Institute of Radiation Biology, Helmholtz Zentrum Munich - German Research Center for Environmental Health; Neuherberg Germany
- Clinical Cooperation Group Osteosarcoma, Helmholtz Zentrum Munich - German Research Center for Environmental Health; Neuherberg Germany
- Pediatric Oncology Center; Department of Pediatrics, Technical University of Munich and Comprehensive Cancer Center; Munich Germany
| | - Hongen Xu
- Department of Bioinformatics; Wissenschaftszentrum Weihenstephan, Technical University of Munich; Freising Germany
| | - Yanping Zhang
- Department of Bioinformatics; Wissenschaftszentrum Weihenstephan, Technical University of Munich; Freising Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Center; Institute of Pathology, University Hospital Basel; Switzerland
| | - Sebastian Ribi
- Bone Tumour Reference Center; Institute of Pathology, University Hospital Basel; Switzerland
| | - Michal Kovac
- Bone Tumour Reference Center; Institute of Pathology, University Hospital Basel; Switzerland
| | - Irene von Luettichau
- Pediatric Oncology Center; Department of Pediatrics, Technical University of Munich and Comprehensive Cancer Center; Munich Germany
| | - Stefan Bielack
- Pediatrics 5 (Oncology, Hematology, Immunology), Klinikum Stuttgart Olgahospital; Stuttgart Germany
| | - Valerie B. O'Leary
- Institute of Radiation Biology, Helmholtz Zentrum Munich - German Research Center for Environmental Health; Neuherberg Germany
| | - Christine Leib-Mösch
- Institute of Virology, Helmholtz Zentrum Munich - German Research Center for Environmental Health; Neuherberg Germany
| | - Dmitrij Frishman
- Department of Bioinformatics; Wissenschaftszentrum Weihenstephan, Technical University of Munich; Freising Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munich - German Research Center for Environmental Health; Neuherberg Germany
- St Petersburg State Polytechnic University; St Petersburg Russia
| | - Michaela Nathrath
- Clinical Cooperation Group Osteosarcoma, Helmholtz Zentrum Munich - German Research Center for Environmental Health; Neuherberg Germany
- Pediatric Oncology Center; Department of Pediatrics, Technical University of Munich and Comprehensive Cancer Center; Munich Germany
- Department of Pediatric Hematology and Oncology; Klinikum Kassel; Germany
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