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Scheepbouwer C, Borland K, Aparicio E, Verschueren H, Wedekind L, Ramaker J, Misovic B, CM Kouwenhoven M, Noske D, Vandertop P, Wesseling P, Wurdinger T, Hackenberg M, Kellner S, Koppers-Lalic D. GENE-60. THE EPITRANSCRIPTOMIC CODE IN LGG: METABOLICALLY REPROGRAMMED IDH-MUTANT GLIOMAS ALTER tRNA MODIFICATION LANDSCAPE. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Diffuse lower grade gliomas (LGGs) are generally slow growing primary central nervous system tumors that occur in early adult life. The prevalence of isocitrate dehydrogenase (IDH) mutations is high in LGG, and induces excess production of the oncometabolite 2-hydroxyglutarate (2-HG). These gain-of-function mutations play a key role in promoting metabolic reprogramming of the cancer cell that affects activity of α-KG dependent demethylases. Inhibition of DNA demethylase activity leads to glioma with a CpG island methylator phenotype (G-CIMP). Whether the activity of RNA demethylases and methylation status of tRNAs in LGG are modulated by changes in IDH-status is unknown. AIM: To investigate whether IDH mutations play a role in reprogramming of tRNA modifications in adult glioma.
MATERIALS AND METHODS
We combined small RNAseq and LC-MS/MS analysis to identify distinct tRNA processing patterns and methylation signatures in LGG tissues. To address important experimental bottlenecks that limit RNAseq-based detection of tRNA and possibly other modified small noncoding RNAs, we employed a tailored small RNAseq method with validation of specific methylation sites by mass-spectrometry.
RESULTS
Our customized small RNAseq approach yielded >100 fold increase in sequencing reads per tRNA type, thereby dramatically improving tRNA detection when compared to currently used small RNAseq approaches. Moreover, LC-MS/MS analysis revealed a higher abundance of modified nucleosides in tRNA from IDH-mutant LGG compared to IDH-wildtype LGG. Analysis of tRNA from IDH-mutant and IDH-wildtype LGG using the combination of our tailored small RNAseq and LC-MS/MS methodology demonstrated strong differential tRNA expression, tRFs processing and tRNA methylation.
CONCLUSION
We described an approach that makes use of tailored small RNA sequencing combined with mass-spectrometry that enables insights into cancer driven alterations in tRNA methylation patterns and differential tRNA processing signatures. Our data implies that tumor metabolic reprogramming deregulates tRNA methylation, contributing to an altered epitranscriptomic code in IDH-mutant LGG.
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Affiliation(s)
- Chantal Scheepbouwer
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Kayla Borland
- Ludwig Maximilians University Munich, Department of Chemistry, Munich, Germany
| | | | - Heleen Verschueren
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Laurine Wedekind
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Jip Ramaker
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Branko Misovic
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Mathilde CM Kouwenhoven
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurology, Amsterdam, Netherlands
| | - David Noske
- Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Peter Vandertop
- Amsterdam UMC/AMC, Neurosurgical Center Amsterdam, Amsterdam, Netherlands
| | | | - Tom Wurdinger
- Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, Netherlands
| | | | - Stefanie Kellner
- Ludwig Maximilians University Munich, Department of Chemistry, Munich, Germany
| | - Danijela Koppers-Lalic
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
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Hendriks G, Derr R, Misovic B, Morolli B, Calléja F, Vrieling H. The novel ToxTracker reporter system provides mechanistic insight into the genotoxic properties of chemicals. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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