Article
Methlyation-based classification of brain tumours through extracellular vesicle DNA
Methlysierungsbasierte Klassifizierung von Hirntumoren durch extrazelluläre Vesikel-DNA
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Published: | June 26, 2020 |
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Objective: Genome-wide methylation profiling has recently been developed into a tool that allows subtype tumor classification in central nervous system (CNS) tumors. Extracellular vesicles (EVs) are released by CNS tumor cells and contain high molecular weight tumor DNA, rendering EVs a potential biomarker source to identify tumor subgroups, stratify patients and monitor therapy by liquid biopsy. We investigated whether the DNA in glioma-derived EVs reflects genome-wide tumor methylation profiles and allows tumor subtype classification.
Methods: DNA was isolated from EVs secreted by cultured glioma stem-like cells (GSC) as well as from the cells of origin and from the original tumor samples (n=6 patients). EVs were classified by nanoparticle analysis (NTA), immunoblotting, imaging flow cytometry (IFCM), multiplex EV assays and electron microscopy. Genome-wide DNA methylation profiling was performed using an 850k Illumina EPIC array and results were classified according to the DKFZ brain tumor classifier. EV DNA was furthermore isolated from brain tumor patients (n=3) and healthy donors (n=3)
Results: The size range of GSC-derived EVs was 120-150 nm. The majority of secreted EVs exhibited high expression of common EV markers. Genome-wide methylation profiling of GSC-derived EVs correctly identified the methylation class of the original tumor, including information on the IDH mutation status and subclass classification (RTK1, RTK2). In addition, copy number alterations and the MGMT metyhlation status matched the pattern of the parental GSCs and original tumor samples. PCA analysis of methylation status of circulating EV DNA showed close relationship to the original tumor profile.
Conclusion: EV DNA faithfully reflects the tumor methylation class as well as the MGMT methylation status and copy number variations present in the parental cells and the original tumor. Methylation profiling of circulating tumor EV DNA could become a useful tool to detect and classify CNS tumors.
Figure 1 [Fig. 1]