Reliable tumor detection by whole-genome methylation sequencing of cell-free DNA in cerebrospinal fluid of pediatric medulloblastoma.

Abstract

Medulloblastoma (MB), the most common form of pediatric brain malignancy, has a low frequency of oncogenic mutations but pronouncedly abnormal DNA methylation changes. Epigenetic analysis of circulating cell-free tumor DNA (ctDNA) by liquid biopsy offers an approach for real-time monitoring of tumor status without tumor dissection. In this study, we identified 6598 differentially methylated CpGs in both MB tumors and the ctDNA isolated from matched cerebrospinal fluid (CSF) compared with normal cerebellum, which could be used to detect MB tumor occurrence and determine its subtype. Furthermore, DNA methylation changes in serial CSF samples could be used to monitor the treatment response and tumor recurrence. Integrating our data with large public datasets, we identified reliable MB DNA methylation signatures in ctDNA that have potential diagnostic and prognostic values. Our study sets the stage for exploiting epigenetic markers in CSF to improve the clinical management of patients with MB.

• Authors: Jia Li, Sibo Zhao, Minjung Lee, Yue Yin, Jin Li, Yubin Zhou, Leomar Y Ballester, Yoshua Esquenazi, Roderick H Dashwood, Peter J A Davies, D Williams Parsons, Xiao-Nan Li, Yun Huang, Deqiang Sun
• Journal: Science advances (Sci Adv) Vol. 6 Issue 42 (10 2020) ISSN: 2375-2548 [Electronic] United States
• PMID: 33067228 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)
• Copyright: Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Chemical References

• Cell-Free Nucleic Acids
• Circulating Tumor DNA

Topics

• Cell-Free Nucleic Acids (genetics)
• Cerebellar Neoplasms (diagnosis, genetics)
• Child
• Circulating Tumor DNA (cerebrospinal fluid, genetics)
• DNA Methylation
• Humans
• Medulloblastoma (diagnosis, genetics)
• Mutation