Base resolution maps reveal the importance of 5-hydroxymethylcytosine in a human glioblastoma

• Main Authors: Eun-Ang Raiber, Dario Beraldi, Sergio Martínez Cuesta, Gordon R. McInroy, Zoya Kingsbury, Jennifer Becq, Terena James, Margarida Lopes, Kieren Allinson, Sarah Field, Sean Humphray, Thomas Santarius, Colin Watts, David Bentley, Shankar Balasubramanian
• Format: Article
• Language: English
• Published: Nature Publishing Group 2017-03-01
• Series: npj Genomic Medicine
• Online Access: https://doi.org/10.1038/s41525-017-0007-6

Abstract Aberrant genetic and epigenetic variations drive malignant transformation and are hallmarks of cancer. Using PCR-free sample preparation we achieved the first in-depth whole genome (hydroxyl)-methylcytosine, single-base-resolution maps from a glioblastoma tumour/margin sample of a patient. Our data provide new insights into how genetic and epigenetic variations are interrelated. In the tumour, global hypermethylation with a depletion of 5-hydroxymethylcytosine was observed. The majority of single nucleotide variations were identified as cytosine-to-thymine deamination products within CpG context, where cytosine was preferentially methylated in the margin. Notably, we observe that cells neighbouring tumour cells display epigenetic alterations characteristic of the tumour itself although genetically they appear “normal”. This shows the potential transfer of epigenetic information between cells that contributes to the intratumour heterogeneity of glioblastoma. Together, our reference (epi)-genome provides a human model system for future studies that aim to explore the link between genetic and epigenetic variations in cancer progression.