Intratumor DNA methylation heterogeneity in glioblastoma: implications for DNA methylation-based classification

Abstract

Background A feature of glioblastoma (GBM) is cellular and molecular heterogeneity, both within and between tumors. This variability causes a risk for sampling bias and potential tumor escape from future targeted therapy. Heterogeneous intratumor gene expression in GBM is well documented, but little is known regarding the epigenetic heterogeneity. Variability in DNA methylation within tumors would have implications for diagnostics, as methylation can be used for tumor classification, subtyping, and determination of the clinically used biomarker O 6 -methylguanine-DNA methyltransferase ( MGMT ) promoter methylation. We therefore aimed to profile the intratumor DNA methylation heterogeneity in GBM and its effect on diagnostic properties. Methods Three to 4 spatially separated biopsies per tumor were collected from 12 GBM patients. We performed genome-wide DNA methylation analysis and investigated intratumor variation. Results All samples were classified as GBM isocitrate dehydrogenase ( IDH ) wild type (wt)/mutated by methylation profiling, but the subclass differed within 5 tumors. Some GBM samples exhibited higher DNA methylation differences within tumors than between, and many cytosine-phosphate-guanine (CpG) sites (mean: 17 000) had different methylation levels within the tumors. MGMT methylation status differed in IDH mutated patients (1/1). Conclusions We demonstrated that intratumor DNA methylation heterogeneity is a feature of GBM. Although all biopsies were classified as GBM IDH wt/mutated by methylation analysis, the assigned subclass differed in samples from the same patient. The observed heterogeneity within tumors is important to consider for methylation-based biomarkers and future improvements in stratification of GBM patients.

The clinical significance of the T2-FLAIR mismatch sign in grade II and III gliomas: a population-based study

“…Methylation analysis and normalization was performed as previously described [21]. Briefly, methylation data were processed with the statistical software R (version 3.6.1) using the Minfi [22] and ChAMP [22][23][24] packages.…”

Immunohistochemically Characterized Intratumoral Heterogeneity Is a Prognostic Marker in Human Glioblastoma

“…By self-renewal of stem cell like neoplastic cells, genetically and phenotypically diverse daughter cells develop, from which different intratumoral subtypes arise [ 9 , 10 ]. Besides these two main hypotheses, it is assumed that tumor heterogeneity is a consequence of a multifactorial process, including epigenetic alterations [ 11 ], intercellular communication, and interaction with the surrounding microenvironment [ 10 , 12 ]. In addition to regional heterogeneity, a chronological heterogeneity can also be observed when comparing pairs of primary and recurrent GBM.…”

DNA methylation classification in diffuse glioma shows little spatial heterogeneity after adjusting for tumor purity

“…A recent study reported intratumor DNA methylation-based subtype heterogeneity in five of twelve glioblastomas in their cohort 24 . We were unable to confirm this extent of heterogeneity in our study.…”