Spatial heterogeneity in DNA methylation and chromosomal alterations in diffuse gliomas and meningiomas

Abstract

Adult-type diffuse gliomas and meningiomas are the most common primary intracranial tumors of the central nervous system. DNA methylation profiling is a novel diagnostic technique increasingly used also in the clinic. Although molecular heterogeneity is well described in these tumors, DNA methylation heterogeneity is less studied. We therefore investigated the intratumor genetic and epigenetic heterogeneity in diffuse gliomas and meningiomas, with focus on potential clinical implications. We further investigated tumor purity as a source for heterogeneity in the tumors. We analyzed genome-wide DNA methylation profiles generated from 126 spatially separated tumor biopsies from 39 diffuse gliomas and meningiomas. Moreover, we evaluated five methods for measurement of tumor purity and investigated intratumor heterogeneity by assessing DNA methylation-based classification, chromosomal copy number alterations and molecular markers. Our results demonstrated homogeneous methylation-based classification of IDH-mutant gliomas and further corroborates subtype heterogeneity in glioblastoma IDH-wildtype and high-grade meningioma patients after excluding samples with low tumor purity. We detected a large number of differentially methylated CpG sites within diffuse gliomas and meningiomas, particularly in tumors of higher grades. The presence of CDKN2A/B homozygous deletion differed in one out of two patients with IDH-mutant astrocytomas, CNS WHO grade 4. We conclude that diffuse gliomas and high-grade meningiomas are characterized by intratumor heterogeneity, which should be considered in clinical diagnostics and in the assessment of methylation-based and molecular markers.

DNA methylation alterations across time and space in paediatric brain tumours

“…In the relapse setting in medulloblastoma, there has however been reports of methylation subclass switches in rare cases [ 20 ], but no details on the methylation alterations. Within adult brain tumours, we previously found spatial intratumour heterogeneity of methylation subclasses in GBM [ 44 ] (according to classifier v11b2 and 11b4) and high-grade meningioma, but not in LGG (v12.5) [ 8 ]. The subclasses in the paediatric brain tumours examined here were however stable for all spatial and temporal patients (classification score ≥ 0.9; MNP classifier v12.5), which is promising for clinical diagnostics.…”

“…It should be noted that the LGG had on average one more biopsy per patient for this analysis, which increases their number of DMPs meaning that differences between the tumour types probably is even larger than the numbers suggest. We have previously reported an average of 21,000 DMPs in adult GBM (grade 4 tumour), 24,000 in adult high-grade meningioma, 17,000 in adult LGG and only 100 in adult low-grade (grade 1) meningioma [ 8 , 44 ]. The pattern of more alterations with increasing tumour grade was also observed here for the paired primary and relapse paediatric patients, where the aggressive and fast-growing AT/RT and HGG had significantly more DMPs than the LGGs etc.…”

“…Previous classifier versions (v11b2 and 11b4) had a cut-off at ≥ 0.5 for successful subclassification. V11b2 and 11b4 were used to analyse intratumour heterogeneity regarding methylation subclass in adult GBM [ 44 ], and v12.5 in LGG studies [ 8 ], which are referenced in this study. Copy-number alterations (CNAs) were inferred from the methylation data using conumee [ 15 ].…”

Regulatory function of DNA methylation mediated lncRNAs in gastric cancer

“…For example, it has been demonstrated that DNA methylation can result in the molecular and phenotypic heterogeneity of primary ADCs and lymph node metastases [ 28 ]. Obviously, it has been reported that global DNA methylation can reflect spatial heterogeneity [ 29 ]. Similarly, the DNA methylation shows extensive heterogeneity in time and space in glioblastoma [ 30 ].…”

Methylation Profiling in Diffuse Gliomas: Diagnostic Value and Considerations

“…Several studies have sampled specimen from different regions of the same glioblastoma tumour and profiled them using methylation-based classification [ 87 , 88 , 89 , 90 ]. We showed that 5 of 12 (42%) glioblastoma tumours had different methylation subclasses within their tumours [ 87 ].…”