Abstract
Little is known about the mutational processes that shape the genetic landscape of gliomas. Numerous mutational processes leave marks on the genome in the form of mutations, copy number alterations, rearrangements or their combinations. To explore gliomagenesis, we hypothesized that gliomas with different underlying oncogenic mechanisms would have differences in the burden of various forms of these genomic alterations. This was an analysis on adult diffuse gliomas, but IDH-mutant gliomas as well as diffuse midline gliomas H3-K27M were excluded to search for the possible presence of new entities among the very heterogenous group of IDH-WT glioblastomas. The cohort was divided into two molecular subsets: (1) Molecularly-defined GBM (mGBM) as those that carried molecular features of glioblastomas (including TERT promoter mutations, 7/10 pattern, or EGFR-amplification), and (2) those who did not (others). Whole exome sequencing was performed for 37 primary tumors and matched blood samples as well as 8 recurrences. Single nucleotide variations (SNV), short insertion or deletions (indels) and copy number alterations (CNA) were quantified using 5 quantitative metrics (SNV burden, indel burden, copy number alteration frequency-wGII, chromosomal arm event ratio-CAER, copy number amplitude) as well as 4 parameters that explored underlying oncogenic mechanisms (chromothripsis, double minutes, microsatellite instability and mutational signatures). Findings were validated in the TCGA pan-glioma cohort. mGBM and “Others” differed significantly in their SNV (only in the TCGA cohort) and CNA metrics but not indel burden. SNV burden increased with increasing age at diagnosis and at recurrences and was driven by mismatch repair deficiency. On the contrary, indel and CNA metrics remained stable over increasing age at diagnosis and with recurrences. Copy number alteration frequency (wGII) correlated significantly with chromothripsis while CAER and CN amplitude correlated significantly with the presence of double minutes, suggesting separate underlying mechanisms for different forms of CNA.
Highlights
Gliomas vary considerably in their phenotype, biology, clinical behavior and response to treatment [1]
We studied the oncogenic processes of the cohort indirectly by quantifying the corresponding genetic alterations that they cause and subsequently correlating these findings with direct measurements of several oncogenic processes
45 IDH-WT diffuse glioma tumor specimens from 39 patients were used, classified as Molecularly-defined GBM (mGBM) (n = 37, 82.22%) or “other diffuse gliomas” (Others)” (n = 8, 17.78%) (Table 1)
Summary
Gliomas vary considerably in their phenotype, biology, clinical behavior and response to treatment [1]. Various distinct tumor entities, including astrocytoma, oligodendroglioma and glioblastoma (GBM), were initially defined by morphological criteria and further characterized by large-scale molecular and genetic studies [2,3,4,5]. Each tumor type has a specific molecular landscape with distinctive methylation profiles indicating their cell of origin and genomic alterations defining oncogenic programs [6,7]. Such divergent molecular-genetic landscapes imply that the causative mechanisms may be different, but little is known on the subject [8]. Other studies have provided evidence that DNA repair deficiency was a central theme in gliomagenesis [10,11]
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