Genetic and epigenetic stability of oligodendrogliomas at recurrence

Abstract

Among diffuse gliomas, oligodendrogliomas show relatively better prognosis, respond well to radiotherapy and chemotherapy, and seldom progress to very aggressive tumors. To elucidate the genetic and epigenetic background for such behavior and tumor evolution during tumor relapse, we comparatively analyzed 12 pairs of primary and recurrent oligodendrogliomas with 1p/19q-codeletion. Initial treatment for these patients was mostly chemotherapy alone. Temozolomide was used for 3, and procarbazine, nimustine and vincristine (PAV chemotherapy) were used for 7 patients. World Health Organization histological grade at recurrence was mostly stable; it was increased in 2, the same in 9, and decreased in 1 cases. Whole-exome sequencing demonstrated that the rate of shared mutation between the primary and recurrent tumors was relatively low, ranging from 3.2-57.9% (average, 33.3%), indicating a branched evolutionary pattern. The trunk alterations that existed throughout the course were restricted to IDH1 mutation, 1p/19q-codeletion, and TERT promoter mutation, and mutation of the known candidate tumor suppressor genes CIC and FUBP1 were not consistently observed between primary and recurrent tumors. Multiple sampling from different regions within a tumor showed marked intratumoral heterogeneity. Notably, in general, the number of mutations was not significantly different after recurrence, remaining under 100, and no hypermutator phenotype was observed. FUBP1 mutation, loss of chr. 9p21, and TCF12 mutation were among a few recurrent de novo alterations that were found at recurrence, indicating that these events were clonally selected at recurrence but were not enough to enhance malignancy. Genome-wide methylation status, measured by Illumina 450 K arrays, was stable between recurrence and the primary tumor. In summary, although oligodendroglioma displays marked mutational heterogeneity, histological malignant transformation accompanying events such as considerable increase in mutation number and epigenetic profile change were not observed at recurrence, indicating that noticeable temporal and spatial genetic heterogeneity in oligodendrogliomas does not result in rapid tumor progression.

Keywords: Heterogeneity; Hypermutator; Methylation; Mutation; Oligodendroglioma.

Fig. 1

Summary of the genomic profiles of the primary and recurrent oligodendrogliomas. The number of non-synonymous mutations, WHO grade, postoperative treatment, MGMT promoter methylation status, mutation profiles and copy number alterations are shown from top to bottom of the panel. On the right of the panel, the percentage of retained and acquired mutations and copy number alterations are depicted

Fig. 2

An example of histopathological and molecular genetic alterations in recurrent anaplastic oligodendroglioma (Patient 3). The patient with anaplastic oligodendroglioma was treated with 12 courses of temozolomide after gross total removal of the tumor, and MRI and ¹¹C-Methionine –PET detected regrowth of the tumor 17 months after this treatment. Histological analysis was anaplastic oligodendroglioma at recurrence, which showed decreased tumor cell density, slight improvement of atypia of the nucleus, and decreased number of mitotic cells compared to the primary tumor. Hemizygous loss of multiple foci was not preserved at recurrence, except for 1p/19q-codeletion. Clinical course, MRI and MET-PET images, pathological images (H&E stained formalin-fixed paraffin-embedded tissue slides), copy number alterations and phylogenetic tree of the primary and recurrent tumor are depicted from top to bottom of the panel

Fig. 3

Summary of genomic profiles in different regions of oligodendrogliomas. Mutation and copy number analysis of samples in different regions of the tumor in four patients. The number of non-synonymous mutations, clinical grade, MGMT promoter methylation status, mutation profiles and copy number alterations are shown from top to bottom of the panel. On the right of the panel, the percentage of retained and acquired mutations and copy number alterations are depicted

Fig. 4

Representative cases illustrating intratumoral heterogeneity. a In patient 14, the Gd-enhanced tumor center and the marginal non-enhanced part of the tumor were separately collected. The TERT promoter mutation was different in each tumor region. b In patient 15, the tumor center with MET-PET high uptake, and the marginal tumor portion with MET-PET low uptake, were separately collected. Only the tissue with MET-PET high uptake had TERT promoter mutation

Fig. 5

Genome-wide methylation status was stable between recurrence and the primary tumor. Heatmap of the methylation levels (β-value) in 319 samples, including the 30 oligodendrogliomas of the present study and 289 lower-grade gliomas from TCGA. Unsupervised clustering was performed using 8000 selected Infinium probes. Each row represents a probe, and each column represents one sample. For each sample, IDH1 mutation and 1p/19q-codeletion status are indicated by colored boxes at the bottom of the map. Samples connected with a line are pairs of primary and recurrent tumors or samples in different regions of the tumor