MGMT promoter methylation is associated with patient age and 1p/19q status in IDH-mutant gliomas

Methylation of the promoter region of the gene encoding O⁶-methylguanine-DNA methyltransferase (MGMT) predicts better response to the alkylating chemotherapeutic temozolomide (TMZ) in glioblastomas (GBM).¹ Testing for MGMT promoter methylation is therefore required for World Health Organization (WHO) grade 4 GBMs, whereas in grade 2-3 gliomas, testing is more variable between institutions.

Mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 (“IDH^mut”) are present in the majority of WHO grade 2-3 astrocytomas, and in ~10% of grade 4 gliomas. The presence of IDH^mut is now required for the diagnosis of oligodendroglioma, along with 1p/19q codeletion.² Because IDH^mut increases overall genomic CpG methylation, it is strongly associated with MGMT promoter methylation. Indeed, one prior report suggested that the MGMT promoter is methylated in virtually all IDH^mut astrocytomas and oligodendrogliomas.³ However, this is controversial.⁴ At Northwestern Memorial Hospital (NMH), which uses a pyrosequencing assay to screen for MGMT promoter methylation in every WHO grade 2-4 glioma, 17/97 (17.5%) of IDH^mut astrocytomas lacked MGMT promoter methylation (Figure 1A). In contrast, only 2/53 (3.8%) of IDH^mut, 1p/19q-codeleted oligodendrogliomas were negative (P = .019 by Fisher’s exact test). In The Cancer Genome Atlas (TCGA), 30/257 (11.7%) of IDH^mut astrocytomas lacked MGMT promoter methylation, but only 1/169 (0.6%) IDH^mut, 1p/19q-codeleted oligodendrogliomas was MGMT-unmethylated (P > .0001 by Fisher’s exact test) (Figure 1A).

Fig. 1.

MGMT promoter methylation in IDH^mut gliomas. (A) Summary of MGMT promoter methylation according to IDH^mut in WHO grade 2-4 gliomas. N = 515 cases from NMH (Northwestern Memorial Hospital) and 626 cases from TCGA (The Cancer Genome Atlas). (B) Pattern of MGMT CpG methylation in IDH^mut oligodendrogliomas vs IDH^mut astrocytomas. Each column represents the mean beta value of 168 IDH^mut, 1p/19q-codeleted oligodendrogliomas, minus the mean beta value of 260 IDH^mut astrocytomas, at a single CpG site associated with the MGMT gene from TCGA. CpG methylation data obtained from http://xena.ucsc.edu. P values were calculated at each site by two-tailed t-tests with Bonferroni correction. (Note that cohort sizes slightly vary compared to (A), due to rare cases in each subgroup lacking sufficient annotation for analysis.)

Detailed analysis of MGMT methylation showed that, compared to IDH^mut astrocytomas, IDH^mut, 1p/19q-codeleted oligodendrogliomas had significantly higher average methylation beta values at 44.9% of all 147 MGMT CpG sites (Figure 1B). At the transcriptionally sensitive north shore and island regions, 69% of sites were significantly more methylated in oligodendrogliomas. None were significantly more methylated in astrocytomas.

At NMH, IDH^mut astrocytomas without MGMT promoter methylation were similar in WHO grade (χ ² = 3.2, P = .19) and survival (hazard ratio = 1.3, P = .57) compared to IDH^mut astrocytomas with MGMT promoter methylation. TCGA IDH^mut astrocytomas also showed no significant correlation between unmethylated MGMT promoter and WHO grade (χ ² = 0.58, P = .75), cytosine-phosphate-guanine (CpG) island methylator phenotype (G-CIMP) status (P = .13 by Fisher’s exact test), or survival (hazard ratio = 1.2, P = .67). Surprisingly, MGMT-unmethylated IDH^mut astrocytomas at NMH tended to occur in slightly younger patients (mean age = 32.5 vs 38.0 years, P = .03). This age difference was nearly identical in TCGA IDH^mut astrocytomas (32.6 vs 38.6 years, P = .01).

In sum, whereas MGMT promoter methylation is more common in IDH^mut astrocytomas than in IDH wild-type astrocytomas, it is even more common in IDH^mut, 1p/19q-codeleted oligodendrogliomas, to the point of being present in nearly all oligodendrogliomas. This comports with data from EORTC 22033⁵; and further shows (i) an inverse association between age and MGMT methylation; (ii) differential methylation between IDH^mut astrocytomas and IDH^mut oligodendrogliomas at specific CpG sites within the MGMT gene; (iii) overall survival in MGMT-methylated vs -unmethylated IDH^mut astrocytomas.

Thus, while IDH^mut increases genomic methylation, the extent to which specific genes are methylated likely depends on other factors, such as cell lineage. While lack of MGMT methylation has been described as an adverse prognostic marker in grade 4 IDH^mut gliomas,⁴ its clinical significance in IDH^mut grade 2-3 astrocytomas and oligodendrogliomas is less clear, perhaps in part because they are not always treated with TMZ upfront. Although overall survival in MGMT-unmethylated IDH^mut astrocytomas was not significantly worse in this current study, the EORTC 22033 study did suggest worse progression-free survival in such tumors.⁵MGMT analysis may also help predict the risk of post-TMZ hypermutation in astrocytomas.⁶ In contrast, since nearly all oligodendrogliomas are MGMT-methylated, its routine testing in oligodendrogliomas might not be necessary. Finally, while the association between younger patient age and increased odds of unmethylated MGMT promoter in IDH^mut astrocytomas is interesting, an explanation for this is not yet apparent.

Funding

This work was supported by National Institutes of Health grants R01NS102669 (C.H.), R01NS117104 (C.H.), R01NS118039 (C.H.), and by the Northwestern SPORE in Brain Cancer P50CA221747.

Conflict of interest statement. The authors disclose no potential conflicts of interest.

Authorship statement. Project conception: C.H. Project implementation: C.H. and K.M. Manuscript preparation and editing: C.H. and R.S.