Unveiling hierarchy and spatial distribution of O6-methylguanine-DNA methyltransferase promoter methylation in World Health Organization grade 2-3 gliomas

Abstract

This study investigated the role of O⁶-methylguanine-DNA methyltransferase promoter (MGMTp) methylation hierarchy and heterogeneity in grade 2-3 gliomas, focusing on variations in chemotherapy benefits and resection dependency. A cohort of 668 newly diagnosed grade 2-3 gliomas, with comprehensive clinical, radiological, and molecular data, formed the basis of this analysis. The extent of resection was categorized into gross total resection (GTR ≥100%), subtotal resection (STR >90%), and partial resection (PR ≤90%). MGMTp methylation levels were examined using quantitative pyrosequencing. Our findings highlighted the critical role of GTR in improving the prognosis for astrocytomas (IDH1/2-mutant and 1p/19q non-codeleted), contrasting with its lesser significance for oligodendrogliomas (IDH1/2 mutation and 1p/19q codeletion). Oligodendrogliomas demonstrated the highest average MGMTp methylation levels (median: 28%), with a predominant percentage of methylated cases (average methylation levels >20%). Astrocytomas were more common in the low-methylated group (10%-20%), while IDH wild-type gliomas were mostly unmethylated (<10%). Spatial distribution analysis revealed a decrement in frontal lobe involvement from methylated, low-methylated to unmethylated cases (72.8%, 59.3%, and 47.8%, respectively). In contrast, low-methylated and unmethylated cases were more likely to invade the temporal-insular region (19.7%, 34.3%, and 40.4%, respectively). Astrocytomas with intermediate MGMTp methylation were notably associated with temporal-insular involvement, potentially indicating a moderate response to temozolomide and underscoring the importance of aggressive resection strategies. In conclusion, our study elucidates the complex interplay of MGMTp methylation hierarchy and heterogeneity among grade 2-3 gliomas, providing insights into why astrocytomas and IDH wild-type lower-grade glioma might derive less benefit from chemotherapy.

Keywords: MGMT promoter; astrocytoma; grade 2–3 gliomas; hierarchy; oligodendroglioma.

FIGURE 1

The relationship between extent of resection (EOR) and prognosis of grade 2–3 gliomas. (A) Typically illustrative examples of patients who received gross total resection (a, gross total resection [GTR]; b, subtotal resection [STR]; and c, partial resection [PR] (c). Pre and post, preoperative and postoperative T2WI, FLAIR, and T1CE images. Orange arrows represent tumor residuals. (B) Progression‐free survival (PFS) comparison among gliomas: (a) oligodendroglioma patients who received STR were not inferior to those who underwent GTR, but both superior to PR patients; (b) astrocytoma patients might achieve significant tumor control benefits from undergoing GTR (median PFS for GTR, STR, and PR: unreached, 52.0 months and 46.0 months, respectively); and (c) limited by the sample size, we observed a clear trend toward IDH wild‐type gliomas (IDHwts) also benefiting from GTR, although this difference was not statistically significant for PFS (median PFS for GTR, STR, and PR: 38.0, 12.0, and 11.0 months, p = 0.107). (C) Overall survival (OS) comparison among grade 2–3 gliomas: (a) the OS between GTR and STR patients was comparable but both were superior to STR patients in oligodendrogliomas; (b) an evident OS hierarchy was observed for GTR, STR, and PR astrocytoma cases; and (c) GTR might improve the survival of IDHwts (median OS for GTR, STR, and PR: unreached, 28.0 months, and 21.0 months, respectively, p = 0.092).

FIGURE 2

Some representative outcomes of grade 2–3 gliomas treated with different tumor removal strategies are shown (A, gross total resection [GTR]; B, subtotal resection [STR]; C, partial resection [PR]). (A) GTR can provide significant benefits for gliomas. (B) Oligodendrogliomas with STR exhibit a better response to chemoradiotherapy, and the residual tumor often regresses following adjuvant treatment. However, the small residuals remaining from astrocytomas and IDH wild‐type gliomas (IDHwts) can be a direct source of tumor progression. (C) Patients who undergo PR experience tumor recurrence within a relatively short follow‐up period. Orange arrows represent tumor residuals and red arrows are radiological outcomes. Pre, preoperative; post, postoperative; mon; months after operation.

FIGURE 3

The difference in O6‐methylguanine‐DNA methyltransferase promoter (MGMTp) methylation status among grade 2–3 gliomas. (A) The heatmap of quantitative MGMTp methylation levels for gliomas. The results showed substantial heterogeneity among CpG sites and hierarchy in gliomas. (B) Representative examples for methylated oligodendrogliomas (a), low‐methylated astrocytomas (b), and unmethylated IDHwts (c). (C) The median methylation results of gliomas. Oligodendrogliomas harbored the highest methylation levels for each CpGs tested, followed by astrocytomas and IDH wild‐type gliomas (IDHwts). (D) The distribution of average results of CpGs 74–81 showed hierarchy among gliomas. (E) Tiered average methylation levels revealed that most oligodendrogliomas were methylated (>20%), while low‐methylated (10%–20%) cases increased in astrocytomas and unmethylated (<10%) cases were common in IDHwt subgroups. (F) Correlation between MGMT promoter methylation levels and genome‐wide methylation levels. DNA methylation data were obtained from TCGA database, and Pearson correlation coefficients were calculated to determine the relationship. The analysis included 502 primary LGG patients, and both the MGMT promoter and genome‐wide methylation levels were computed as average beta values of the respective CpG sites. The MGMT promoter methylation levels had a moderate relationship with overall methylation levels in TCGA‐LGGs (r = 0.57, p < 0.001), which implied that MGMTp methylation might only partially serve as a surrogate for G‐CIMP.

FIGURE 4

Spatial distribution of grade 2–3 gliomas. (A) Gliomas frequently invaded the frontal lobe and then the temporal‐insular and parieto‐occipital lobes. (B) Oligodendrogliomas (a), astrocytomas (b), and IDH wild‐type gliomas (IDHwts) (c) displayed different spatial preferences. Most of the oligodendrogliomas located in the frontal lobe, and more astrocytomas, showed temporal‐insular involvement. (C) Based on the average results of all CpG sites tested, we simply classified gliomas as (a) methylated (>20%), (b) low methylation (10%–20%), and (c) unmethylated (<10%), and we noticed a decrement of frontal invasion while an inverse trend of temporal‐insular infringement (frontal lobe involvement: 72.8% (262/360) of methylated, 59.3% (102/172) of low‐methylated, and 47.8% (65/136) of unmethylated LGGs, temporal‐insular invasion: 19.7% (71/360) of methylated, 34.3% (59/172) of low‐methylated, and 40.4% (55/136) of unmethylated LGGs, Table 2).