MGMT Promoter Methylation Predicts Overall Survival after Chemotherapy for 1p/19q-Codeleted Gliomas

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1p/19q-codeleted oligodendrogliomas are relatively less common primary brain tumors with a favorable prognosis compared with isocitrate dehydrogenase (IDH)–wild-type and IDH-mutant gliomas with 1p/19q-intact (1, 2). Standard treatment generally includes maximal safe resection and radiotherapy (3, 4), with adjuvant alkylating chemotherapy as the backbone of systemic treatment (5–10). Given favorable long-term outcomes, there is interest in strategies to de-escalate therapy regimens, either with substitution of procarbazine, lomustine, and vincristine (PCV) with temozolomide (TMZ) or omission of radiotherapy, both of which are currently being evaluated in phase III randomized clinical trials (RCT; refs. 11, 12). Level 1 evidence supports adjuvant radiotherapy and PCV for high-risk or anaplastic 1p/19q-codeleted oligodendrogliomas (5–7, 12). However, in practice, selection of therapy is highly variable and may be provider- or institution-dependent (11, 13–15). There are currently no validated biomarkers that predict response to alkylating chemotherapy or guide more personalized management for these tumors.

O⁶-methylguanine-DNA methyltransferase (MGMT) is a DNA-repair protein that removes alkyl groups from the O⁶ position of guanine, an important site of DNA alkylation (16). Epigenetic silencing of MGMT through promoter methylation is an important biomarker that predicts response to TMZ in glioblastoma (9). Multiple phase III trials have demonstrated that MGMT methylation can be used to consider de-escalation of therapy for elderly patients with glioblastoma or those with poor performance status (16–18). However, the role of MGMT status remains unresolved in grade 2 and 3 gliomas due to molecular heterogeneity and the lack of sufficiently large datasets for this analysis (11, 19, 20). The World Health Organization (WHO) now classifies grade 2 and 3 gliomas based on molecular features, rather than tumor morphology alone (21). 1p/19q chromosomal codeletion in the presence of the IDH mutation is the defining characteristic of molecular oligodendrogliomas and is present in approximately 70%, 4%, and 2% of histologic oligodendrogliomas, astrocytomas, and glioblastomas, respectively (22). Analyses of historical clinical trials that recruited patients based on histologic features represent mixed populations of patients by current standards. Prior studies did not determine the effect of mMGMT in the context of molecular classifications and, therefore, reported mixed results (20). The IDH mutation leads to accumulation of 2-hydroxyglutarate, an oncometabolite that results in CpG island hypermethylation, including MGMT promoter region sites (23). The MGMT promoter is more frequently methylated in IDH-mutant (1p/19q-codeleted or -intact) versus IDH–wild-type tumors (5, 7, 8, 20, 24, 25). Previous studies generally have not resolved the predictive value of mMGMT in IDH-mutant tumors independently of 1p/19q-codeletion status (5, 7, 8, 10, 26–28).

We recently found that MGMT status is predictive of response to alkylating chemotherapy in IDH-mutant and 1p/19q-codeleted but not IDH-mutant and 1p/19q-intact gliomas (20). While the effect of MGMT methylation on progression-free survival (PFS) was impressive, we did not find a statistically significant effect on overall survival (OS), likely due to the low number of deaths observed. However, the lack of survival benefit could also be explained by effective salvage therapies or acquired resistance through TMZ-induced hypermutation. TMZ-induced hypermutation occurs more commonly in methylated gliomas and is associated with worse outcomes after progression (29–33). We queried the nation's largest cancer database to determine the association of MGMT methylation and OS in these tumors.

The National Cancer Database (NCDB) is a retrospective nationwide dataset sponsored by the American College of Surgeons and the American Cancer Society, constituting 70% of incident invasive cancer cases in the United States. Data were collected at more than 1,500 Commission on Cancer (CoC)–accredited hospitals between 2004 and 2022 (34).

We queried the NCDB (2022 submission) to identify all cases of diffuse/anaplastic gliomas, including oligodendroglioma, [International Classification of Diseases (ICD)-O-3 code 9450], anaplastic oligodendroglioma (9451, 9460), diffuse astrocytoma (9400), anaplastic astrocytoma (9401), mixed oligoastrocytic (9382), or glioma, not otherwise specified (9380) within the brain (ICD-O-3 codes C70.0, C71.0–71.9) newly diagnosed between January 1, 2010 and December 31 2019 (3). Data were submitted from COC-accredited cancer programs with follow-up through December 31, 2022. The following variables were collected and coded: age at diagnosis, sex, race, Charlson–Deyo Comorbidity Index, primary site, ICD-O-3 histology, collaborative staging (CS) site-specific factor 1 (WHO grade), CS site-specific factor 2 (MGMT promoter status), CS site-specific factor 5 (1p chromosomal deletion status), CS site-specific factor 6 (19q chromosomal deletion status), surgery at the primary site, chemotherapy, and radiation therapy. Additional brain-specific variables were collected and coded for patients diagnosed from 2018 to 2019: brain molecular markers (including IDH and 1p/19q-codeletion status), loss of heterozygosity of chromosome 1p and chromosome 19q, and methylation of O6-methylguanine-methyltransferase. Patients were included if they tested positive for both chromosome 1p and 19q loss of heterozygosity and positive or negative for MGMT gene promoter methylation. Patients diagnosed from 2018 to 2019 were additionally required to test positive for both IDH-mutation and 1p and 19q loss of heterozygosity. Patients were excluded if they had incomplete or less than 1 month of follow-up or unknown grade, extent of resection, receipt of chemotherapy, or receipt of radiotherapy.

Age, sex, race, Charlson–Deyo Comorbidity Index, WHO grade, extent of resection, chemotherapy, radiotherapy, and mMGMT status were included as covariables. The method of molecular marker testing is not specified in national cancer registries. The Charlson-Deyo Comorbidity Index is mapped from ICD-9-CM or ICD-10 secondary diagnosis codes and was categorized as 0, 1, and 2 or greater (35). WHO grade was coded as 2 or 3, consistent with WHO 2021 guidelines for IDH-mutant, 1p/19q-codeleted oligodendrogliomas (21). Extent of resection was based on definitions in the American College of Surgeons CoC's Facility Oncology Registry Data System manual and coded as previously described (3, 4, 36–40). All cancer-directed treatments submitted by CoC-accredited cancer registries, including surgical resection, chemotherapy, and radiotherapy are recorded only if they are administered as a first course of treatment to destroy, modify, control, or remove cancer tissue.

The primary outcome was OS in patients who received chemotherapy. Exploratory analyses included OS in all patients, regardless of treatment, and in patients who did not receive chemotherapy (Fig. 1). Subgroup analyses stratified patients by WHO grade and use of single- versus multiagent chemotherapy. A prior study validated that single- and multiagent regimens in patients with 1p/19q-codeleted tumors submitted to the NCDB from three academic medical centers represented TMZ and PCV, respectively, in 100% of cases (15).

All statistical analyses were conducted using the RStudio software Version 1.4.1106 (RStudio, Inc., Boston, Massachusetts). For our primary analysis, we measured the association between MGMT promoter status and OS in patients who received chemotherapy, adjusted for covariables. Descriptive statistics were generated and stratified by MGMT promoter status. Associations between MGMT promoter status and other clinical variables were determined using the Pearson χ² test and the Wilcoxon rank-sum test. Kaplan–Meier estimates were obtained for OS and compared using the log‐rank test. Univariable and multivariable Cox proportional hazards regressions were conducted. Variables that were statistically significant on univariable analysis were included in the multivariable model. Schoenfeld test of weighted residuals was utilized to assess proportional hazard assumptions in the primary analysis. If the proportional hazards assumptions for a variable were violated, the variable was removed and used as a stratification factor in the Cox models. Exploratory analyses were not corrected for multiple hypothesis testing. All analyses were performed at the 0.05 significance level based on two‐sided statistical testing. This report follows the STROBE and REMARK reporting guidelines for observational and biomarker studies, respectively.

Raw data for the NCDB Participant User Data File can be accessed by request to the American College of Surgeons (https://www.facs.org/quality-programs/cancer-programs/national-cancer-database/puf/). The code used to generate the datasets that were analyzed are available upon request to the corresponding author. The generated datasets cannot be shared, as stated in the NCDB Participant User File Data Use Agreement.

Of 5,247 patients with 1p/19q-codeleted gliomas, we identified 1,398 (26.6%) cases with known mMGMT status (Fig. 1). After excluding patients with unknown WHO grade, extent of resection, chemotherapy, and radiotherapy (N = 101, 7.2%), there were 1,297 patients included in the analysis. Clinical and demographic characteristics are displayed in Table 1. A total of 938 patients (72.3%) received chemotherapy as first-line treatment. Among patients who received chemotherapy, 783 (83.5%) received single-agent regimens and 134 (14.3%) received multiagent regimens. The MGMT promoter was methylated in 1,009 (77.8%) patients. mMGMT was associated with older age (median 47 vs. 42, P < 0.001). Median follow-up time was 38 months (interquartile range, 25–58) with 220 deaths (16.9%).

Median survival time for all patients was not reached. Among all patients, the 5-year OS rates were 70% [95% confidence interval (CI), 64%–77%] and 81% (95% CI, 78%–85%) for unmethylated (uMGMT) and methylated (mMGMT) tumors, respectively (P < 0.001; Fig. 2A). uMGMT remained an independent predictor of survival after adjusting for other covariables [HR, 2.35 (95% CI, 1.77–3.14); P < 0.001; Supplementary Table S1].

In patients who received chemotherapy, uMGMT was associated with worse survival [5-year survival 63% (95% CI, 55%–73%) vs. 80% (95% CI, 76%–84%); P < 0.001; adjusted HR (aHR) 2.61 (95% CI, 1.89–3.60); Fig. 2B; Table 2]. mMGMT was not prognostic in patients who did not receive chemotherapy [5-year survival 82% (95% CI, 74%–92%) vs. 86% (95% CI, 81%–92%) for uMGMT vs. mMGMT, respectively; P = 0.38; HR, 1.31 (95% CI, 0.71–2.42); Fig. 2C; Supplementary Table S2].

Subgroup analyses in patients who received chemotherapy were stratified by chemotherapy regimen and WHO grade (Figs. 3 and 4). The effect-sizes were similar across subgroups. mMGMT was prognostic in patients who received single-agent (log-rank P < 0.001) and multiagent (P = 0.006) chemotherapy regimens and with grade 2 (P = 0.02) and 3 tumors (P < 0.001). A similar effect was observed for patients with high-risk low-grade gliomas, defined per RTOG 9802 as patients with grade 2 tumors and less than gross-total resection (P = 0.02; Figs. 3D and 4; refs. 6, 10). Most patients who received chemotherapy also received radiotherapy as part of their first course of treatment (N = 801, 85.4%). In patients who received both chemotherapy and radiotherapy, uMGMT was associated with worse survival [5-year survival 59% (95% CI, 49%–71%) vs. 79% (95% CI, 75–83); aHR, 2.72 (95% CI, 1.93–3.84); P < 0.001; Supplementary Fig. S1]. No effect was observed in patients who received chemotherapy alone (P = 0.64).

We tested the proportional hazards assumption with the Schoenfeld method for our primary analysis of OS in patients who received chemotherapy. While the univariable test indicated a violation of the proportional hazards assumption for MGMT status (P = 0.04; Supplementary Fig. S2), the residual plot was inconsistent with a specific time-period interaction. As sensitivity analyses, we analyzed patients diagnosed through 2017 (median follow-up 55 months) and patients with longer than 1 year of follow-up and found similar results with no violations of the proportional hazards assumption (Supplementary Fig. S3). The proportional hazards assumption in the multivariable model remained unviolated (Supplementary Table S3). In addition, the univariable tests indicated a violation for age, grade, and Charlson-Deyo Comorbidity Index (Supplementary Fig. S5). Similar results were observed after stratifying our analyses by these factors (Fig. 3, Supplementary Fig. S4).

IDH mutation status was not available in national cancer registries before 2018. Although virtually all tumors with 1p/19q codeletion are mutated for IDH1 or IDH2, false-positives for 1p/19q codeletion may occur (41). Because false-positive 1p/19q-codeletions are rare in properly worked-up samples (i.e., patients with oligodendroglial histology or retained ATRX expression; ref. 42), we performed a sensitivity analysis that only included patients with oligodendroglial histology (ICD-O-3 codes 9450, 9451, 9460, and 9382). Among patients with oligodendroglial tumors that received chemotherapy (N = 852, 90.8%), uMGMT was associated with worse survival [aHR, 2.63 (95% CI, 1.78–3.92); P < 0.001; Supplementary Fig. S5A]. Both 1p/19q status and IDH status were available for patients diagnosed from 2018 to 2019. In the 418 patients diagnosed from 2018–2019 with IDH-mutant and 1p/19q-codeleted tumors, uMGMT was associated with worse survival [aHR, 3.00 (95% CI, 1.43–6.31); P = 0.004; Supplementary Fig. S5B].

In the current study, we found that mMGMT is predictive of OS in patients with 1p/19q-codeleted tumors who receive chemotherapy. Similar results were observed in subgroups of patients who were treated with single- and multiagent chemotherapy and with WHO grade 2 and 3 tumors. The effect was strongest in patients who received multimodality therapy with chemotherapy and radiotherapy. MGMT status was not associated with outcomes in patients who did not receive chemotherapy. This is the largest study to evaluate the predictive value of MGMT status in 1p/19q-codeleted oligodendrogliomas and the first to identify an OS benefit. On the basis of our findings, we suggest that MGMT status be used as a stratification factor in future clinical trials of 1p/19q-codeleted gliomas that use OS as an endpoint.

There are currently three major RCT evaluating treatment de-escalation for patients with 1p/19q-codeleted oligodendrogliomas, with alkylating chemotherapy being a component of every arm (Supplementary Fig. S6). CODEL (NCT00887146) is an international phase III RCT, jointly sponsored by the European Organization for Research and Treatment of Cancer (EORTC), North Central Cancer Treatment Group/Alliance for Clinical Trials in Oncology, and Canadian Cancer Trials Group. The initial design compared radiotherapy alone, radiotherapy with TMZ, or TMZ alone and was terminated after the RTOG 9402 and EORTC 26951 trials demonstrated improved OS with the addition of PCV to radiotherapy in patients with anaplastic oligodendrogliomas (43). The current iteration is randomizing patients with grade 2 or 3 1p/19q-codeleted gliomas to radiotherapy plus TMZ versus radiotherapy with PCV, with PFS as the primary endpoint and OS as a secondary endpoint.

The French POLCA (NCT02444000) trial seeks to determine if radiotherapy can be deferred until the time of progression and randomizes patients with anaplastic 1p/19q-codeleted gliomas to PCV alone versus radiotherapy followed by PCV. The primary endpoint is survival without neurocognitive deterioration, with PFS and OS being secondary endpoints. Similarly, the German IMPROVE CODEL (NOA-18, NCT05331521) trial seeks to improve “qualified overall survival,” defined as OS without functional, cognitive, or quality-of-life deterioration (44). This phase III trial will randomize patients with grade 2 or 3 1p/19q-codeleted gliomas to TMZ and lomustine (CETEG) versus radiotherapy and PCV, testing if chemoradiotherapy can be deferred until progression.

MGMT status will be collected and analyzed in the CODEL and IMPROVE CODEL trials but is not included as a stratification factor. Correlation between exploratory biomarkers (i.e., MGMT status) and survival is a prespecified secondary goal of the CODEL trial. In the IMPROVE CODEL trial, MGMT status will be included in a multivariable Cox proportional hazards model. The POLCA trial does not prespecify prospective analysis of MGMT methylation as a study goal, however, conclusions from our study suggest that MGMT promoter status may be evaluated in a post-hoc manner when available. Overall, our results suggest that MGMT status may affect patients with 1p/19q-codeleted tumors that receive alkylating chemotherapy (regardless of grade and chemotherapy regimen) and is thus relevant in every arm of these three major ongoing RCT.

Level 1 evidence supports the use of radiotherapy plus PCV in high-risk low-grade or anaplastic 1p/19q-codeleted oligodendrogliomas based on the RTOG 9802, RTOG 9402, and EORTC 26951 studies (5–7, 12). PCV monotherapy, TMZ monotherapy, and radiotherapy with TMZ have been investigated in the EORTC 22033, NOA-04, RTOG 0424, and CODEL (initial design) trials (7, 8, 28, 43); however, none of these regimens has demonstrated superiority compared with radiotherapy alone. Despite there being less data to support the use of TMZ in 1p/19q-codeleted oligodendrogliomas and some evidence suggesting it may be inferior (8, 15, 45), this regimen is often favored by neuro-oncologists, given its favorable hematological toxicity profile (11). Providers at academic centers more often treat with TMZ than PCV (13, 14). This is reflected in national data as well, which suggest that TMZ is given to approximately 89% of patients with grade 3 1p/19q-codeleted oligodendrogliomas (15). Furthermore, while the National Comprehensive Cancer Network Guidelines recommend radiotherapy unless the patient has a low-risk tumor or poor performance status (46), radiotherapy is reportedly administered in less than half of patients nationally (3, 4). The POLCA, CODEL, and IMPROVE CODEL trials are expected to be completed in 2024, 2025, and 2029, respectively. Therefore, results will not be reported for many years and OS data will likely take much longer to mature (47). In the meantime, incorporating MGMT status into decision strategies may aid in selecting appropriate therapies for patients.

Advantages of our study include the analysis of a large national cohort that may be generalizable to the US population. The large sample size decreases the likelihood of a type II error when studying this relatively uncommon tumor. Disadvantages include retrospective analysis and lack of central histologic and molecular review. There are risks of biases that cannot be accounted for. For oligodendrogliomas, the follow-up time was relatively short, as median survival time was not reached. IDH status was not available in tumor registries before 2018. To address this, we performed sensitivity analyses limited to tumors with oligodendroglial histology, in which false-positives are expected to be exceedingly rare (41, 42), and in patients diagnosed after 2018 with information on both IDH-mutation and 1p/19q-codeletion status. 1p/19q and MGMT status are not uniformly reported in national cancer registries, and nationwide disparities in molecular marker testing have been described (48, 49). Given that MGMT testing is not routinely performed for oligodendrogliomas, it is expected that a large percentage of cases had missing values. Patients with missing data may be systematically different than those included in the analysis, which may potentially limit the generalizability of our findings. However, it is reassuring that the frequency of mMGMT (77.8%) in the current study closely matches that of our previously reported prospective cohort (74%) (20). Overall, our study highlights an opportunity to increase MGMT testing nationwide for oligodendroglial tumors. However, widespread adoption will likely not be realized until further guidance is given from authoritative sources, such as the WHO or the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT-NOW).

We found that MGMT status is predictive of OS in patients with 1p/19q-codeleted gliomas who receive chemotherapy. Our results appear to be generalizable to patients who receive single- or multiagent chemotherapy and with grade 2 or 3 tumors. We therefore suggest that MGMT status be considered as a stratification factor in future clinical trials that evaluate alkylating chemotherapy in 1p/19q-codeleted gliomas. These findings are particularly salient in the context of the ongoing CODEL, POLCA, and IMPROVE CODEL trials and in a disease when daily practice often diverges from evidence-based standard of care.

G.M. McKhann reports personal fees from Koh Young Inc. and NeuroOne Technologies and grants from NIH outside the submitted work. F.M. Iwamoto reports personal fees from Advarra, Mimivax, Novocure, Ono Pharmaceutics, AbbVie, Alexion, Gennao Bio, Guidepoint, Kaytec, MassiveBio, Medtronic, Merck, Regeneron, Tocagen, XCures, Praesidia Biotherapeuthics, Oncoceutics, and Anheart; other support from Northwest Biotherapeutics; grants from Roche/Genentech; and grants and personal fees from BMS outside the submitted work. D.P. Horowitz reports other support from SWOG outside the submitted work. L.A. Kachnic reports grants from Varian, Inc.; personal fees from New Beta Innovation Limited, and Data Safety Monitoring Board; other support from UpToDate (royalties/licenses — editor of Bones Metastasis chapter); and nonfinancial support from RTOG Foundation board member outside the submitted work. A.I. Neugut reports consulting work for Otsuka, GlaxoSmithKline, United Biosource Corp., Hospira, Value Analytics, and Organon. In addition, A.I. Neugut is a member of the medical advisory board of EHE Intl. J.B. Yu reports grants and personal fees from Pfizer/Myovant and personal fees from Boston Scientific outside the submitted work. S.K. Cheng reports grants from Janssen outside the submitted work. T.J. Wang reports personal fees and nonfinancial support from AbbVie; personal fees from Cancer Panels, Doximity, Elekta, Novocure Wolters Kluwer, and Iylon Precision Oncology; nonfinancial support from Merck; and grants and nonfinancial support from RTOG Foundation, Genentech, and Varian outside the submitted work. No disclosures were reported by the other authors.

C.J. Kinslow: Conceptualization, data curation, software, formal analysis, validation, investigation, visualization, methodology, writing–original draft, writing–review and editing. A.I. Rae: Resources, supervision, validation, investigation, methodology, writing–review and editing. K. Taparra: Resources, data curation, validation, investigation, writing–review and editing. P. Kumar: Data curation, software, formal analysis, methodology, writing–review and editing. M.D. Siegelin: Supervision, investigation, methodology, writing–review and editing. J. Grinband: Supervision, validation, investigation, methodology, writing–review and editing. B.J.A. Gill: Supervision, investigation, writing–review and editing. G.M. McKhann: Supervision, investigation, methodology, project administration, writing–review and editing. M.B. Sisti: Supervision, investigation, methodology, project administration, writing–review and editing. J.N. Bruce: Supervision, investigation, methodology, project administration, writing–review and editing. P.D. Canoll: Resources, supervision, validation, investigation, methodology, project administration, writing–review and editing. F.M. Iwamoto: Supervision, investigation, methodology, writing–original draft. D.P. Horowitz: Resources, supervision, investigation, methodology, project administration, writing–review and editing. L.A. Kachnic: Resources, supervision, investigation, methodology, project administration, writing–review and editing. A.I. Neugut: Resources, supervision, investigation, methodology, project administration, writing–review and editing. J.B. Yu: Resources, data curation, supervision, validation, investigation, methodology, project administration, writing–review and editing. S.K. Cheng: Resources, supervision, funding acquisition, investigation, methodology, project administration, writing–review and editing. T.J. Wang: Conceptualization, supervision, investigation, visualization, methodology, writing–original draft, project administration, writing–review and editing.

The NCDB is a joint project of the CoC of the American College of Surgeons and the American Cancer Society. The data used in the study are derived from a deidentified NCDB file. The American College of Surgeons and the CoC have not verified and are not responsible for the analytical or statistical methodology employed, or the conclusions drawn from these data by the investigator.

A preliminary version of this study was submitted for presentation at the American Society for Radiation Oncology (ASTRO) Annual Meeting 2023 (October 1–4, 2023, San Diego, California).

This study was supported by NCI grant P30 CA13696.

The National Cancer Institute had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

The publication costs of this article were defrayed in part by the payment of publication fees. Therefore, and solely to indicate this fact, this article is hereby marked “advertisement” in accordance with 18 USC section 1734.