Methylation Of The O6-methylguanine-DNA Methyltransferase Promoter Methylation Research Articles

Development of A Radiomic Model for MGMT Promoter Methylation Detection in Glioblastoma Using Conventional MRI.

The methylation of the O6-methylguanine-DNA methyltransferase (MGMT) promoter is a molecular marker associated with a better response to chemotherapy in patients with glioblastoma (GB). Standard pre-operative magnetic resonance imaging (MRI) analysis is not adequate to detect MGMT promoter methylation. This study aims to evaluate whether the radiomic features extracted from multiple tumor subregions using multiparametric MRI can predict MGMT promoter methylation status in GB patients. This retrospective single-institution study included a cohort of 277 GB patients whose 3D post-contrast T1-weighted images and 3D fluid-attenuated inversion recovery (FLAIR) images were acquired using two MRI scanners. Three separate regions of interest (ROIs) showing tumor enhancement, necrosis, and FLAIR hyperintensities were manually segmented for each patient. Two machine learning algorithms (support vector machine (SVM) and random forest) were built for MGMT promoter methylation prediction from a training cohort (196 patients) and tested on a separate validation cohort (81 patients), based on a set of automatically selected radiomic features, with and without demographic variables (i.e., patients' age and sex). In the training set, SVM based on the selected radiomic features of the three separate ROIs achieved the best performances, with an average of 83.0% (standard deviation: 5.7%) for accuracy and 0.894 (0.056) for the area under the curve (AUC) computed through cross-validation. In the test set, all classification performances dropped: the best was obtained by SVM based on the selected features extracted from the whole tumor lesion constructed by merging the three ROIs, with 64.2% (95% confidence interval: 52.8-74.6%) accuracy and 0.572 (0.439-0.705) for AUC. The performances did not change when the patients' age and sex were included with the radiomic features into the models. Our study confirms the presence of a subtle association between imaging characteristics and MGMT promoter methylation status. However, further verification of the strength of this association is needed, as the low diagnostic performance obtained in this validation cohort is not sufficiently robust to allow clinically meaningful predictions.

Using variant allelic fraction of driver mutations to determine the reliability of MGMT promoter methylation testing in adult-type diffuse gliomas.

e14034 Background: Methylation of the O6-methylguanine-DNA methyltransferase ( MGMT) promoter predicts response to temozolomide (TMZ) in adult-type diffuse gliomas. MGMT testing is thus standard practice. However, accurate results depend on adequate tumor cellularity in the analyzed sample. If the sample contains too many admixed nonneoplastic cells (which are consistently MGMT unmethylated), a false-negative result may be generated. Currently, ̃70% tumor cells are considered the minimum for reliable testing, but that is based on visual estimation by light microscopy; such estimation varies between observers and is often inaccurate. Since next-generation sequencing (NGS) is also frequently done on adult-type diffuse gliomas, and such tumors usually have heterozygous driver mutations known to be present in nearly 100% of tumor cells (IDH mutations in astrocytomas and oligodendrogliomas; TERT promoter mutations in ̃85% of IDH wild-type GBM), we sought to determine whether the variant allelic fraction (VAF) of these mutations could improve quality assurance in MGMT promoter methylation testing. Methods: We used an in-house cohort of 175 WHO gliomas (112 IDHwt, TERTmut GBM, 34 WHO grade 2-4 IDHmut astrocytomas, 29 WHO grade 2-3 IDHmut oligodendrogliomas), all with MGMT pyrosequencing and NGS data obtained from the same tissue blocks. Gliomas with average 10% methylation across all four CpG sites in the MGMT promoter were considered positive, as per standard cutoffs for that assay. Results: Overall, there was a positive correlation between driver VAF and amount of MGMT promoter methylation (slope = 0.25, R2= 0.33, P = 0.016). The largest dropoff in average methylation was when VAF was below 13% (7.4% average CpG methylation when VAF < 13% vs. 19.0% when VAF≥13%, P= 0.029). Based on our prior published study (PMID: 33830235), 36.5% of IDHwt GBMs, 86.7% of IDHmut astrocytomas, and 98.6% of IDHmut oligodendrogliomas should have MGMT promoter methylation. Among our GBMs, only 1/7 (14.0%) below a TERT mutant VAF of 13% reached the cutoff for MGMT promoter methylation, whereas 39/105 (37.0%) of GBMs VAF≥13% did. However, this did not reach statistical significance, likely because our cohort was underpowered for GBMs with TERTmut VAF < 13%. Among 34 IDHmut astrocytomas, only 1 had a VAF below 13%, and was reported as MGMT promoter unmethylated; all others had VAF between 21-56%, and showed consistent rates of MGMT methylation positivity across that entire range. All 29 oligodendrogliomas had VAFs of at least 26%; 2/29 were MGMT-negative, and both had VAFs at or above 36%. Conclusions: Additional cases are being prospectively collected to boost statistical power. Still, our existing data suggest that, when driver mutation VAF falls below ̃13% (i.e., tumor cellularity ̃26%), the risk of false-negative MGMT methylation results increases, and caution is warranted in such cases.

Federated Learning Approach for Measuring the Response of Brain Tumors to Chemotherapy

Brain tumor is a fatal disease and one of the major causes of rising death rates in adults. Predicting methylation of the O6-Methylguanine-DNA Methyltransferase (MGMT) gene status utilizing Magnetic resonance imaging (MRI) imaging is highly important since it is a predictor of brain tumor responses to chemotherapy, which reduces the number of needed surgeries. Deep Learning (DL) approaches became powerful in extracting meaningful relationships and making accurate predictions. DL-based models require a large database and accessing or transferring patient data to train the model. Federated machine learning has recently gained popularity, as it offers practical solutions for data privacy, centralized computation, and high computing power. This study aims to investigate the feasibility of federated learning (FL) by developing a FL-based approach to predict MGMT promoter methylation status using the BraTs2021 dataset for the four sequence types, (Fluid Attenuated Inversion Recovery (FLAIR), T1-weighted (T1w), T1-weighted Gadolinium Post Contrast (T1wCE/T1Gd), and T2-weighted (T2w)) MRI images. The FL model compared to the DL-based and the experimental results show that even with imbalanced and heterogeneous datasets, the FL approach reached the training model to 99.99% of the model quality achieved with centralized data after 300 communication rounds between 10 institutions using OpenFl framework and the improved EfficentNet-B3 neural network architecture.

Changes of O6-Methylguanine DNA Methyltransferase (MGMT) Promoter Methylation in Glioblastoma Relapse-A Meta-Analysis Type Literature Review.

Methylation of the O6-methylguanine DNA methyltransferase (MGMT) promoter has emerged as strong prognostic factor in the therapy of glioblastoma multiforme. It is associated with an improved response to chemotherapy with temozolomide and longer overall survival. MGMT promoter methylation has implications for the clinical course of patients. In recent years, there have been observations of patients changing their MGMT promoter methylation from primary tumor to relapse. Still, data on this topic are scarce. Studies often consist of only few patients and provide rather contrasting results, making it hard to draw a clear conclusion on clinical implications. Here, we summarize the previous publications on this topic, add new cases of changing MGMT status in relapse and finally combine all reports of more than ten patients in a statistical analysis based on the Wilson score interval. MGMT promoter methylation changes are seen in 115 of 476 analyzed patients (24%; CI: 0.21–0.28). We discuss potential reasons like technical issues, intratumoral heterogeneity and selective pressure of therapy. The clinical implications are still ambiguous and do not yet support a change in clinical practice. However, retesting MGMT methylation might be useful for future treatment decisions and we encourage clinical studies to address this topic.

Pyrosequencing Analysis of MGMT Promoter Methylation in Meningioma.

Methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is a well-established predictor of response to the DNA-alkylating agent temozolomide in patients with glioblastoma. Pyrosequencing analysis was used to determine the MGMT promoter methylation status in 61 meningiomas, to clarify whether it might have a predictive role. Only two tumors (3%) had a mean methylation frequency higher than the cut-off value of 10% for the four CpG sites examined. The methylation of the MGMT promoter is uncommon, or occurs at a low frequency in meningiomas. There is no convincing rationale to test such tumors for their MGMT methylation status in a clinical setting.

Clinical and Molecular Prognostic Factors for Long-Term Survival of Patients with Glioblastomas in Single-Institutional Consecutive Cohort.

The purpose of this study was to clarify the clinical and molecular characteristics associated with long-term survival in patients with glioblastoma. We analyzed the characteristics of 96 glioblastoma patients. Long-term survivors (LTSs) were classified into moderate LTSs (mLTSs), who survived >3 years, and LTSs, who survived >5 years, and compared with short-term survivors (STSs). Clinical and molecular factors were investigated. Younger age, better recursive partitioning analysis class, lack of subventricular zone (SVZ) involvement, promoter methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene, and loss of 19q were associated with mLTSs as compared with STSs. After adjustment for these factors, younger age and MGMT methylation remained independently associated with mLTSs. Younger age, better recursive partitioning analysis class, lack of SVZ involvement, and loss of 19q were associated with LTSs as compared with STSs. After adjustment, younger age and better preoperative Karnofsky performance scale (KPS) score remained independently associated with LTSs. Kaplan-Meier analyses revealed that younger age (<50 years), better preoperative KPS score (≥70), lack of SVZ involvement, and loss of 19q were associated with longer overall survival. In the multivariate analysis, only age was significantly associated with overall survival. Younger age and better preoperative KPS score were the characteristics associated with LTSs as compared with STSs. MGMT promoter methylation was associated with mLTSs, but not with LTSs. In addition, lack of SVZ involvement and loss of 19q might be prognostic for longer survival.

A novel truncated form of HMGA2 in tumors of the ovaries.

Neoplasms of the ovary are the second most common tumor of the female reproductive system, and the most lethal of the gynecological malignancies. Ovarian tumors are divided into a copious number of different groups reflecting their different features. The present study analyzed 187 ovarian tumors (39 sex-cord stromal tumors, 22 borderline tumors and 126 carcinomas) for the expression of the high-mobility group AT-hook 2 (HMGA2) gene, for mutations in the isocitrate dehydrogenase (NADP(+)) 1, cytosolic (IDH1), isocitrate dehydrogenase (NADP(+)) 2, mitochondrial (IDH2) and telomerase reverse transcriptase (TERT) genes, and for methylation of the O6-methylguanine-DNA methyltransferase (MGMT) promoter. Reverse transcription-polymerase chain reaction analysis showed that HMGA2 was expressed in 74.5% of the samples (120/161). A truncated transcript of HMGA2 was identified in 11 cases. A novel truncated form of HMGA2 was found in 4 serous high-grade carcinomas. Only 4 tumors (4/185) showed the TERT C228T mutation. No IDH1 or IDH2 mutations were found. Methylation of the promoter of MGMT was found in 2 borderline tumors (2/185). HMGA2 was expressed, in its truncated and native form, in different ovarian tumors, even the less aggressive types, underscoring the general importance of this gene in ovarian tumorigenesis. Mutations involving TERT, as well as MGMT promoter methylation, are rare events in ovarian tumors.

New insights into acquired temozolomide resistance in glioblastoma?

This scientific commentary refers to ‘c-Myc–miR-29c–REV3L signalling pathway drives the acquisition of temozolomide resistance in glioblastoma’ by Luo et al. (doi:10.1093/brain/awv287) The emergence of tumour cell resistance to chemotherapy represents a major challenge for the development of durable therapeutic strategies across most solid cancers including glioblastoma, the most malignant primary brain tumour in adults. The standard of care for glioblastoma is maximum surgery as safely feasible followed by radiotherapy, with concomitant and maintenance chemotherapy with the alkylating agent temozolomide (TMZ/RT→TMZ). This results in a median overall survival in the range of 12 months on a population level (Weller et al. , 2014). Radiotherapy alone doubled median survival in early studies, but the best radiological response is commonly stable disease, progression is inevitable, and the efficacy of radiotherapy may be partly related to anti-angiogenic rather than intrinsic tumour cell cytotoxic effects. Mechanisms underlying resistance to radiotherapy remain poorly understood, but extensive hypoxia may be an important factor. TMZ was approved for the treatment of newly diagnosed glioblastoma because of a moderate prolongation of median survival (Stupp et al. , 2005). Subgroup analyses revealed that the benefit from TMZ was largely restricted to patients with glioblastomas that exhibit a particular epigenetic alteration, promoter methylation of the O6-methylguanine DNA methyltransferase ( MGMT ) gene (Hegi et al. , 2005). However, even these patients eventually all progress and succumb to their disease, in the absence of changes in MGMT promoter methylation …

P108: Participation of the genes MVP/LRP and YB-1 in the determination of the rate of sensitivity of glioblastoma cells to temodal

Background Glioblastomas (GBL) are most aggressive brain tumors in adults. They are often radio- and chemotherapy resistant. The standard therapy of GBL includes surgery followed by radiotherapy with concomitant chemotherapy with temozolomide named temodal (imidazotetrazine derivative). Methylation of the O6-methylguanine-DNA-methyltransferase (MGMT) gene promoter is considered as predictor of better outcome of temodal therapy in comparison with the cases without MGMT promoter methylation (Stupp et al., 2009). The aim of this study is finding of additional predictors of temozolomide therapy effectiveness. Materials and methods We obtained primary cultures of GBL. The rate of GBL sensitivity to temozolomide was revealed by MTT test. Expression of multidrug resistance genes and genes which mediate temozolomide sensitivity (YB1, MDR1, MRP1, LRP, BCRP and MGMT) was determined by real time PCR. Protein localization and expression was revealed by immunohistochemical technique. Results We developed 14 primary GBL cultures. Staining for nestin was used for demonstration of neuronal origin of cell cultures. Analysis of gene expression and the rate of cell proliferation of the cultures showed that the rate of YB1 gene expression in slow proliferating cultures is significantly lower than in quickly proliferating cell populations. Cell cultures differed in temodal sensitivity 2–2.5-fold. We analyzed whether GBL cell sensitivity to temodal and the rate of several genes’ expression are correlated. We did not find the correlation between cell temodal sensitivity and the rate of MGMT gene expression. These data are in accordance with some results of another authors (Mullins et al., 2013; Brennan et al., 2013). However, we revealed positive correlation of the temodal sensitivity of GBL cultures and MVP/LRP expression (r = 0.5592, p = 0.04). We found also the trend to negative correlation between GBL temodal sensitivity and YB1 gene expression (r = −0.43602, p = 0.02) as well as MDR1 expression (r = −0.4195, p = 0.02). Conclusion The rate of temodal sensitivity of GBL primary cultures is connected with the rate of the expression of MVP/LRP, YB1 and MDR1genes. It is likely that YB-1 protein affects temodal sensitivity by influence on DNA reparation. YB1 could also have an effect on MDR1 expression. MVP/LRP expression is independent factor of GBL prognosis. This paper was completed with partial support from the Russian Foundation for Basic Research – Russia (Grant No. 23-04-40204 ).

P04.18 * PROGNOSIS IMPACT OF THE REGIONAL DISTRIBUTION OF MGMT GENE METHYLATION ACCORDING TO THE CPGISLAND METHYLATOR PHENOTYPE AND AGE IN HIGH-GRADE GLIOMAS

Clinical and molecular prognostic factors in gliomas include age, IDH mutation, the glioma CpG island methylator phenotype (G-CIMP) and promoter methylation of the O6-methylguanine DNA-methyltransferase (MGMT) gene, among others. Clinical trials supported the predictive value of MGMT promoter methylation for benefit from alkylating chemotherapy in elderly GBM patients. In this study, methylation data were obtained from 46 oligodendroglial samples with the Illumina 450K platform, and were analyzed with external data to reach a total 247 glioma samples. MGMT gene methylation analysis with this platform revealed two significant survival-associated CpG regions, one within the promoter (cg12981137) and the other within the gene body (cg07933035), both significantly associated with better overall survival (OS) and strongly correlated with the G-CIMP+ status. However, although around 50% of G-CIMP- tumors were MGMT methylated on these CpG sites, their prognostic relevance were not observed in these patients. Only the gene body methylation was prognostic, but in the context of age, showing significant differences of OS in elderly patients. The absence of the MGMT promoter prognostic value in G-CIMP- tumors was validated in an independent series of 59 chemoradiated GBM patients by MSP and qMSP assays. Our study suggests that the prognostic value of MGMT methylation should be reviewed in the context of specific G-CIMP profiles and age groups. Further analysis on the impact of MGMT methylation on gene and protein expression is necessary for better clinical treatment settings. The routine use of MGMT methylation for the individual treatment of patients should be still viewed with caution.

MGMT promoter methylation in plasma of glioma patients receiving temozolomide

Promoter methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene plays a role in cellular response to alkylating agents. In the present study aimed to: (i) evaluate the concordance between MGMT promoter methylation status in tumor tissue and plasma; (ii) monitor MGMT promoter methylation status in plasma taken before and during temozolomide treatment; (iii) explore the value of MGMT promoter methylation status in plasma as a prognostic/predictive biomarker in glioma patients. We enrolled 58 patients with histologically confirmed glioma at different grades of malignancy. All patients underwent surgical resection and temozolomide treatment. Paraffin-embedded tumor tissue was available for 48 patients. Blood samples were collected from all patients before temozolomide treatment (baseline) and at each MRI examination for a 12-month period. MGMT promoter methylation status was assessed in both sample types by real time PCR with a specific probe. The frequency of MGMT promoter methylation was 60.4% in tumor tissue and 41.38% in plasma. MGMT promoter methylation status was concordant in the two sample types (Kappa=0.75, 95% confidence interval (CI) 0.57-0.93; p value<0.001). Overall and progression-free survival were longer in patients with methylated MGMT promoter. Mortality was higher in patients with unmethylated MGMT promoter, whether in tumor tissue [hazard ratio (HR) 2.21; 95% CI 0.99-4.95] or plasma (HR 2.19; 95% CI 1.02-4.68). Progression-free survival was shorter in patients with unmethylated MGMT promoter, whether in tissue (HR 2.30; 95% CI 1.19-4.45) or plasma (HR 1.77; 95% CI 0.95-3.30). The cumulative incidence of unmethylated MGMT promoter in plasma at baseline was 58%, and reached virtually 100% at 12months. In conclusion MGMT promoter methylation status in tumor tissue and plasma was highly concordant, and both were associated with longer survival, supporting the role of the detection of methylated MGMT promoter in predicting treatment response. However we suggest caution in using plasma as a surrogate of tumor tissue due to possible false-negative results.

Epigenetic modulation of the drug resistance genes MGMT, ABCB1 and ABCG2 in glioblastoma multiforme

BackgroundResistance of the highly aggressive glioblastoma multiforme (GBM) to drug therapy is a major clinical problem resulting in a poor patient’s prognosis. Beside promoter methylation of the O 6 -methylguanine-DNA-methyltransferase (MGMT) gene the efflux transporters ABCB1 and ABCG2 have been suggested as pivotal factors contributing to drug resistance, but the methylation of ABCB1 and ABCG2 has not been assessed before in GBM.MethodsTherefore, we evaluated the proportion and prognostic significance of promoter methylation of MGMT, ABCB1 and ABCG2 in 64 GBM patient samples using pyrosequencing technology. Further, the single nucleotide polymorphisms MGMT C-56 T (rs16906252), ABCB1 C3435T (rs1045642) and ABCG2 C421A (rs2231142) were determined using the restriction fragment length polymorphism method (RFLP). To study a correlation between promoter methylation and gene expression, we analyzed MGMT, ABCB1 and ABCG2 expression in 20 glioblastoma and 7 non-neoplastic brain samples.ResultsDespite a significantly increased MGMT and ABCB1 promoter methylation in GBM tissue, multivariate regression analysis revealed no significant association between overall survival of glioblastoma patients and MGMT or ABCB1 promoter methylation. However, a significant negative correlation between promoter methylation and expression could be identified for MGMT but not for ABCB1 and ABCG2. Furthermore, MGMT promoter methylation was significantly associated with the genotypes of the MGMT C-56 T polymorphism showing a higher methylation level in the T allele bearing GBM.ConclusionsIn summary, the data of this study confirm the previous published relation of MGMT promoter methylation and gene expression, but argue for no pivotal role of MGMT, ABCB1 and ABCG2 promoter methylation in GBM patients’ survival.

Chronic treatment with fluoxetine for more than 6 weeks decreases neurogenesis in the subventricular zone of adult mice

The purpose of this study was to clarify the clinical and molecular characteristics associated with long-term survival in patients with glioblastoma.We analyzed the characteristics of 96 glioblastoma patients. Long-term survivors (LTSs) were classified into moderate LTSs (mLTSs), who survived >3 years, and LTSs, who survived >5 years, and compared with short-term survivors (STSs). Clinical and molecular factors were investigated.Younger age, better recursive partitioning analysis class, lack of subventricular zone (SVZ) involvement, promoter methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene, and loss of 19q were associated with mLTSs as compared with STSs. After adjustment for these factors, younger age and MGMT methylation remained independently associated with mLTSs. Younger age, better recursive partitioning analysis class, lack of SVZ involvement, and loss of 19q were associated with LTSs as compared with STSs. After adjustment, younger age and better preoperative Karnofsky performance scale (KPS) score remained independently associated with LTSs. Kaplan-Meier analyses revealed that younger age (<50 years), better preoperative KPS score (≥70), lack of SVZ involvement, and loss of 19q were associated with longer overall survival. In the multivariate analysis, only age was significantly associated with overall survival.Younger age and better preoperative KPS score were the characteristics associated with LTSs as compared with STSs. MGMT promoter methylation was associated with mLTSs, but not with LTSs. In addition, lack of SVZ involvement and loss of 19q might be prognostic for longer survival.

MGMT promoter gene methylation in pediatric glioblastoma: analysis using MS-MLPA

Promoter methylation of the O⁶-methylguanine-DNA-methyltransferase (MGMT) gene is widely recognized as an important predictive factor in the treatment of glioblastoma (GBM) patients with temozolomide. However, data regarding the methylation status of the MGMT promoter in pediatric GBM are yet to be elucidated. Nineteen tissue samples of pediatric GBM were evaluated for the MGMT promoter methylation status using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Methylation status was also evaluated using methylation-specific polymerase chain reaction (MSP) for 17 of the 19 patients. The correlation between MGMT promoter methylation and clinical outcome was assessed. Three of the 19 patients (16%) showed methylation of the MGMT promoter, according to MS-MLPA, as did 1 of the 17 (6%), according to MSP. The methylation status did not seem to have a definite effect on clinical outcome. Pediatric GBMs rarely have methylated MGMT promoters. With a better clinical outcome and lower methylation rate than their adult counterparts, it may be suggested that, for pediatric GBM, MGMT promoter methylation does not play a significant role as a prognostic factor.

Determination of O6-Methylguanine DNA Methyltransferase Promoter Methylation in Non-Small Cell Lung Cancer

Aberrant methylation of promoter CpG islands is known to be a major inactivation mechanism of the tumor-related genes including DNA repair genes. The objective of this study was to determine the frequency of promoter methylation of the O⁶-methylguanine DNA methyltransferase (MGMT) gene as a DNA repair gene in nonsmall cell lung cancer (NSCLC) and to analyze the correlation with clinicopathological parameters including age, gender, smoking status, histological subtype, and clinical stage. Eighty patients with NSCLC were included in this study. The analysis of DNA methylation was performed on formalin-fixed, paraffin-embedded lung cancer tissues. Following DNA isolation and bisulfite treatment, DNA methylation was analyzed by methylation-specific real-time polymerase chain reaction. MGMT promoter methylation was detected in 51 of 80 (64%) NSCLC patients. There was a significant correlation between MGMT methylation and tumor stage (p = 0.01). The frequencies of the promoter methylation of MGMT gene in smokers and older patients were higher than in their counterparts. In conclusion, the present study provides strong evidence for a higher frequency of promoter methylation of the MGMT gene in NSCLC, indicating that it is a common event during the carcinogenesis of NSCLC.

Extent and Patterns ofMGMTPromoter Methylation in Glioblastoma- and Respective Glioblastoma-Derived Spheres

Quantitative methylation-specific tests suggest that not all cells in a glioblastoma with detectable promoter methylation of the O6-methylguanine DNA methyltransferase (MGMT) gene carry a methylated MGMT allele. This observation may indicate cell subpopulations with distinct MGMT status, raising the question of the clinically relevant cutoff of MGMT methylation therapy. Epigenetic silencing of the MGMT gene by promoter methylation blunts repair of O6-methyl guanine and has been shown to be a predictive factor for benefit from alkylating agent therapy in glioblastoma. Ten paired samples of glioblastoma and respective glioblastoma-derived spheres (GS), cultured under stem cell conditions, were analyzed for the degree and pattern of MGMT promoter methylation by methylation-specific clone sequencing, MGMT gene dosage, chromatin status, and respective effects on MGMT expression and MGMT activity. In glioblastoma, MGMT-methylated alleles ranged from 10% to 90%. In contrast, methylated alleles were highly enriched (100% of clones) in respective GS, even when 2 MGMT alleles were present, with 1 exception (<50%). The CpG methylation patterns were characteristic for each glioblastoma exhibiting 25% to 90% methylated CpGs of 28 sites interrogated. Furthermore, MGMT promoter methylation was associated with a nonpermissive chromatin status in accordance with very low MGMT transcript levels and undetectable MGMT activity. In MGMT-methylated glioblastoma, MGMT promoter methylation is highly enriched in GS that supposedly comprise glioma-initiating cells. Thus, even a low percentage of MGMT methylation measured in a glioblastoma sample may be relevant and predict benefit from an alkylating agent therapy.

Should Biomarkers Be Used to Design Personalized Medicine for the Treatment of Glioblastoma?

Significant progress has been made in understanding the molecular pathogenesis of gliomas and in predicting general outcome depending on a limited set of clinical parameters and molecular markers. However, methylation of the O⁶-methylguanine DNA methyltransferase (MGMT) gene promoter is the only molecular marker linked to sensitivity of a specific treatment, that is, alkylating agent chemotherapy, and this predictive value may be limited to glioblastoma. Moreover, in the absence of potent alternative drugs, temozolomide chemotherapy should not be withheld from patients with newly diagnosed glioblastoma without MGMT promoter methylation in general practice. In the context of clinical trials, however, irrespective of whether classical cytotoxic drugs, tyrosine kinase inhibitors or antiangiogenic agents are used, tissue should be centrally collected. Appropriate research programs should seek to define enriched patient populations for future trials and ultimately facilitate individualized cancer treatments.

The temozolomide O6-methylguanine-DNA methyltransferase (MGMT) study: A phase II trial to evaluate the effect of low-dose preoperative neoadjuvant temozolomide on brain tumour MGMT activity in glioma patients

e13027 Background: Epigenetic methylation of the O6-methylguanine-DNA methyltransferase (MGMT) DNA repair gene promoter in tumor tissue from glioblastoma multiforme patients is associated with improved survival after treatment with radiotherapy plus concomitant and adjuvant temozolomide (TMZ). We hypothesized that MGMT promoter methylation mosaicism exists in glial tumors and would affect response to TMZ. Methods: This is a nonrandomized, prospective, open-label, two cohort, single-center phase II study. Twenty-three patients with brain tumors detected by MRI scan and suspected to be gliomas were evaluated. All eligible patients were treatment naive and were self-selected into a TMZ group or a control group. The primary goal of the study was to evaluate the effect of TMZ 75 mg/m2 daily prior to surgery on the brain tumor MGMT expression. Secondary endpoints included safety, tolerability, and MGMT promoter methylation mosaicism in glial tumors. Samples were obtained from multiple regions of each tumor intra-operatively and were analyzed by methylation specific PCR. Results: Our results on MGMT promoter methylation demonstrate that three groups of patients can be identified: Type I: all sites assessed in the tumor demonstrate no methylation of the MGMT promoter; Type II: all sites demonstrate high levels of MGMT promoter methylation; and Type III: a mixed promoter methylation pattern is observed. Conclusions: These results suggest that 1) preoperative neoadjuvant temozolomide is not associated with increased postoperative complications; 2) glial tumors can have very heterogeneous areas of MGMT promoter methylation; and 3) three patterns of MGMT promoter methylation can be discerned. This experimental paradigm may be a useful experimental platform for the assessment of the effect of new drugs at the tumor level. [Table: see text]

Promoter methylation of O6-methylguanine-DNA-methyltransferase in lung cancer is regulated by p53

Methylation of the O6-methylguanine-DNA-methyltransferase (MGMT) promoter is associated with G:C to A:T transitions in the p53 gene in various human cancers, including lung cancer. In tumors with p53 mutation, MGMT promoter methylation is more common in advanced tumors than in early tumors. However, in tumors with wild-type p53, MGMT promoter methylation is independent of tumor stage. To elucidate whether p53 participates in MGMT promoter methylation, we engineered three cell models: A549 cells with RNA interference (RNAi)-mediated knockdown of p53, and p53 null H1299 cells transfected with either wild-type p53 (WT-p53) or mutant-p53 (L194R, and R249S-p53). Knockdown of endogenous p53 increased MGMT promoter methylation in A549 cells, and transient expression of WT-p53 in p53 null H1299 cells diminished MGMT promoter methylation, whereas the MGMT promoter methylation status were unchanged by expression of mutant-p53. Previous work showed that p53 modulates DNA-methyltransferase 1 (DNMT1) expression; we additionally examined chromatin remodeling proteins expression levels of histone deacetylase 1 (HDAC1). We found that p53 knockdown elevated expression of both DNMT1 and HDAC1 in A549 cells. Conversely, expressing WT-p53 in p53 null H1299 cells reduced DNMT1 and HDAC1 expression, but the reduction of both proteins was not observed in expressing mutant-p53 H1299 cells. CHIP analysis further showed that DNMT1 and HDAC1 binding to the MGMT promoter was increased by MGMT promoter methylation and decreased by MGMT promoter demethylation. In conclusion, MGMT promoter methylation modulated by p53 status could partially promote p53 mutation occurrence in advanced lung tumors.