scholarly journals P14.02 Influence of individual CpG methylation status on outcome in adult patients with glioblastoma multiforme receiving alkylating agent treatment

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii66-iii66
Author(s):  
S Siller ◽  
M Lauseker ◽  
A Giese ◽  
J Tonn ◽  
K Niyazi ◽  
...  
Keyword(s):  
Glioblastoma Multiforme ◽  
Mrna Expression ◽  
Alkylating Agents ◽  
Methylation Status ◽  
Tumor Resection ◽  
Cpg Methylation ◽  
Karnofsky Performance Score ◽  
Cpg Sites ◽  
Promotor Region ◽  
The Individual

Abstract Background: Methylation of the O-6-methylguanine-DNA methyltransferase (MGMT) promotor causes gene silencing and has been associated with a favourable prognosis in patients with glioblastoma multiforme (GBM) receiving alkylating chemotherapy. However, analysis of MGMT promotor methylation is usually reported as a cut-off depending on the results of the correspondent CpG site testing. This approach disregards a possible heterogeneity concerning the methylation status within the individual CpG sites and its possible association with prognosis in GBM patients. The current study aimed at elucidating the association between methylation of CpG sites 74–98 within the MGMT promotor region and outcome in GBM patients receiving alkylating agents. Material and Methods: Individual methylation status of 230 patients with histologically proven GBM following concomitant radio-chemotherapy with TMZ after stereotactic biopsy or open tumor resection (OTR) was assessed by the Sanger sequencing (Sseq) approach. Methylation of CpG sites 74–98 within the MGMT promotor region was defined according to a ratio of cytosine /thymine peak >50%. The total number of methylated CpG sites as well as clinical factors such as age, Karnofsky Performance Score (KPS) and mode of surgical procedure were correlated with outcome using proportional hazards models. In a subset of 34 patients, a correlation between individual CpG methylation and MGMT mRNA expression was performed. Results: Median progression-free (PFS) and overall survival (OS) were 7.8 and 14.6 months, respectively. Alongside younger age, KPS> 80 and OTR, the cumulative total number of methylated loci within the CpG sites 74–98 was strongly associated with both PFS and OS and retained its prognostic influence on outcome in multivariate models (p <0.001). Furthermore, a linear coherence between the total number of methylated CpG sites 74–98 and survival parameters could be observed. Moreover, low number of methylated CpG sites was observed in tumor specimen with a high mRNA expression and vice versa (Spearman correlation coefficient: -0.62). Conclusion: In contrast to the concept of dichotomizing the MGMT promotor status into ‘methylated’ and ‘non-methylated’, our approach shows a clear heterogeneity within the methylation status of the CpG sites 74–98 within the GBM tumor specimens. Our data suggest a strong correlation between outcome and the total number of methylated CpG sites, thus an up-front analysis of the individual GpC site methylation status prior to initiation of alkylating chemotherapy might help to improve treatment response in GBM patients.

scholarly journals PATH-04. INFLUENCE OF INDIVIDUAL CpG METHYLATION STATUS OF THE MGMT PROMOTOR ON OUTCOME IN ADULT PATIENTS WITH GLIOBLASTOMA MULTIFORME RECEIVING ALKYLATING AGENT TREATMENT

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi143-vi143
Author(s):  
Sebastian Siller ◽  
Michael Lauseker ◽  
Armin Giese ◽  
Joerg-Christian Tonn ◽  
Karim-Maximilian Niyazi ◽  
...  
Keyword(s):  
Glioblastoma Multiforme ◽  
Mrna Expression ◽  
Dna Methyltransferase ◽  
Alkylating Agents ◽  
Methylation Status ◽  
Tumor Resection ◽  
Cpg Sites ◽  
Cpg Site ◽  
Promotor Region ◽  
The Individual

Abstract BACKGROUND Methylation of O-6-methylguanine-DNA-methyltransferase (MGMT) promotor causes gene silencing and has been associated with a favourable prognosis in patients with glioblastoma multiforme (GBM) receiving alkylating chemotherapy. However, analysis of MGMT promotor methylation is usually reported as a cut-off depending on the results of the correspondent CpG-site testing. This approach disregards a possible heterogeneity concerning the methylation status within the individual CpG-sites and its possible association with prognosis in GBM patients. The current study aimed at elucidating the association between methylation of CpG-sites 74–98 within the MGMT promotor region and outcome in GBM patients receiving alkylating agents. METHODS Individual methylation status of 230 patients with histologically proven GBM following concomitant radio-chemotherapy with TMZ after stereotactic biopsy or open tumor resection was assessed by the Sanger-sequencing approach. Methylation of CpG-sites 74–98 within the MGMT promotor region was defined according to a ratio of cytosine/thymine peak > 50%. The total number of methylated CpG-sites was correlated with outcome using proportional hazards models. In a subset of 34 patients, a correlation between individual CpG-site methylation and MGMT mRNA-expression was performed. RESULTS Median progression-free (PFS) and overall survival (OS) were 7.8 and 14.6months, respectively. The cumulative total number of methylated loci within the CpG-sites 74–98 was strongly associated with both PFS and OS and retained its prognostic influence on outcome in multivariate models (p< 0.001). Furthermore, a linear coherence between the total number of methylated CpG-sites 74–98 and survival parameters could be observed. Moreover, low number of methylated CpG-sites was observed in tumor specimen with a high mRNA-expression and vice versa (Spearman-correlation-coefficient: -0.62). CONCLUSION Our data suggest a strong linear coherence between outcome and the total number of methylated CpG-sites 74–98, thus an up-front analysis of the individual GpC-site methylation status prior to initiation of alkylating chemotherapy might help improving treatment response in GBM patients.

scholarly journals The number of methylated CpG sites within the MGMT promoter region linearly correlates with outcome in glioblastoma receiving alkylating agents

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sebastian Siller ◽  
Michael Lauseker ◽  
Philipp Karschnia ◽  
Maximilian Niyazi ◽  
Sabina Eigenbrod ◽  
...  
Keyword(s):  
Promoter Methylation ◽  
Promoter Region ◽  
Proportional Hazards ◽  
Alkylating Agents ◽  
Methylation Status ◽  
Tumor Resection ◽  
Absolute Number ◽  
Cumulative Number ◽  
Cpg Sites ◽  
A Site

AbstractMGMT-promoter methylation is associated with favorable outcome in glioblastoma. The aim of this study was to determine whether the absolute number of methylated Cytosine-Guanine-dinucleotide-(CpG-)sites within the DMR-2 island of the MGMT-promoter may correlate with outcome in a qualitative or quantitative fashion. In a cohort of newly diagnosed glioblastoma patients treated with stereotactic biopsy or open tumor resection plus concomitant chemoradiotherapy, we assessed MGMT-promoter methylation by methylation-specific polymerase-chain-reaction (MSP). Methylation of the CpG-sites 74–98 within the MGMT-promoter region was additionally analysed by Sanger sequencing, and the total number of methylated CpG-sites was correlated with outcome using proportional hazards models. 215 patients with glioblastoma were identified and stratified per MSP (positive: 53%, negative: 47%). Among MSP-positive tumors, hierarchical clustering identified three subgroups with different methylation rates (median: 80% vs. 52% vs. 47%), indicating a site-dependent methylation propagation. The methylation status of a given CpG-site indicated a neighborhood-dependent methylation propagation. Survival was linearly associated with the cumulative number of methylated CpG-sites. This was particularly true in patients who received at least one adjuvant cycle of temozolomide. Notably, all CpG-sites analyzed contributed similarly to effect size; this enabled a further predictive substratification of MSP-positive tumors with median OS ranging from as low as 17.1 months (< 18 methylated CpG-sites) to as high as 26.2 months (≥ 18 methylated CpG-sites) in the overall cohort. All in all, total number of methylated CpG-sites may correlate with outcome in a linear fashion. Such analysis may therefore add further predictive value to conventional methods of determining the MGMT-promoter status.

MGMT methylation in newly-diagnosed glioblastoma multiforme (GBM): From the S0001 phase III study of radiation therapy (RT) and O6-benzylguanine, (O6BG) plus BCNU versus RT and BCNU alone for newly diagnosed GBM

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 1512-1512 ◽  
Author(s):  
D. T. Blumenthal ◽  
M. Wade ◽  
C. J. Rankin ◽  
F. Fitzpatrick ◽  
K. Stelzer ◽  
...  
Keyword(s):  
Glioblastoma Multiforme ◽  
Median Survival ◽  
Promoter Methylation ◽  
Promoter Region ◽  
Alkylating Agents ◽  
Methylation Status ◽  
Phase Iii ◽  
Newly Diagnosed ◽  
Tissue Samples ◽  
Mgmt Promoter

1512 Background: Glioblastoma multiforme (GBM) is a high grade primary brain neoplasm associated with a median survival of less than a year. Historically, one-third of patients seem to benefit from treatment with alkylating chemotherapy. This minority may correspond to a population with decreased levels of active O6-methylguanine- methyltransferase enzyme (MGMT). MGMT repairs tumor DNA damaged by chemotherapy, allowing continued replication after exposure to treatment. Patients with low tumor MGMT activity may be more likely to respond to alkylating treatment. Hypermethylation of the MGMT promoter region leads to decreased transcription of the enzyme and is associated with improved outcome in GBM patients treated with radiation and alkylating chemotherapy. Methods: We studied a patient cohort with newly diagnosed GBM registered on Southwest Oncology Group protocol S0001, a phase III randomized, two arm clinical trial investigating an inhibitor of MGMT (O6-benzylguanine, O6BG). Both groups received standard radiation and BCNU (carmustine). The experimental group additionally received O6BG. We determined polymerase chain reaction (PCR) methylation status of the promoter region of MGMT in 88 patients with adequate tissue samples. In 41 cases, we were able to obtain successful PCR results. Results: 28 of 41 samples (68%) were found to be unmethylated and 13 of 41 (32%, 95% c. i. 18% to 50%) were methylated. Patients with methylated MGMT had a median survival of 12.6 months (95% c.i. of 7.8–15.8 months). Patients with unmethylated MGMT had a median survival of 10.6 months (95% c.i. of 8.7–12.0 months). Median progression-free survivals were 4.5 and 3.1 months respectively, for the methylated and unmethylated groups. Conclusions: This result is consistent with prior studies which showed that approximately two-thirds of patients express MGMT, and accordingly, are resistant to alkylating agents. The subgroup of patients without promoter methylation may be more likely to benefit from treatment with O6BG. Analysis of MGMT promoter methylation status per study treatment group, and correlation with median survival and progression-free survival will be presented. No significant financial relationships to disclose.

scholarly journals Ethnic Differences in MicroRNA-375 Expression Level and DNA Methylation Status in Type 2 Diabetes of Han and Kazak Populations

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Xiangyun Chang ◽  
Siyuan Li ◽  
Jun Li ◽  
Liang Yin ◽  
Ting Zhou ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Methylation Status ◽  
Cpg Methylation ◽  
Expression Level ◽  
Related Factor ◽  
Expression Levels ◽  
Relative Expression ◽  
Cpg Sites ◽  
Significant Difference

Han population is six times as likely as Kazak population to present with type 2 diabetes mellitus (T2DM) in China. We hypothesize that differential expression and CpG methylation of miR-375 may be an ethnic-related factor that influences the incidence of T2DM. The expression level of miR-375 was examined using real-time PCR on Kazak and Han T2DM plasma samples. Furthermore, the methylation levels of CpG sites of miR-375 promoter were determined by MassARRAY Spectrometry in these samples. The relative expression levels of plasma miR-375 in Kazak T2DM samples are 1, and the relative expression levels of plasma miR-375 in Han T2DM samples are 3. The mean level of miR-375 methylation, calculated from the methylation levels of the CpG sites, was 8.47% for the Kazak T2DM group and 10.38% for the Han T2DM group. Further, five CpG units showed a statistically significant difference between Kazak and Han T2DM samples, and, among them, four were hypomethylated and only one CpG unit showed hypermethylation in Kazak T2DM samples. These findings indicate that the expression levels of plasma miR-375 and its CpG methylation in the promoter region are ethnically different, which may contribute to the different incidence of diabetes observed in Kazak and Han populations.

scholarly journals PATH-28. EXTENT AND PROGNOSTIC VALUE OF MGMT PROMOTOR METHYLATION DEPEND ON IDH MUTATION AND 1p19q CO-DELETION IN GLIOMA WHO GRADE II

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii170-ii170
Author(s):  
Philipp Karschnia ◽  
Nico Teske ◽  
Sebastian Siller ◽  
Mario M Dorostkar ◽  
Jonathan Weller ◽  
...  
Keyword(s):  
Overall Survival ◽  
Dna Methyltransferase ◽  
Methylation Status ◽  
Malignant Progression ◽  
Wild Type ◽  
Who Grade ◽  
Cpg Sites ◽  
Idh Mutations ◽  
Promotor Region ◽  
Grade Ii

Abstract INTRODUCTION Methylation of the promotor region of the O6-methylguanin-DNA-methyltransferase (MGMT) gene is associated with increased survival in low- and high-grade glioma. It is unknown whether this association also applies to the 2016 WHO categories of glioma WHO grade II. MATERIAL AND METHODS We retrospectively searched the institutional database of the Center for Neuro-Oncology for patients with glioma WHO grade II. Patients were assigned to one of three groups according to the 2016 WHO classification system: 1. 1p19q co-deleted oligodendroglioma, IDH mutant; 2. 1p19q non-codeleted astrocytoma, IDH mutant; 3. 1p19q non-codeleted astrocytoma, IDH wild-type. MGMT methylation status was analysed using Sanger sequencing of the CpG sites 74-98 within the MGMT promotor region. The total number of methylated CpG sites was calculated for each patient. RESULTS 155 patients with glioma WHO grade II were encountered, including 81 1p19q co-deleted, IDH mutant oligodendrogliomas; 54 IDH mutant astrocytomas; and 20 IDH wild-type astrocytomas. The mean number of methylated CpG sites among oligodendrogliomas was significantly higher when compared to IDH mutant astrocytomas (18.9 ± 0.4 vs. 16.3 ± 0.6; p = 0.001). In turn, the number of methylated CpG sites among IDH mutant astrocytomas was higher when compared to IDH wild-type astrocytomas (16.3 ± 0.6 vs. 12.3 ± 1.9; p = 0.007). Median follow-up was estimated at 35 months. Median time to malignant progression was 87 months for all patients, and median overall survival was not reached. In the entire cohort, a larger number of methylated CpG sites was prognostic of overall survival and time to malignant progression. When analysed separately for the three WHO subgroups, a similar association was only retained in IDH wild-type astrocytoma. CONCLUSION In our series of WHO II gliomas, MGMT promotor methylation appeared strongly associated with 1p19q codeletion and IDH mutations. MGMT promotor methylation was only prognostic in IDH wild-type astrocytoma.

scholarly journals Interleukin-4 Induces CpG Site-Specific Demethylation of the Pendrin Promoter in Primary Human Bronchial Epithelial Cells

2017 ◽  
Vol 41 (4) ◽  
pp. 1491-1502 ◽  
Author(s):  
Giada Scantamburlo ◽  
Simone Vanoni ◽  
Silvia Dossena ◽  
Selma M. Soyal ◽  
Emanuele Bernardinelli ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Methylation Status ◽  
Bronchial Epithelial Cells ◽  
Cpg Methylation ◽  
Interleukin 4 ◽  
Mrna Levels ◽  
Primary Cells ◽  
Bronchial Epithelial ◽  
Cpg Sites ◽  
Cpg Site

Pendrin is upregulated in bronchial epithelial cells following IL-4 stimulation via binding of STAT6 to an N4 GAS motif. Basal CpG methylation of the pendrin promoter is cell-specific. We studied if a correlation exists between IL-4 sensitivity and the CpG methylation status of the pendrin promoter in human bronchial epithelial cell models. Methods: Real-time PCR and pyrosequencing were used to respectively quantify pendrin mRNA levels and methylation of pendrin promoter, with and without IL-4 stimulation, in healthy and diseased primary HBE cells, as well as NCI-H292 cells. Results: Increases in pendrin mRNA after IL-4 stimulation was more robust in NCI-H292 cells than in primary cells. The amount of gDNA methylated varied greatly between the cell types. In particular, CpG site 90 located near the N4 GAS motif was highly methylated in the primary cells. An additional CpG site (90bis), created by a SNP, was found only in the primary cells. IL-4 stimulation resulted in dramatic demethylation of CpG sites 90 and 90bis in the primary cells. Conclusions: IL-4 induces demethylation of specific CpG sites within the pendrin promoter. These epigenetic alterations are cell type specific, and may in part dictate pendrin mRNA transcription.

Prognostic value of AKAP13 methylation and expression in lung squamous cell carcinoma

2020 ◽  
Vol 14 (7) ◽  
pp. 503-512
Author(s):  
Hui-lin Wang ◽  
Ke-zhi Li ◽  
Ji-lin Li ◽  
Bang-li Hu
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Mrna Expression ◽  
Squamous Cell ◽  
Prognostic Value ◽  
Methylation Status ◽  
Lung Squamous Cell Carcinoma ◽  
Prognostic Indicators ◽  
Cpg Sites

Aim: This study aimed to analyze the prognostic value and clinical significance of AKAP13 mRNA expression and AKAP13 methylation in lung squamous cell carcinoma (LUSC). Materials & methods: The mRNA expression and methylation of AKAP13 data of LUSC patients were downloaded from the Broad GDAC Firehose database and analyzed. Results: AKAP13 mRNA expression was downregulated and methylation was upregulated in LUSC tissue. Three CpG sites of AKAP13 were associated with overall survival. Combination of AKAP13 mRNA and methylation revealed 11 CpG sites associated with overall survival of LUSC patients. AKAP13 mRNA expression was associated with distant metastasis of LUSC, no associations were found between methylation status of CpG sites and clinical features. Conclusion: AKAP13 mRNA and its methylated CpG sites are potential prognostic indicators in LUSC patients.

scholarly journals MGMT promoter methylation testing to predict overall survival in people with glioblastoma treated with temozolomide: a comprehensive meta-analysis based on a Cochrane Review

2021 ◽  
Author(s):  
Sebastian Brandner ◽  
Alexandra McAleenan ◽  
Claire Kelly ◽  
Francesca Spiga ◽  
Hung-Yuan Cheng ◽  
...  
Keyword(s):  
Overall Survival ◽  
Dna Methyltransferase ◽  
Meta Analysis ◽  
Alkylating Agents ◽  
Cochrane Review ◽  
Predictive Biomarker ◽  
Test Method ◽  
Sufficient Information ◽  
Cpg Sites ◽  
Hazard Ratios

Abstract BACKGROUND The DNA repair protein O6 methylguanine-DNA methyltransferase (MGMT) causes resistance of tumour cells to alkylating agents. It is a predictive biomarker in high grade gliomas treated with temozolomide, however there is no consensus on which test method, methylation sites, and cut-off values to use. METHODS We performed a Cochrane Review to examine studies using different techniques to measure MGMT and predict survival in glioblastoma patients treated with temozolomide. Eligible longitudinal studies included adults with glioblastoma treated with temozolomide with or without radiotherapy, or surgery; where MGMT status was determined in tumour tissue, and assessed by one or more technique; and where overall survival was an outcome parameter, with sufficient information to estimate hazard ratios. Two or more methods were compared in 32 independent cohorts with 3474 patients. RESULTS Methylation-specific PCR (MSP) and pyrosequencing (PSQ) techniques were more prognostic than immunohistochemistry for MGMT protein, and PSQ is a slightly better predictor than MSP. CONCLUSIONS We cannot draw strong conclusions about use of frozen tissue versus formalin-fixed paraffin embedded in MSP and PSQ. Also, our meta-analysis does not provide strong evidence about the best CpG sites or threshold. MSP has been studied mainly for CpG sites 76-80 and 84-87 and Pyrosequencing at CpG sites ranging from 72 to 95. A cut-off threshold of 9% for CpG sites 74-78 performed better than higher thresholds of 28% or 29% in two of three good-quality studies. 190 studies were identified presenting hazard ratios from survival analysis in patients in which MGMT methylation was measured by one technique only.

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