PATH-27. MGMT PROMOTER STATUS IN IDH1/2 MUTANT ANAPLASTIC ASTROCYTOMA PATIENTS ASSESSED BY DNA METHYLATION PROFILING AND QMS-PCR: A REPORT FROM THE EORTC BRAIN TUMOR GROUP

Abstract BACKGROUND Temozolomide efficacy in high-grade glioma is related to MGMTp methylation. We compared the prognostic and predictive effect of MGMTp between DNA methylation profiling (MGMT-STP27 model) and qMS-PCR in IDH1/2mt anaplastic astrocytoma patients. METHODS The 2x2 factorial design phase III CATNON trial randomized 751 adult patients with newly diagnosed 1p/19q non-codeleted anaplastic glioma to 59.4Gy radiotherapy, radiotherapy with concurrent temozolomide, radiotherapy with 12 cycles of adjuvant temozolomide, or radiotherapy with concurrent and adjuvant temozolomide. MGMTp methylation status was assessed with the MGMT-STP27 model using 850k EPIC data, and qMS-PCR. IDH1/2 mutation status was determined with next-generation sequencing. OS was measured from randomization date. RESULTS We identified 444 IDH1/2mt anaplastic astrocytoma patients. MGMTp was methylated in 365/440 patients (83.0%) with MGMT-STP27 data, and 168/361 patients (46.5%) with qMS-PCR data. The agreement between both modalities is 59.9% (Cohen’s Kappa score 0.229). At database lock, 289 patients with MGMT-STP27 data were alive and 236 patients with qMS-PCR data. The median OS of MGMTp methylated glioma patients was 9.1 yrs [95%CI 7.5-not reached] for the MGMT-STP27 model, and not reached [95%CI 9.1-not reached] for qMS-PCR. For MGMTp unmethylated glioma patients, the median OS was 6.9 yrs [95%CI 6.2-not reached] for the MGMT-STP27 model, and 6.8 yrs [95%CI 6.2-9.7] for qMS-PCR. The HR for OS based on MGMTp methylation was 0.88 [95%CI 0.58-1.31] for the MGMT-STP27 model, and 0.72 [95%CI 0.50-1.03]) for qMS-PCR. The HR for OS after radiotherapy with any temozolomide vs radiotherapy alone for the MGMT-STP27 model was 0.53 [95%CI 0.37-0.78] for MGMTp methylated, and 0.54 [95%CI 0.25-1.18] for MGMTp unmethylated glioma patients; and for MS-PCR was 0.34 [95%CI 0.19-0.61] for MGMTp methylated, and 0.53 [95%CI 0.33-0.85] for MGMTp unmethylated glioma patients. CONCLUSION MGMTp methylation, regardless of assay, was neither prognostic nor predictive for outcome to temozolomide in IDH1/2mt anaplastic astrocytoma patients.

Download Full-text

OS05.2.A MGMT promoter status in IDH1/2 mutant anaplastic astrocytoma patients assessed by DNA methylation profiling and qMS-PCR: a report from the EORTC Brain Tumor Group

Neuro-Oncology ◽

10.1093/neuonc/noab180.019 ◽

2021 ◽

Vol 23 (Supplement_2) ◽

pp. ii6-ii7

Author(s):

C M S Tesileanu ◽

P J French ◽

M Sanson ◽

A A Brandes ◽

W Wick ◽

...

Keyword(s):

Dna Methylation ◽

Anaplastic Astrocytoma ◽

Dna Methyltransferase ◽

Methylation Status ◽

High Grade Glioma ◽

Phase Iii ◽

Isocitrate Dehydrogenase 1 ◽

Kappa Score ◽

Dna Methylation Profiling ◽

Methylation Profiling

Abstract BACKGROUND Temozolomide (TMZ) efficacy in high-grade glioma is related to O 6-methylguanine DNA methyltransferase promoter (MGMTp) methylation. We compared the prognostic and predictive effect of MGMTp between DNA methylation profiling (the MGMT-STP27 model) and quantitative methylation specific polymerase chain reaction (qMS-PCR) in isocitrate dehydrogenase 1 and 2 (IDH1/2) mutant (mt) anaplastic astrocytoma patients. MATERIAL AND METHODS The 2x2 factorial design phase III CATNON trial randomized 751 adult patients with newly diagnosed 1p/19q non-codeleted anaplastic glioma to 59.4 Gy radiotherapy (RT), RT with concurrent TMZ, RT with 12 cycles of adjuvant TMZ, or RT with concurrent and adjuvant TMZ. MGMTp methylation status was assessed with the MGMT-STP27 model using 850k EPIC data, and qMS-PCR. IDH1/2 mutation status was determined with a next-generation sequencing panel. Overall survival (OS) was measured from date of randomization. RESULTS We identified 444 IDH1/2mt anaplastic astrocytoma patients of which MGMT-STP27 data was available for 440 patients (99.1%), qMS-PCR data for 361 patients (81.3%), and both for 357 patients (80.4%). MGMTp was methylated in 365 patients (83.0%) for the MGMT-STP27 model, and 168 patients (46.5%) for qMS-PCR. The agreement between the MGMT-STP27 model and qMS-PCR is 59.9% with a Cohen’s Kappa score of 0.229. At database lock, 289 patients with MGMT-STP27 data were still alive and 236 patients with qMS-PCR data. The median OS of MGMTp methylated glioma patients was 9.1 yrs [95 % confidence interval (CI) 7.5-not reached] for the MGMT-STP27 model, and not reached [95 % CI 9.1-not reached] for the qMS-PCR data. For MGMTp unmethylated glioma patients, the median OS was 6.9 yrs [95% CI 6.2-not reached] for the MGMT-STP27 model, and 6.8 yrs [95% CI 6.2–9.7] for the qMS-PCR data. The hazard ratio (HR) for OS based on MGMTp methylation was 0.88 [95% CI 0.58–1.31] for the MGMT-STP27 data, and 0.72 [95% CI 0.50–1.03]) for the qMS-PCR data. The HR for OS after RT with any TMZ vs RT alone for the MGMT-STP27 model was 0.53 [95% CI 0.37–0.78] for MGMTp methylated, and 0.54 [95% CI 0.25–1.18] for MGMTp unmethylated glioma patients; and for the MS-PCR data was 0.34 [95% CI 0.19–0.61] for MGMTp methylated, and 0.53 [95% CI 0.33–0.85] for MGMTp unmethylated glioma patients. CONCLUSION MGMTp methylation, regardless of assay, was neither prognostic nor predictive for outcome to temozolomide in IDH1/2mt anaplastic astrocytoma patients.

Download Full-text

Implication of DNA Methylation Profiling in Oral Epithelium for Lung Cancer Screening

ISRN Pulmonology ◽

10.5402/2012/973203 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6

Author(s):

Hiroaki Harada ◽

Kazuaki Miyamoto ◽

Yoshinori Yamashita ◽

Kikuo Nakano ◽

Kiyomi Taniyama ◽

...

Keyword(s):

Lung Cancer ◽

Dna Methylation ◽

Cancer Patients ◽

Methylation Status ◽

Lung Cancer Screening ◽

High Specificity ◽

Oral Epithelium ◽

Molecular Alterations ◽

Dna Methylation Profiling ◽

Methylation Profiling

In lung cancer, the roles of molecular alterations in blood, sputum, bronchial brushing, and exhaled gas samples, which are relatively easy to obtain, have been evaluated for clinical availability. This study was based on the hypothesis that similar molecular alterations occur in the lung and oral cavity because both are exposed to the same environmental or tobacco-derived carcinogens. Because epigenetic alterations due to exposure to carcinogens are thought to play a major role in the development of lung cancer, the DNA methylation status of 11 genes in the oral epithelium was analyzed in lung cancer patients (n=16) and control individuals without lung cancer (n=32). DNA methylation profiling revealed that GDNF, RARB, and HS3ST2 were methylated more frequently in cancer patients than in the control participants (P=0.0017, 0.0062, and 0.0193, resp.). Combined analysesindicatedthat 6 of 16 cancer patients (37.5%), but only 1 of 32 control individuals (3.1%) showed DNA methylation in 2-3 of these 3 genes (P=0.0015). These combined analyses showed the high specificity and positive predictive value in total and subgroup analyses. Our data suggest that DNA methylation profiling using oral epithelium may help in the identification of individuals with a high risk of lung cancer.

Download Full-text

Discovery and Validation of Hypermethylated Markers for Colorectal Cancer

Disease Markers ◽

10.1155/2016/2192853 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 11

Author(s):

Jiufeng Wei ◽

Guodong Li ◽

Shuwei Dang ◽

Yuhui Zhou ◽

Kai Zeng ◽

...

Keyword(s):

Dna Methylation ◽

Operating Characteristic ◽

Malignant Tumors ◽

Methylation Status ◽

Roc Curves ◽

Gene Expression Omnibus ◽

Data Sets ◽

Dna Methylation Profiling ◽

Aberrant Dna Methylation ◽

Methylation Profiling

Colorectal carcinoma (CRC) is one of the most prevalent malignant tumors worldwide. Screening and early diagnosis are critical for the clinical management of this disease. DNA methylation changes have been regarded as promising biomarkers for CRC diagnosis. Here, we map DNA methylation profiling on CRC in six CRCs and paired normal samples using a 450 K bead array. Further analysis confirms the methylation status of candidates in two data sets from the Gene Expression Omnibus. Receiver operating characteristic (ROC) curves are calculated to determine the diagnostic performances. We identify 1549 differentially methylated regions (DMRs) showing differences in methylation between CRC and normal tissue. Two genes (ADD2andAKR1B1), related to the DMRs, are selected for further validation. ROC curves show that the areas under the curves ofADD2andAKR1B1are higher than that ofSEPT9, which has been clinically used as a screening biomarker of CRC. Our data suggests that aberrant DNA methylation ofADD2andAKR1B1could be potential screening markers of CRC.

Download Full-text

Genetic Alterations Precede DNA Methylation Changes in Juvenile Myelomonocytic Leukemia

Blood ◽

10.1182/blood-2020-143443 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 19-20

Author(s):

Astrid Behnert ◽

Julia Meyer ◽

Jahan-Yar Parsa ◽

Aaron Hechmer ◽

Mignon L. Loh ◽

...

Keyword(s):

Dna Methylation ◽

Somatic Mutation ◽

Methylation Status ◽

Juvenile Myelomonocytic Leukemia ◽

Genetic Mutations ◽

P Value ◽

International Consensus ◽

Consensus Definition ◽

Dna Methylation Profiling ◽

Methylation Profiling

Introduction Juvenile myelomonocytic leukemia (JMML) is a rare and highly aggressive myeloid malignancy of early childhood. Approximately 95% of patients have at least one mutation that leads to hyperactive RAS signaling. Both the presence of multiple mutations at diagnosis as well as altered DNA methylation are associated with a poor prognosis. Whether altered DNA methylation leads to the acquisition of additional genetic mutations or is a secondary event to genetic mutations is unknown. In this study, we analyzed a total of 33 newborn blood screening (NBS) cards from children who went on to develop JMML later in childhood. Using next generation sequencing to detect both genetic mutations and DNA methylation status we sought to determine the sequence of events that lead to the development of JMML. Patients and Methods We identified 33 patients that were born in the state of California from 1990 to 2017 who were confirmed to have JMML and were previously consented to participate in a JMML tissue bank study. Guthrie cards from these 33 patients as well as 12 healthy controls were obtained from the California Biobank Program. DNA samples (20 ng) were sequenced for mutations using a custom amplicon-based sequencing approach (Paragon Genomics, Hayward, CA) targeting 26 genes that are recurrently mutated in JMML. For DNA methylation profiling, 300ng of genomic DNA was processed for bisulfite conversion using the TrueMethyl oxBS Module (Tecan Genomics Inc., Redwood City, CA.) according to manufacturer's guidelines and next generetation sequencing (NGS) libraries were prepared by targeting 3000 CpG loci using custom probes for Targeted Methyl-Seq assay (Tecan Genomics Inc., Redwood City, CA). Sequence reads were trimmed using Cutadapt to remove adapters and methylation status called using Bismark. Samples were classified into one of three methylation subgroups: Low, Intermediate, or High using 1386 probes according to an international consensus definition. Results At diagnosis of JMML, somatic mutations were identified in 32 of 33 patients. Of the 32 patients with a somatic mutation present upon diagnosis, the same mutations were found in NBS cards in 13 (41%) patients using a mutant allele fraction (MAF) cut-off of 1%. Clonal mutations (MAF >15%) were found in 9 of 32 (28%) patients. Patients who had a somatic mutation detected at birth were significantly younger at diagnosis with a median age of 7.1 months (range 2.5-91.6 months) compared to patients who had none (19.8 months; p-value = 0.042). However, no difference was observed in overall or event-free survival for patients with or without somatic mutations at birth. Methylation profiling classified all NBS cards as having "low" DNA methylation using an international, consensus definition (Figure 1A). Of the 33 patients, ten also had DNA methylation profiling performed on their diagnostic JMML sample which were classified as low (LM), intermediate (IM) or high methylation (HM) (Figure 1B). Amongst patients with both NBS and JMML methylation data available, 5 had mutations present in the NBS card and all 5 had lower methylation (β values) in their NBS card compared to their JMML sample (mean 0.38 vs 0.29, p-value = 0.002). Discussion We identified somatic Ras pathway mutations at birth in 13/32 (41%) of newborns that developed JMML later in their childhood. We found that patients with a somatic mutation detected at birth were significantly younger at diagnosis compared to patients who had no mutations at birth. DNA methylation profiling of NBS cards from children who went on to develop JMML revealed methylation signatures that were similar to normal age-matched controls. All newborn cards were classified as low methylation at birth. Specifically, amongst patients who had genetic mutations present at birth, methylation changes that were eventually detected in JMML samples were not present in the NBS cards. Therefore, we conclude that aberrant DNA methylation is a secondary event to genetic changes in JMML. Figure 1: Panel A: Methylation profiling of JMML NBS and control NBS samples, classified according to the international JMML methylation consensus signature. Panel B: Methylation profiling of paired NBS and diagnosis samples from JMML patients. The star indicates the NBS methylation profile. Heatmaps (A and B) show the beta values of 1386 CpG loci used for methylation classification. Figure 1 Disclosures Loh: Pfizer: Other: Institutional Research Funding; Medisix Therapeutics: Membership on an entity's Board of Directors or advisory committees.

Download Full-text

Diagnosis and Prognostication of Ductal Adenocarcinomas of the Pancreas Based on Genome-Wide DNA Methylation Profiling by Bacterial Artificial Chromosome Array-Based Methylated CpG Island Amplification

Journal of Biomedicine and Biotechnology ◽

10.1155/2011/780836 ◽

2011 ◽

Vol 2011 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Masahiro Gotoh ◽

Eri Arai ◽

Saori Wakai-Ushijima ◽

Nobuyoshi Hiraoka ◽

Tomoo Kosuge ◽

...

Keyword(s):

Dna Methylation ◽

Bacterial Artificial Chromosome ◽

Cpg Island ◽

Methylation Status ◽

Artificial Chromosome ◽

Prognostic Indicators ◽

Bac Clones ◽

Genome Wide ◽

Dna Methylation Profiling ◽

Methylation Profiling

To establish diagnostic criteria for ductal adenocarcinomas of the pancreas (PCs), bacterial artificial chromosome (BAC) array-based methylated CpG island amplification was performed using 139 tissue samples. Twelve BAC clones, for which DNA methylation status was able to discriminate cancerous tissue (T) from noncancerous pancreatic tissue in the learning cohort with a specificity of 100%, were identified. Using criteria that combined the 12 BAC clones, T-samples were diagnosed as cancers with 100% sensitivity and specificity in both the learning and validation cohorts. DNA methylation status on 11 of the BAC clones, which was able to discriminate patients showing early relapse from those with no relapse in the learning cohort with 100% specificity, was correlated with the recurrence-free and overall survival rates in the validation cohort and was an independent prognostic factor by multivariate analysis. Genome-wide DNA methylation profiling may provide optimal diagnostic markers and prognostic indicators for patients with PCs.

Download Full-text