scholarly journals MPC-1 DNA methylome analysis suggested the presence of “true” IDH-wildtype lower-grade gliomas

2021 ◽  
Vol 3 (Supplement_6) ◽  
pp. vi15-vi16
Author(s):  
Kaishi Satomi ◽  
Kenji Fujimoto ◽  
Hideyuki Arita ◽  
Kai Yamasaki ◽  
Yuko Matsushita ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heterogeneous Group ◽  
Lower Grade ◽  
Diffuse Glioma ◽  
Tumor Type ◽  
Adult Type ◽  
Molecular Features ◽  
Tert Promoter ◽  
Methylome Analysis ◽  
Data Files

Abstract Background: There will be significant changes in the diagnosis of IDH-wildtype adult-type gliomas in the upcoming 5th edition of the WHO Classification of Central Nervous System Tumours. IDH-wildtype lower grade gliomas (IDHwt LGGs) that harbor molecular features of glioblastoma (EGFR amplification, the combination of whole chromosome 7 gain and whole chromosome 10 loss (7+/10-), or TERT promoter mutations) will be diagnosed as glioblastomas (GBMs), while IDH-wildtype astrocytomas will not be included as a separate tumor type. However, IDHwt LGGs are a very heterogeneous group of tumors, and further investigation is warranted particularly in those without molecular features of glioblastoma. To elucidate the biology of IDHwt LGGs, we analyzed DNA methylation profile and survival time. Materials and Methods: Of the 724 adult-type diffuse glioma samples from a multi-institutional study, 64 IDHwt LGG, including 54 without any of molecular features of GBM and 10 with PDGFRA amplification or TERT promoter mutation, were examined using Infinium MethylationEPIC BeadChip. The raw data files (IDAT files) were analyzed by the web-based DNA methylation classifier provided by DKFZ (MolecularNeuropathology.org) or by R (Version 4.0.4) using the minfi (1.34.0) and Rtsne (0.15) packages. [Result] Twenty-three out of 54 IDHwt LGGs matched known methylation classes using the DKFZ methylation classifier. In t-Distributed Stochastic Neighbor Embedding clustering analysis, 20 cases formed a cluster within the methylation class family glioblastoma, IDH-wildtype, mainly subclass RTK I (“GBM” cluster). Another 29 IDHwt LGGs formed an independent cluster (“LGG” cluster) separate from any of the existing reference groups near but not overlapping with several subtypes of pediatric-type lower grade gliomas. The “LGG” cluster cases had significantly longer overall survival than the “GBM” cluster cases. Discussion: Methylation profiling showed that IDHwt LGGs without molecular features of GBM were heterogeneous group of tumors. Our data suggested the presence of “true” IDHwt LGGs with intermediate prognosis.

EPID-17. COMPARATIVE EPIDEMIOLOGY OF PRIMARY BRAIN TUMORS AMONG ADOLESCENTS AND YOUNG ADULTS (AYA)

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi89-vi89
Author(s):  
Nayan Lamba ◽  
Bryan Iorgulescu
Keyword(s):  
Brain Tumor ◽  
Brain Tumors ◽  
Cox Regression ◽  
Adolescent And Young Adult ◽  
Lower Grade ◽  
Diffuse Glioma ◽  
Tumor Type ◽  
Primary Brain Tumors ◽  
Diffuse Gliomas ◽  
Hiv Aids

Abstract INTRODUCTION We utilized national registry data to evaluate the unique epidemiology of primary adolescent and young adult (AYA) brain tumors according to the WHO2016 classification. METHODS AYA patients (15≤age≤39) presenting between 2004-2017 with a brain tumor were identified by ICD-O-3 coding from the National Cancer Database (comprising >70% of newly-diagnosed cancers in the U.S.), and compared to pediatric and adult populations. Epidemiology and overall survival (estimated by Kaplan-Meier techniques and multivariable Cox regression) were assessed by WHO2016 tumor type. RESULTS 108,705 AYA brain tumor patients were identified (56.9% female), compared to 23,928 pediatric (46.8% female) and 748,272 adult (55.6% female) patients. Among the 69.4% of AYA brain tumors with pathological diagnosis, diffuse gliomas (31.4%), sellar tumors (19.2%), and meningiomas (15.3%) predominated in both sexes. Diffuse glioma (31.4%), sellar (19.2%), cranial nerve (7.3%), and mesenchymal non-meningothelial (4.1%) tumors represented a greater proportion of AYA brain tumors than in either pediatric or adult populations. A majority of all intracranial GCTs (59.2%) and neuronal & mixed neuronal-glial tumors (51.6%) presented during AYA. Although the prevalence of diffuse gliomas was similar between AYAs and adults, AYA gliomas were more likely to be grade 2-3 astrocytomas (38.9% vs 14.3%) and oligodendrogliomas (19.3% vs 4.3%) than in adults. GBMs represented 76.0% of adult diffuse gliomas vs. only 25.7% of AYA diffuse gliomas, but with a similar prevalence of MGMT promoter methylation (40.8% vs 38.4%). Notably, 50.7% of AYA PCNSLs were associated with HIV/AIDS, vs only 7.1% in adults (p< 0.001). CONCLUSIONS The distribution, epidemiology, and survival outcomes of primary brain tumors in the AYA population are distinct from their pediatric and adult counterparts. Notably, AYA infiltrative gliomas were more often of lower grade than adults and AYA PCNSL were far more likely to be associated with HIV/AIDS. Primary brain tumors in AYA patients require specialized management.

scholarly journals OS10.1 Survival analysis of IDH wildtype astrocytomas with molecular features of glioblastoma, WHO grade IV

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii20-iii20 ◽  
Author(s):  
C M S Tesileanu ◽  
J A F Koekkoek ◽  
L Dirven ◽  
H J Dubbink ◽  
J M Kros ◽  
...  
Keyword(s):  
Molecular Data ◽  
Lower Grade ◽  
Who Grade ◽  
Historical Cohort ◽  
Molecular Features ◽  
Tert Promoter ◽  
Significant Difference ◽  
Tert Promoter Mutations ◽  
Grade Ii ◽  
Promoter Mutations

Abstract BACKGROUND Recently, isocitrate dehydrogenase wildtype (IDHwt) lower grade gliomas (LGGs) that have a telomerase reverse transcriptase (TERT) promoter mutation and/or gain of chromosome 7 combined with loss of chromosome 10 and/or epidermal growth factor receptor amplification have been reclassified as IDHwt astrocytomas with molecular features of glioblastoma, WHO grade IV (‘astrocytomas IDHwt, WHO IV’). Survival of these tumors meeting the criteria of these tumors is less well studied. The objective of this study is to compare the overall survival (OS) between the IDHwt astrocytomas, WHO IV and histological glioblastomas (GBMs). MATERIAL AND METHODS In this retrospective multicenter cohort study, all adult patients with a newly diagnosed IDHwt LGG (histologically WHO grade II or III) and with molecular data available were selected from the Erasmus MC and the LUMC from October 2002 to April 2019. LGG patients showing contrast enhancement with necrosis on the MRI at the time of histological diagnosis were excluded. Molecular data were determined using a diagnostic NGS panel. A historical cohort of 195 patients with IDHwt GBMs with molecular data available was used to compare OS. OS was measured from the date of the first diagnostic MR scan. RESULTS 79 IDHwt LGG patients were identified of which 62 patients had molecular features of glioblastoma (‘astrocytomas IDHwt, WHO IV’), 11 patients did not have these molecular features (‘astrocytomas IDHwt, WHO II & III’). In the remaining 6 patients the molecular data were not conclusive (astrocytomas IDHwt, WHO NOS). Patients with astrocytomas IDHwt, WHO IV were slightly older at diagnosis (median age = 57 years) than patients with GBMs IDHwt in the reference cohort or astrocytomas IDHwt, WHO II & III (respectively: median age 55 years, p=0.032 and 47 years, p=0.035). The relatively young age of our GBM IDHwt cohort reflects more extensive molecular testing in younger patients and histologically lower grade tumors. The median OS of astrocytomas IDHwt, WHO IV (23.8 months) was similar to the median OS of GBMs (19.2 months, log-rank test p=0.37). The median OS in 19 patients with only TERT promoter mutations was 16.8 months, similar to GBMs (p=0.94). CONCLUSION There is no statistically significant difference between the OS of IDHwt astrocytomas with molecular features of glioblastoma and the OS of true glioblastomas. Grade II and III IDHwt astrocytoma with molecular features of glioblastoma should be designated WHO grade IV. The presence of TERT promoter mutations alone in this histological context also qualifies for this designation.

scholarly journals Downregulation of Brain Enriched Type 2 MAGEs Is Associated With Immune Infiltration and Poor Prognosis in Glioma

2020 ◽  
Vol 10 ◽  
Author(s):  
Mohit Arora ◽  
Sarita Kumari ◽  
Jay Singh ◽  
Anita Chopra ◽  
Shyam S. Chauhan
Keyword(s):  
Dna Methylation ◽  
Hedgehog Signaling ◽  
Neuronal Development ◽  
Cox Regression ◽  
Lower Grade ◽  
Poor Overall Survival ◽  
Cox Regression Analysis ◽  
Immune Infiltration ◽  
Molecular Features

Melanoma associated antigen (MAGE) is an extensively studied family of tumor-associated genes that share a common MAGE homology domain (MHD). Based upon their expression pattern, MAGE genes have been broadly classified into type 1 MAGEs (T1Ms) and type 2 MAGEs (T2Ms) categories. Interestingly, several T2Ms are highly expressed in the brain and involved in the regulation of neuronal development, differentiation, and survival. Available literature suggests possible tumor suppressor functions of a few T2Ms, while information available about their expression, regulation, and clinical significance in glioma is scanty. This prompted us to perform a comprehensive analysis of T2M expression in glioma. Gene expression data from glioma datasets: Oncomine, TCGA, and REMBRANDT study, were used to assess the mRNA expression of T2M genes (MAGED1, MAGED2, MAGED3, MAGED4, MAGED4B, MAGEE1, MAGEE2, MAGEF1, MAGEH1, MAGEL2, NSMCE3, and NDN), and their association with clinical characteristics and composition of the tumor microenvironment. Further, mutation, copy number alteration, and DNA methylation data from TCGA were assessed for determining potential mechanisms of T2Ms expression in glioma. Expression analysis revealed overexpression of MAGED subfamily genes in glioma, while other genes of this family exhibited reduced expression in advanced grades of this malignancy. Further, the expression of T2Ms exhibited varying extent of positive correlations with each other. Amongst downregulated T2Ms, MAGEH1 expression exhibited negative correlations with DNA methylation. Additionally, genes associated with MAGEH1 were enriched in Myc and Hedgehog signaling. Furthermore, T2Ms downregulation was associated with immune infiltration in glioma tissues and poor overall survival of glioma patients. In multivariate Cox regression analysis, MAGEH1 emerged as an independent prognosticator in lower grade glioma. Conclusively, these results suggest that expression of T2Ms is associated with important clinical and molecular features in glioma. Mechanistic studies may further provide novel insights into their role in glioma progression.

scholarly journals Pleomorphic xanthoastrocytoma is a heterogeneous entity with pTERT mutations prognosticating shorter survival

2022 ◽  
Vol 10 (1) ◽  
Author(s):  
Azadeh Ebrahimi ◽  
Andrey Korshunov ◽  
Guido Reifenberger ◽  
David Capper ◽  
Joerg Felsberg ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Pleomorphic Xanthoastrocytoma ◽  
Histopathological Diagnosis ◽  
Lower Grade ◽  
Tumor Type ◽  
Methylation Analysis ◽  
Diagnostic Challenge ◽  
Methylation Array ◽  
Who Grade ◽  
Dna Methylation Analysis

AbstractPleomorphic xanthoastrocytoma (PXA) in its classic manifestation exhibits distinct morphological features and is assigned to CNS WHO grade 2 or grade 3. Distinction from glioblastoma variants and lower grade glial and glioneuronal tumors is a common diagnostic challenge. We compared a morphologically defined set of PXA (histPXA) with an independent set, defined by DNA methylation analysis (mcPXA). HistPXA encompassed 144 tumors all subjected to DNA methylation array analysis. Sixty-two histPXA matched to the methylation class mcPXA. These were combined with the cases that showed the mcPXA signature but had received a histopathological diagnosis other than PXA. This cohort constituted a set of 220 mcPXA. Molecular and clinical parameters were analyzed in these groups. Morphological parameters were analyzed in a subset of tumors with FFPE tissue available. HistPXA revealed considerable heterogeneity in regard to methylation classes, with methylation classes glioblastoma and ganglioglioma being the most frequent mismatches. Similarly, the mcPXA cohort contained tumors of diverse histological diagnoses, with glioblastoma constituting the most frequent mismatch. Subsequent analyses demonstrated the presence of canonical pTERT mutations to be associated with unfavorable prognosis among mcPXA. Based on these data, we consider the tumor type PXA to be histologically more varied than previously assumed. Histological approach to diagnosis will predominantly identify cases with the established archetypical morphology. DNA methylation analysis includes additional tumors in the tumor class PXA that share similar DNA methylation profile but lack the typical morphology of a PXA. DNA methylation analysis also assist in separating other tumor types with morphologic overlap to PXA. Our data suggest the presence of canonical pTERT mutations as a robust indicator for poor prognosis in methylation class PXA.

scholarly journals DNA methylation classification in diffuse glioma shows little spatial heterogeneity after adjusting for tumor purity

2020 ◽  
Author(s):  
N. Verburg ◽  
F.B. Barthel ◽  
K.J. Anderson ◽  
K.C. Johnson ◽  
T. Koopman ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Spatial Heterogeneity ◽  
Three Dimensional ◽  
Diffuse Glioma ◽  
Tumor Type ◽  
Tumor Purity ◽  
Genome Wide ◽  
Dimensional Reconstruction ◽  
Diffuse Gliomas ◽  
Molecular Aberrations

AbstractIntratumoral heterogeneity is a hallmark of diffuse gliomas. We used neuronavigation to acquire 133 image-guided and spatially-separated stereotactic biopsy samples from 16 adult patients with a diffuse glioma, which we characterized using DNA methylation arrays. Samples were obtained from regions with and without imaging abnormalities. Methylation profiles were analyzed to devise a three-dimensional reconstruction of genetic and epigenetic heterogeneity. Molecular aberrations indicated that tumor was found outside imaging abnormalities, underlining the infiltrative nature of this tumor and the limitations of current routine imaging modalities. We demonstrate that tumor purity is highly variable between samples and largely explains apparent epigenetic spatial heterogeneity. Indeed, we observed that DNA methylation subtypes are highly conserved in space after adjusting for tumor purity. Genome-wide heterogeneity analysis showed equal or increased heterogeneity among normal tissue when compared to tumor. These findings were validated in a separate cohort of 61 multi-sector tumor and 64 normal samples. Our findings underscore the infiltrative nature of diffuse gliomas and suggest that heterogeneity in DNA methylation is innate to somatic cells and not a characteristic feature of this tumor type.

scholarly journals DNA methylation profiling for molecular classification of adult diffuse lower-grade gliomas

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sandra Ferreyra Vega ◽  
Thomas Olsson Bontell ◽  
Alba Corell ◽  
Anja Smits ◽  
Asgeir Store Jakola ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Classification ◽  
Lower Grade ◽  
Who Grade ◽  
Class Prediction ◽  
Mutation Status ◽  
Molecular Features ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

Abstract Background DNA methylation profiling has facilitated and improved the classification of a wide variety of tumors of the central nervous system. In this study, we investigated the potential utility of DNA methylation profiling to achieve molecular diagnosis in adult primary diffuse lower-grade glioma (dLGG) according to WHO 2016 classification system. We also evaluated whether methylation profiling could provide improved molecular characterization and identify prognostic differences beyond the classical histological WHO grade together with IDH mutation status and 1p/19q codeletion status. All patients diagnosed with dLGG in the period 2007–2016 from the Västra Götaland region in Sweden were assessed for inclusion in the study. Results A total of 166 dLGG cases were subjected for genome-wide DNA methylation analysis. Of these, 126 (76%) were assigned a defined diagnostic methylation class with a class prediction score ≥ 0.84 and subclass score ≥ 0.50. The assigned methylation classes were highly associated with their IDH mutation status and 1p/19q codeletion status. IDH-wildtype gliomas were further divided into subgroups with distinct molecular features. Conclusion The stratification of the patients by methylation profiling was as effective as the integrated WHO 2016 molecular reclassification at predicting the clinical outcome of the patients. Our study shows that DNA methylation profiling is a reliable and robust approach for the classification of dLGG into molecular defined subgroups, providing accurate detection of molecular markers according to WHO 2016 classification.

scholarly journals DNA Methylation Analysis Identifies Patterns in Progressive Glioma Grades to Predict Patient Survival

2021 ◽  
Vol 22 (3) ◽  
pp. 1020
Author(s):  
Jing Yin Weng ◽  
Nicole Salazar
Keyword(s):  
Dna Methylation ◽  
Survival Probability ◽  
Patient Survival ◽  
Human Life ◽  
Malignant Gliomas ◽  
Methylation Pattern ◽  
The Cancer Genome Atlas ◽  
Lower Grade ◽  
Diffuse Glioma ◽  
Cpg Sites

DNA methylation is an epigenetic change to the genome that impacts gene activities without modification to the DNA sequence. Alteration in the methylation pattern is a naturally occurring event throughout the human life cycle which may result in the development of diseases such as cancer. In this study, we analyzed methylation data from The Cancer Genome Atlas, under the Lower-Grade Glioma (LGG) and Glioblastoma Multiforme (GBM) projects, to identify methylation markers that exhibit unique changes in DNA methylation pattern along with tumor grade progression, to predict patient survival. We found ten glioma grade-associated Cytosine-phosphate-Guanine (CpG) sites that targeted four genes (SMOC1, KCNA4, SLC25A21, and UPP1) and the methylation pattern is strongly associated with glioma specific molecular alterations, primarily isocitrate dehydrogenase (IDH) mutation and chromosome 1p/19q codeletion. The ten CpG sites collectively distinguished a cohort of diffuse glioma patients with remarkably poor survival probability. Our study highlights genes (KCNA4 and SLC25A21) that were not previously associated with gliomas to have contributed to the poorer patient outcome. These CpG sites can aid glioma tumor progression monitoring and serve as prognostic markers to identify patients diagnosed with less aggressive and malignant gliomas that exhibit similar survival probability to GBM patients.

98-OR: Placental DNA Methylation Changes Associated with Birthweight and Overlaps with Adult Type 2 Diabetes

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 98-OR
Author(s):  
FASIL TEKOLA-AYELE ◽  
TSEGASELASSIE WORKALEMAHU ◽  
XUEHUO ZENG
Keyword(s):  
Type 2 Diabetes ◽  
Dna Methylation ◽  
Adult Type

scholarly journals PATH-11. PROSPECTIVE (EPI-)GENETIC CLASSIFICATION OF > 1,000 PEDIATRIC CNS TUMORS—THE MNP 2.0 STUDY

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii426-iii426
Author(s):  
Dominik Sturm ◽  
Felix Sahm ◽  
Felipe Andreiuolo ◽  
David Capper ◽  
Marco Gessi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Panel ◽  
Cns Tumors ◽  
Lower Grade ◽  
High Grade ◽  
Sequencing Data ◽  
Cns Tumor ◽  
Gene Panel Sequencing ◽  
Tumor Entities ◽  
Panel Sequencing

Abstract The large variety of CNS tumor entities affecting children and adolescents, some of which are exceedingly rare, results in very diverging patient outcomes and renders accurate diagnosis challenging. To assess the diagnostic utility of routine DNA methylation-based CNS tumor classification and gene panel sequencing, the Molecular Neuropathology 2.0 study prospectively integrated these (epi-)genetic analyses with reference neuropathological diagnostics as an international trial for newly-diagnosed pediatric patients. In a four-year period, 1,215 patients with sufficient tissue were enrolled from 65 centers, receiving a reference neuropathological diagnosis according to the WHO classification in >97%. Using 10 FFPE sections as input, DNA methylation analysis was successfully performed in 95% of cases, of which 78% with sufficient tumor cell content were assigned to a distinct epigenetic tumor class. The remaining 22% did not match any of 82 represented classes, indicating novel rare tumor entities. Targeted gene panel sequencing of >130 genes performed for 96% of patients with matched blood samples detected diagnostically, prognostically, or therapeutically relevant somatic alterations in 48%. Germline DNA sequencing data indicated potential predisposition syndromes in ~10% of patients. Discrepant results by neuropathological and epigenetic classification (29%) were enriched in histological high-grade gliomas and implicated clinical relevance in 5% of all cases. Clinical follow-up suggests improved survival for some patients with high-grade glioma histology and lower-grade molecular profiles. Routine (epi-)genetic profiling at the time of primary diagnosis adds a valuable layer of information to neuropathological diagnostics and will improve clinical management of CNS tumors.

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