DNA methylation profiles for the SIOP Ependymoma I Study
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PROVIDER: PRJNA757457 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation profiles were generated for cases in the SIOP ependymoma I study. Samples were analysed using the Illumina 450k BeadChip and processed using the Heidelberg classifier (v11.2b). The aim of the biological studies aspect of the trial was to perform a retrospective analysis of the methylation profiles of the participants in the trial.
2021-08-25 | GSE182707 | GEO
Project description:DNA Methylation profiles were generated for retrospective cases to support work into investigation of the immune environment in pediatric ependymoma. Samples were analyzed using the Illumina 450k beadchip and processed using the Heidelberg classifier (v11.2b and subsequently v12.3 for subgrouping/subtyping). The aim of the study was to better understand the immune-tumor microenvironment in pediatric ependymoma and the methylation profiles support the diagnoses of each case.
2023-10-02 | GSE190798 | GEO
Project description:DNA methylation profiles for Sister Study duplicate samples
| PRJNA729778 | ENA
Project description:Ependymomas exist within distinct genetic subgroups, but the molecular diversity within individual ependymomas is unknown. We performed multiplatform molecular profiling of 6 spatially-distinct samples from an ependymoma with C11orf95-RELA fusion. DNA methylation and RNA sequencing distinguished clusters of samples according to neuronal development gene expression programs that could also be delineated by differences in magnetic resonance blood perfusion. Exome sequencing and phylogenetic analysis revealed epigenomic intratumor heterogeneity, and suggested that chromosomal structural alterations may precede accumulation of single nucleotide variants during ependymoma tumorigenesis. In sum, these findings shed new light on the oncogenesis and intratumor heterogeneity of ependymoma.
2019-12-20 | GSE142320 | GEO
Project description:Pediatric ependymoma has relatively low frequencies of DNA mutations, which suggest that epigenetics may drive tumors. However, the epigenetic mechanisms for recurrent ependymoma are still poorly understood. Here, we performed longitudinal and comprehensive DNA methylation and gene expression analysis for recurrent pediatric ependymoma tumors from 10 patients, total 46 DNA methylomes (including primary tumors and matched recurrent tumors; normal pediatric brain tissues and PDOX tumors). Both RELA and PFA tumors maintained the subtype DNA methylation signatures during repeated relapses. We further identified the potential DNA methylation predictors, drivers and boosters and their potential regulated genes for recurrent ependymoma tumors. Increased DNA methylation levels within H3K4me1 enriched regions indicates disturbed functions of LSD1 gene in recurrent ependymoma tumors. Combining novel LSD1 inhibitor SYC-836 with radiation (XRT) significantly prolonged animal survival times in PDOX models of recurrent PFA ependymoma. Our PDOX models provide a unique platform for preclinical testing drugs and development of new therapy for pediatric recurrent ependymoma.
2022-07-12 | GSE156619 | GEO
Project description:Background: A methylation-based classification of ependymoma has recently found broad application. However, the diagnostic advantage and implications for treatment decisions remain unclear. Here, we retrospectively evaluate the impact of surgery and radiotherapy on outcome after molecular reclassification of adult intracranial ependymomas. Methods: Tumors diagnosed as intracranial ependymomas from 170 adult patients collected from eight diagnostic institutions were subjected to DNA methylation profiling. Molecular classes, patient characteristics, and treatment were retrospectively correlated with progression-free survival (PFS). Results: The classifier indicated an ependymal tumor in 73.5%, a different tumor entity in 10.6% and non-classifiable tumors in 15.9% of cases, respectively. The most prevalent molecular classes were posterior fossa ependymoma group B (EPN-PFB, 32.9%), posterior fossa subependymoma (PF-SE, 25.9%), and supratentorial ZFTA fusion-positive ependymoma (EPN-ZFTA, 11.2%). With a median follow-up of 60.0 months, the 5- and 10-year-PFS rates were 64.5% and 41.8% for EPN-PFB, 67.4% and 45.2% for PF-SE and 60.3% and 60.3% for EPN-ZFTA. In EPN-PFB, but not in other molecular classes, gross total resection (p=0.009) and postoperative radiotherapy (p=0.007) were significantly associated with improved PFS in multivariable analysis. Histological tumor grading (WHO 2 vs. 3) was not a predictor of prognosis within molecularly defined ependymoma classes. Conclusions: DNA methylation profiling improves diagnostic accuracy and risk stratification in adult intracranial ependymoma. The molecular class of PF-SE is unexpectedly prevalent among adult tumors with ependymoma histology and relapsed as frequently as EPN-PFB, despite the supposed benign nature. Gross total resection and radiotherapy may represent key factors in determining the outcome of EPN-PFB patients.
2023-02-21 | GSE224218 | GEO
Project description:PROGRESS/ELEMENT DNA Methylation Study
| PRJNA792632 | ENA
Project description:PROGRESS/ELEMENT DNA Methylation Study
| PRJNA792633 | ENA
Project description:DNA methylation analysis was perfomed using Infinium EPIC Methylation BeadChip platform on 65 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.
2023-06-01 | GSE226895 | GEO
Project description:Multiplatform molecular profiling reveals epigenomic intratumor heterogeneity in ependymoma, DNA Methylation
| PRJNA596639 | ENA