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A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors [Illumina HumanMethylation]

ABSTRACT: We have generated and comprehensively characterized 30 patient-derived orthotopic xenograft (PDOX) models and 7 cell lines represeneting subgroups of medulloblastoma, high-grade glioma, atypical teratoid/rhabdoid tumor, ependymoma and pineoblastoma.

ORGANISM(S): Homo sapiens

PROVIDER: GSE99994 | GEO | 2018/10/25

REPOSITORIES: GEO

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A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors [Affymetrix]

Project description:We have generated and comprehensively characterized 30 patient-derived orthotopic xenograft (PDOX) models and 7 cell lines represeneting subgroups of medulloblastoma, high-grade glioma, atypical teratoid/rhabdoid tumor, ependymoma and pineoblastoma.

2018-10-25 | GSE99961 | GEO

A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-10-25 | GSE99996 | GEO

Transcriptome analysis in medulloblastoma groups

Project description:Embryonal tumors of the central nervous system (CNS) represent a highly malignant tumor group of medulloblastoma (MB), atypical teratoid/rhabdoid tumor (AT/RT), and primitive neuroectodermal tumor (PNET) that frequently afflict children. In this study, we report transcriptome traits in MB by using gene expression microarray analyses. We also compare MB dataset with AT/RT cases and AT/RT-like cases. 22 MB cases are subjected to transcriptome analysis

2015-04-15 | E-GEOD-67850 | biostudies-arrayexpress

Human pluripotent stem cell-derived brain tumor model uncovered embryonic stem cell signature as a key driver in atypical teratoid/rhabdoid tumor (microarray)

Project description:Atypical teratoid/rhabdoid tumor (AT/RT), which harbors INI1 mutation and exhibits a characteristic histology of rhabdoid cells, has a poor prognosis because of the lack of effective treatments. Here we established human INI1-deficient pluripotent stem cells (hPSCs), which developed AT/RT formation in vivo. However, INI1-deficient hPSC-derived neural progenitor cell (NPC) gave rise to mostly medulloblastoma-like tumors when transplanted into the mouse brain.

2019-06-20 | GSE118653 | GEO

Epigenetic Landscape of Pediatric Ependymoma Recurrence

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

Malignant rhabdoid tumors originating within and outside the central nervous system are clinically and molecularly heterogeneous

Project description:Multifocal synchronous or metachronous central nervous system (CNS) and extra-CNS malignant rhabdoid tumors (MRTs) are rare and deadly cancers. To further understand these cancers, we performed genome-wide DNA methylation and CNA analysis in 27 tumors (16 of which were paired samples). 26 samples were newly generated and one sample was from a previously published cohort of MRTs. We compared our results with the previously published reference group of 150 atypical teratoid rhabdoid tumors. We showed that that CNS and extra-CNS MRTs for the most part clustered in distinct methylation groups and had heterogeneous molecular characteristics.

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The lncRNA HHIP-AS1 is required for oncogenic SHH signaling in humans

Project description:Here we show that the non-conserved lncRNA HHIP-AS1 promotes tumorigenesis in human SHH-driven brain tumors, including medulloblastoma, atypical teratoid / rhabdoid tumors (AT/RT). We reveal that GLI2 regulates a bidirectional promoter shared between the well-characterized SHH regulator HHIP and HHIP-AS1. We found a novel regulatory lncRNA mechanism, termed blocking endogenous RNA (beRNA), extending the concept of competing endogenous RNA (ceRNA), where HHIP-AS1 binds its target DYCN1I2 to avoid miRNA-425-based degradation.

2022-05-23 | GSE140741 | GEO

Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma.

Project description:Despite histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymomas reveals the existence of two demographically, transcriptionally, genetically and clinically distinct groups of posterior fossa (PF) ependymoma. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis, and death as compared to Group B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third group of independent ependymomas using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients. This SuperSeries is composed of the following subset Series: GSE27283: Human ependymoma samples [expression] GSE27286: Human ependymoma samples, Subgrouping [aCGH - German Cancer Research Center human 33K BAC array] Refer to individual Series

2011-08-14 | E-GEOD-27287 | biostudies-arrayexpress

Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

Project description:Gene expression (mRNA) profiling of human ependymomas Despite the histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymoma. Group-A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, secondary metastasis, and death as compared to Group-B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third independent group of tumors using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients. We analyzed 102 primary ependymomas on the Affymetrix Exon 1.0ST platform (Gene Level).

2011-08-14 | E-GEOD-27279 | biostudies-arrayexpress

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